Extract optional-file synchronisation workflow owners

docs/adr/2026_09_customisation_and_hidden_file_sync_ownership.md

@@ -20,13 +20,15 @@ one writer for raw events, scheduled scans, and automatic database-to-local
 reflection. The constructor-name add-on lookup and the `ConfigSync` and
 `HiddenFileSync` add-on identities have been retired.
 
-The Customisation Sync private context coordinates its snapshot operations,
+The Customisation Sync private context coordinates lifecycle, raw-event
-scan queues, periodic work, and focused path and transient-state owners. The
+admission, configuration and periodic policy, view composition, and the
-Hidden File Sync private context coordinates reconciliation, periodic work,
+lifetimes of focused path, snapshot, application, scan, and catalogue owners.
-and the lifetimes of focused path-admission, notification, processed-state,
+The Hidden File Sync private context coordinates lifecycle and handler
-change-processing, and conflict-resolution owners. Each receives live settings
+admission around focused path-admission, notification, processed-state,
-and database projections, focused storage, path, and exact-revision
+change-processing, conflict-resolution, and reconciliation owners. Each
-capabilities, and explicit host effects rather than `LiveSyncCore`.
+receives live settings and database projections, focused storage, path, and
+exact-revision capabilities, and explicit host effects rather than
+`LiveSyncCore`.
 
 The corresponding implemented topology is documented in
 [Optional-file synchronisation architecture](../design_docs/optional_file_sync_architecture.md).
@@ -203,14 +205,35 @@ operations receive this capability through one narrow `processedState` port;
 they do not receive bundles of individual state callbacks or implement state
 keys themselves.
 
-`CustomisationSyncCatalogueState` separately owns the transient catalogue
+`CatalogueState` separately owns the transient catalogue rows, manifest lookup
-rows, manifest lookup and mtime cache, their reactive stores, and catalogue
+and mtime cache, their reactive stores, and catalogue update progress. A small
-update progress. A small recent-event deduplicator owns raw-event admission
+recent-event deduplicator owns raw-event admission history. These Customisation
-history. These Customisation Sync owners are deliberately not implementations
+Sync owners are deliberately not implementations of a shared Hidden File Sync
-of a shared Hidden File Sync state abstraction: the former state is a derived,
+state abstraction: the former state is a derived, in-memory projection, while
-in-memory projection, while Hidden File Sync markers are persisted operational
+Hidden File Sync markers are persisted operational reconciliation state with
-reconciliation state with different identity, invalidation, and deletion
+different identity, invalidation, and deletion rules.
-rules.
+
+`CatalogueOperations` owns catalogue enumeration, one queue and its progress
+subscription, and composes `CatalogueV1`, `CatalogueV2`, and
+`CatalogueMigration`. V1 and V2 are mutually exclusive as the selected write
+format, but both persisted formats can coexist during migration. Queue work
+therefore reads the live setting when it starts, and the shared state continues
+to recognise V2 rows independently of that setting. `CatalogueMigration`
+remains the distinct bridge from grouped V1 binders to per-file V2 documents.
+
+`SnapshotPersistence` owns the host-neutral V1 grouped and V2 per-file writes
+and logical deletion. It returns explicit mutation and refresh outcomes, so it
+neither owns catalogue state nor calls back through the context.
+`SnapshotOperations` applies those outcomes with the inherited awaited V1 or
+fire-and-forget V2 timing. `ApplicationOperations` owns compare, apply,
+duplicate, and delete workflows, while `ScanOperations` owns configuration-file
+enumeration and V1/V2 reconciliation. Both depend on narrow snapshot and
+catalogue ports instead of the context.
+
+The newly extracted catalogue, snapshot, application, scan, and reconciliation
+modules omit a Customisation Sync or Hidden File Sync prefix because their
+feature directories already supply that scope. Public contexts and views retain
+their domain names for compatibility.
 
 `CustomisationSyncPathOperations` binds live configuration-directory, mode,
 and device-name projections to the pure category and V1/V2 key functions. It
@@ -232,6 +255,12 @@ This boundary keeps event concurrency and settlement directly testable without
 giving the processor full scan, initialisation, notification, or host
 responsibilities.
 
+`Reconciliation` owns storage and database enumeration, full scans, offline
+comparison, rebuild direction and ordering, processed-state adoption,
+initialisation sequencing, and the scoped rebuild interceptor used by maintained
+real-Obsidian tests. Storage and database scans remain together because every
+offline and initialisation path coordinates both sides.
+
 The joint composition may return several views backed by those contexts:
 
 - a Customisation Sync catalogue and operation view for its dialogue;
@@ -372,11 +401,17 @@ to the non-owner.
 
 The private context, path module, codec module, focused presentation view, and
 resource teardown are implemented. A focused path capability binds live
-settings and device identity to the pure path functions. A focused
+settings and device identity to the pure path functions. A focused catalogue
-catalogue-state owner holds the rows, manifests, manifest mtime cache, reactive
+owner holds one queue, its progress subscription, and shared state, while
-stores, and update progress, while a bounded deduplicator owns recent raw-event
+separate V1, V2, and migration modules hold format-specific behaviour. A
-keys. Enumeration and scan queues remain with the orchestrating context. The
+bounded deduplicator owns recent raw-event keys. Host-neutral snapshot
-context accepts only narrow, live projections and explicit effects; an
+persistence owns V1 grouped and V2 per-file writes, unchanged-content checks,
+and logical deletion. A snapshot coordinator applies its explicit refresh
+outcomes without a catalogue-to-context callback cycle. Focused application
+and scan owners contain selected-snapshot workflows and full local/database
+reconciliation, respectively. The context retains raw-event admission and
+scheduling, configuration and periodic policy, owner lifetime, and view
+composition. It accepts only narrow, live projections and explicit effects; an
 Obsidian adapter at the composition edge owns dialogues, Notices, plug-in
 reload, restart, lifecycle, Vault access, and compatibility scan telemetry.
 
@@ -397,9 +432,10 @@ the ownership, static-path, pattern, and ignore-file sequence. A focused change
 notifier owns folder batching, delayed delivery, and teardown of its scheduled
 work and Notice effect. A focused change processor owns storage and database
 event processing, bounded concurrency, per-path serialisation, activity
-publication, and compatibility settlement order. The context retains scan,
+publication, and compatibility settlement order. A focused reconciliation
-initialisation, and reconciliation orchestration. A focused
+owner owns storage and database scans, offline comparison, rebuilds,
-conflict-resolution owner owns pending-path admission,
+processed-state adoption, initialisation direction and ordering, and its scoped
+testing interceptor. A focused conflict-resolution owner owns pending-path admission,
 the parallel classification and serial interaction queues, automatic merge,
 newer-revision selection, interactive JSON application, settlement, and queue
 disposal. An Obsidian adapter owns JSON conflict dialogue instances, progress
@@ -499,12 +535,13 @@ migration without first establishing narrow dependencies.
 - The legacy add-on identity and constructor-name lookup are removed.
 - The two contexts coordinate separate synchronisation workflows, but their
   dependency surfaces are explicit and do not include the complete core.
-  Customisation Sync delegates its path binding, derived catalogue, and
+  Customisation Sync delegates its path binding, snapshot persistence and
-  recent-event state, while Hidden File Sync delegates path admission,
+  refresh sequencing, selected-snapshot application, scan reconciliation,
-  notification, processed-state, change-processing, and conflict lifecycles,
+  derived catalogue, catalogue queue, and recent-event state, while Hidden File
-  to focused owners. Further extraction should follow a concrete behavioural
+  Sync delegates path admission, notification, processed-state,
-  boundary rather than create additional serviceFeatures for private
+  change-processing, reconciliation, and conflict lifecycles to focused owners.
-  operations.
+  Further extraction should follow a concrete behavioural boundary rather than
+  create additional serviceFeatures for private operations.
 
 ## References
 

docs/design_docs/optional_file_sync_architecture.md

@@ -32,9 +32,19 @@ Obsidian composition (`main.ts`)
   |      |
   |      +--> `CustomisationSyncContext`
   |      |      +-- `CustomisationSyncPathOperations`
-  |      |      +-- `CustomisationSyncCatalogueState`
+  |      |      +-- `SnapshotPersistence`
+  |      |      +-- `SnapshotOperations`
+  |      |      +-- `ApplicationOperations`
+  |      |      +-- `ScanOperations`
   |      |      +-- recent-event deduplicator
   |      |      +-- immutable service-handler and testing views
+  |      |      |
+  |      |      +--> `CatalogueOperations`
+  |      |             +-- `CatalogueState`
+  |      |             +-- one catalogue queue and progress lifecycle
+  |      |             +-- `CatalogueV1`
+  |      |             +-- `CatalogueV2`
+  |      |             +-- `CatalogueMigration`
   |      |      ^
   |      |      +-- narrow dependencies from
   |      |          `customisationSyncObsidianAdapter`
@@ -64,6 +74,10 @@ Obsidian composition (`main.ts`)
   |             |      +-- changed-folder batching and scheduled delivery
   |             |      +-- suppression and Notice-effect teardown
   |             |
+  |             +--> `Reconciliation`
+  |             |      +-- storage and database scans
+  |             |      +-- offline reconciliation, rebuilds, and initialisation
+  |             |
   |             +-- immutable service-handler, command, repair, and testing views
   |
   +--> `useCustomisationSyncUI`
@@ -84,37 +98,65 @@ application core.
 
 ## Ownership
 
-| Owner                                 | Owns                                                                                                                                                                                                          | Does not own                                                                                                          |
+| Owner                                 | Owns                                                                                                                                                                                                          | Does not own                                                                                                                                                                                                     |
-| ------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------- |
+| ------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `useOptionalFileSync`                 | Construction of both contexts, handler registration and removal, local-owner selection, namespace dispatch, compatibility callback order, and context disposal order.                                         | Persisted feature state, synchronisation algorithms, commands, dialogues, or Notices.                                 |
+| `useOptionalFileSync`                 | Construction of both contexts, handler registration and removal, local-owner selection, namespace dispatch, compatibility callback order, and context disposal order.                                         | Persisted feature state, synchronisation algorithms, commands, dialogues, or Notices.                                                                                                                            |
-| `CustomisationSyncContext`            | The `ix:` scan and snapshot workflow, snapshot storage and application, periodic scan state, and the lifetimes of its focused owners.                                                                         | Path derivation, catalogue mutations, recent-event history, Obsidian dialogues, ribbon actions, or handler registration. |
+| `CustomisationSyncContext`            | Lifecycle and view composition, raw-event admission and scheduling, configuration transitions, periodic scan policy, and focused-owner lifetimes.                                                             | Scan reconciliation, snapshot writes or refresh sequencing, catalogue internals, application and comparison algorithms, Obsidian dialogues, ribbon actions, or handler registration.                             |
-| `CustomisationSyncPathOperations`     | Binding live configuration-directory, mode, and device-name projections to the pure category, target-path, V1 key, V2 key, and device-prefix functions.                                                       | I/O, mutable state, local-owner selection, or persistence.                                                             |
+| `CustomisationSyncPathOperations`     | Binding live configuration-directory, mode, and device-name projections to the pure category, target-path, V1 key, V2 key, and device-prefix functions.                                                       | I/O, mutable state, local-owner selection, or persistence.                                                                                                                                                       |
-| `CustomisationSyncCatalogueState`     | Transient catalogue rows, manifest lookup and mtime cache, reactive catalogue and manifest stores, and catalogue update progress.                                                                             | Database or storage I/O, scan scheduling, routing, or persistence.                                                    |
+| `SnapshotPersistence`                 | V1 grouped and V2 per-file local-to-database writes, unchanged-content checks, logical deletion, and explicit catalogue-refresh outcomes.                                                                     | Catalogue state or refresh execution, scans, lifecycle policy, application, dialogues, or plug-in reload.                                                                                                        |
-| Customisation Sync event deduplicator | The bounded, newest-first keys used to admit raw configuration events once.                                                                                                                                   | Scheduling, path ownership, catalogue state, or persisted data.                                                       |
+| `SnapshotOperations`                  | Applying persistence outcomes to the catalogue with the inherited awaited V1 and fire-and-forget V2 refresh timing.                                                                                           | Snapshot encoding, catalogue state, scans, lifecycle policy, or host effects.                                                                                                                                    |
-| `HiddenFileSyncContext`               | The `i:` scan and reconciliation workflow, exact-revision repair composition, periodic scan state, and focused-owner lifetimes.                                                                               | Path admission state, change-event serialisation, processed-state representation, notification batching, conflict queue state, Obsidian dialogues, or service handler registration. |
+| `ApplicationOperations`               | Comparing, applying, duplicating, and deleting selected Customisation Sync snapshots through narrow storage, snapshot, and catalogue ports.                                                                   | Catalogue enumeration, raw-event admission, periodic scheduling, or view composition.                                                                                                                            |
-| `HiddenFileSyncProcessedState`        | Three device-local autosaved maps, exact storage and database keys, retained known mtime, reset behaviour, and storage/database settlement effects.                                                           | File transfer, scan scheduling, conflict handling, or presentation.                                                   |
+| `ScanOperations`                      | Configuration-file enumeration and V1/V2 reconciliation with local and database state.                                                                                                                        | Periodic scheduling, raw-event admission, snapshot persistence details, or catalogue state.                                                                                                                      |
-| `HiddenFileSyncChangeProcessor`       | Storage and database change processing, same-path event serialisation, bounded concurrency, activity counts, and the inherited event-consumption and settlement order.                                      | Full scans, initialisation policy, notification presentation, or conflict interaction.                               |
+| `CatalogueOperations`                 | Catalogue enumeration and publication, one format-dispatching queue and its progress lifecycle, and composition of the state, V1, V2, and migration modules.                                                  | Local-file scanning, snapshot application, raw-event routing, dialogues, or handler registration.                                                                                                                |
-| `HiddenFileSyncConflictResolution`    | Conflict admission and deduplication, pending paths, the parallel classification and serial interaction queues, automatic merge, newer-revision policy, interactive JSON resolution, and conflict settlement. | Obsidian dialogue instances, general Hidden File Sync scans, processed-state caches, or Service handler registration. |
+| `CatalogueState`                      | Transient catalogue rows, manifest lookup and mtime cache, reactive catalogue and manifest stores, and catalogue update progress.                                                                             | Database or storage I/O, scan scheduling, routing, or persistence.                                                                                                                                               |
-| `HiddenFileSyncPathAdmission`         | The ownership-first eligibility sequence, hidden-path and pattern policy, asynchronous ignore-file check, and the per-context parsed-pattern cache.                                                           | Composition-level owner selection, scans, transfer, or persistence.                                                   |
+| `CatalogueV1`                         | Loading and publishing grouped V1 catalogue rows.                                                                                                                                                             | V2 decoding, migration, queue lifetime, or local-file scanning.                                                                                                                                                  |
-| `HiddenFileSyncChangeNotifier`        | Changed-folder deduplication, delayed delivery, live suppression and configuration-directory checks, scheduled-task cancellation, and the host Notice show/hide effects.                                     | The Obsidian Notice instance, file extraction, or scan policy.                                                        |
+| `CatalogueV2`                         | Building and updating per-file V2 rows and manifests.                                                                                                                                                         | V1 loading, migration, queue lifetime, or local-file scanning.                                                                                                                                                   |
-| Customisation Sync Obsidian adapter   | Obsidian conflict selection, Notice presentation, plug-in reload, restart requests, Vault enumeration, progress telemetry, and platform-derived fallback device names.                                        | Catalogue state, routing, or persisted document operations.                                                           |
+| `CatalogueMigration`                  | Translating a grouped V1 binder into V2 per-file documents, deleting the migrated binder, and applying its required V1 refresh.                                                                               | General catalogue enumeration, queue ownership, or local-file scanning.                                                                                                                                          |
-| Hidden File Sync Obsidian adapter     | JSON conflict dialogue lifetime, progress presentation, grouped change Notices, plug-in reload actions, restart scheduling, Vault enumeration, and compatibility activity publication.                        | Transfer, reconciliation, processed-state, or conflict decisions.                                                     |
+| Customisation Sync event deduplicator | The bounded, newest-first keys used to admit raw configuration events once.                                                                                                                                   | Scheduling, path ownership, catalogue state, or persisted data.                                                                                                                                                  |
-| `useCustomisationSyncUI`              | Command, ribbon, dialogue, open-request subscription, and their unload teardown.                                                                                                                              | Synchronisation state or Hidden File Sync initialisation behaviour.                                                   |
+| `HiddenFileSyncContext`               | Lifecycle and view composition, handler admission, configuration transitions, periodic scan state, exact-revision repair composition, and focused-owner lifetimes.                                            | Scan and rebuild algorithms, path admission state, change-event serialisation, processed-state representation, notification batching, conflict queue state, Obsidian dialogues, or service handler registration. |
-| `useHiddenFileSyncCommands`           | Hidden File Sync command registration, setting-change subscription, and their unload teardown.                                                                                                                | Synchronisation state or command implementation.                                                                      |
+| `HiddenFileSyncProcessedState`        | Three device-local autosaved maps, exact storage and database keys, retained known mtime, reset behaviour, and storage/database settlement effects.                                                           | File transfer, scan scheduling, conflict handling, or presentation.                                                                                                                                              |
+| `HiddenFileSyncChangeProcessor`       | Storage and database change processing, same-path event serialisation, bounded concurrency, activity counts, and the inherited event-consumption and settlement order.                                        | Full scans, initialisation policy, notification presentation, or conflict interaction.                                                                                                                           |
+| `Reconciliation`                      | Storage and database enumeration, full scans, offline reconciliation, rebuild direction and ordering, processed-state adoption, initialisation sequencing, and the scoped rebuild interceptor.                | Individual transfer implementation, conflict interaction, path-pattern state, periodic scheduling, or host lifecycle.                                                                                            |
+| `HiddenFileSyncConflictResolution`    | Conflict admission and deduplication, pending paths, the parallel classification and serial interaction queues, automatic merge, newer-revision policy, interactive JSON resolution, and conflict settlement. | Obsidian dialogue instances, general Hidden File Sync scans, processed-state caches, or Service handler registration.                                                                                            |
+| `HiddenFileSyncPathAdmission`         | The ownership-first eligibility sequence, hidden-path and pattern policy, asynchronous ignore-file check, and the per-context parsed-pattern cache.                                                           | Composition-level owner selection, scans, transfer, or persistence.                                                                                                                                              |
+| `HiddenFileSyncChangeNotifier`        | Changed-folder deduplication, delayed delivery, live suppression and configuration-directory checks, scheduled-task cancellation, and the host Notice show/hide effects.                                      | The Obsidian Notice instance, file extraction, or scan policy.                                                                                                                                                   |
+| Customisation Sync Obsidian adapter   | Obsidian conflict selection, Notice presentation, plug-in reload, restart requests, Vault enumeration, progress telemetry, and platform-derived fallback device names.                                        | Catalogue state, routing, or persisted document operations.                                                                                                                                                      |
+| Hidden File Sync Obsidian adapter     | JSON conflict dialogue lifetime, progress presentation, grouped change Notices, plug-in reload actions, restart scheduling, Vault enumeration, and compatibility activity publication.                        | Transfer, reconciliation, processed-state, or conflict decisions.                                                                                                                                                |
+| `useCustomisationSyncUI`              | Command, ribbon, dialogue, open-request subscription, and their unload teardown.                                                                                                                              | Synchronisation state or Hidden File Sync initialisation behaviour.                                                                                                                                              |
+| `useHiddenFileSyncCommands`           | Hidden File Sync command registration, setting-change subscription, and their unload teardown.                                                                                                                | Synchronisation state or command implementation.                                                                                                                                                                 |
 
 The two domain contexts coordinate one cohesive synchronisation workflow each.
 Their private operations and focused owners are not additional serviceFeatures:
 they do not independently register host integration or have separate
-application lifetimes. `CustomisationSyncPathOperations` is a stateless
+application lifetimes. The newly extracted catalogue, snapshot, application,
-capability which binds live inputs to pure path functions. The Hidden File Sync
+scan, and reconciliation modules omit the domain prefix because their feature
-path-admission owner holds the parsed-pattern cache, and its change notifier
+directories already supply that scope; public context and view names retain it
-holds the pending folder set and scheduled-task lifetime.
+for compatibility. `CustomisationSyncPathOperations` is a stateless capability
+which binds live inputs to pure path functions.
+`SnapshotPersistence` is a host-neutral operation boundary: it returns
+structured mutation and refresh outcomes without reaching into the catalogue
+or presentation. `SnapshotOperations` consumes those outcomes and preserves
+their refresh timing. `ApplicationOperations` and `ScanOperations` depend on
+those narrow ports instead of calling back through the context.
+
+`CatalogueOperations` owns one catalogue queue, its progress subscription, and
+the shared state projected by the format-specific modules. The live V2 setting
+selects V1 loading or V1-to-V2 migration when each queued item starts. Persisted
+V1 and V2 documents can coexist during migration, so V2 documents remain
+recognisable regardless of the currently selected write format. `CatalogueV1`
+and `CatalogueV2` contain only their format-specific catalogue behaviour, while
+`CatalogueMigration` remains the explicit bridge between them. The Hidden File
+Sync path-admission owner holds the parsed-pattern cache, and its change
+notifier holds the pending folder set and scheduled-task lifetime.
 `HiddenFileSyncChangeProcessor` is a focused resource owner because its
 semaphore, per-path serialisation, activity counters, and event settlement form
 one independently testable lifecycle.
 `HiddenFileSyncConflictResolution` is another focused resource owner because
 conflict admission, pending-path identity, two serialisation stages, and
 disposal form a separate lifecycle.
+`Reconciliation` keeps storage and database enumeration together because
+offline comparison, rebuilds, and each initialisation direction depend on both
+sides and their ordered processed-state adoption.
 
 The two state owners intentionally do not implement a common generic state
 contract. Customisation Sync projects transient catalogue and presentation
@@ -214,12 +256,16 @@ than being re-exported through a broad context testing view.
 The composition is created after the Service Hub and required ServiceModules
 exist, and before lifecycle-driven feature work begins. Each context creates
 its own periodic processor and focused resource owners.
-`CustomisationSyncContext` creates one path capability, one catalogue-state
+`CustomisationSyncContext` creates one path capability, one snapshot-persistence
-owner, and one recent-event deduplicator. `HiddenFileSyncContext` creates one
+boundary, one snapshot coordinator, one application owner, one scan owner, one
+catalogue owner, and one recent-event deduplicator. The catalogue owner creates
+its shared state, one queue and progress subscription, and the V1, V2, and
+migration modules. `HiddenFileSyncContext` creates one
 path-admission owner, one change notifier, and one processed-state owner before
 composing database write and extraction operations around their narrow ports.
-It then creates one change processor and one conflict-resolution owner. The
+It then creates one change processor, one conflict-resolution owner, and one
-change processor owns its semaphore and activity state.
+reconciliation owner. The change processor owns its semaphore and activity
+state; the reconciliation owner owns its scoped testing interceptor.
 Full conflict scans admit discovered paths into the same queue without
 suspending it, so ordinary database conflict notifications continue during a
 slow scan. After enumeration, the operation waits for both classification and
@@ -255,10 +301,14 @@ appropriate, a migration decision.
 Focused unit tests cover routing, path-option binding, Hidden File Sync
 admission ordering and cache invalidation, semantic handler views, context
 owner isolation, teardown, initial cache selection, exact-revision repair,
-change-event serialisation and settlement, notification batching, conflict
+Customisation Sync scan reconciliation and context delegation, single-queue
-queue admission, revision selection, automatic and interactive merge effect
+catalogue disposal and publication, live V1/V2 dispatch, V1 and V2 snapshot
-ordering, conflict dialogue adaptation, grouped Notices, and compatibility
+persistence outcomes, logical-deletion idempotence, refresh ordering,
-activity publication.
+application operations, Hidden File Sync change-event serialisation and
+settlement, reconciliation direction and scan ordering, notification batching,
+conflict queue admission, revision selection, automatic and interactive merge
+effect ordering, conflict dialogue adaptation, grouped Notices, and
+compatibility activity publication.
 The boundary test prevents either domain context from regaining core or
 Obsidian dependencies.
 

src/features/ConfigSync/applicationOperations.ts

@@ -0,0 +1,346 @@
+import { diff_match_patch, parseYaml } from "@/deps.ts";
+import type {
+    diff_result,
+    FilePath,
+    FilePathWithPrefix,
+    LOG_LEVEL,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_NOTICE, LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { delay, getDocData, getDocDataAsArray, isDocContentSame } from "@vrtmrz/livesync-commonlib/compat/common/utils";
+import { decodeBinary } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/convert";
+import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
+import { serialized } from "octagonal-wheels/concurrency/lock";
+import { base64ToArrayBuffer, base64ToString } from "octagonal-wheels/binary/base64";
+
+import { LiveSyncError } from "@vrtmrz/livesync-commonlib/compat/common/LSError";
+import type { StorageAccess } from "@vrtmrz/livesync-commonlib/compat/interfaces/StorageAccess";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+import { createCustomisationSyncCodec, type PluginDataEx } from "./customisationSyncCodec.ts";
+import type { CatalogueOperations } from "./catalogueOperations.ts";
+import type { CustomisationSyncPathOperations } from "./customisationSyncPathOperations.ts";
+import type { SnapshotOperations } from "./snapshotOperations.ts";
+import { PluginDataExDisplayV2 } from "./customisationSyncModel.ts";
+import type { IPluginDataExDisplay, LoadedEntryPluginDataExFile } from "./customisationSyncView.ts";
+
+const { deserialize } = createCustomisationSyncCodec({ digestHash, parseYaml });
+
+type ApplicationDatabase = Pick<LiveSyncLocalDB, "getDBEntry">;
+type ApplicationStorage = Pick<
+    StorageAccess,
+    "ensureDir" | "readHiddenFileBinary" | "readHiddenFileText" | "writeHiddenFileAuto"
+>;
+type ApplicationPath = Pick<CustomisationSyncPathOperations, "filenameToUnifiedKey">;
+type ApplicationSnapshotOperations = Pick<
+    SnapshotOperations,
+    "isV2Enabled" | "storeCustomisationFileV2" | "storeCustomizationFiles" | "deleteConfigOnDatabase"
+>;
+type ApplicationCatalogue = Pick<
+    CatalogueOperations,
+    "findPlugins" | "manifestLookup" | "updatePluginList" | "updatePluginListV2"
+>;
+
+export type ApplicationOperationsDependencies = {
+    getLocalDatabase(): ApplicationDatabase;
+    storageAccess: ApplicationStorage;
+    path: ApplicationPath;
+    log: LogFunction;
+    getConfigDir(): string;
+    getDeviceAndVaultName(): string;
+    resolveJsonConflict(
+        path: FilePath,
+        files: [LoadedEntryPluginDataExFile, LoadedEntryPluginDataExFile],
+        remoteName: string,
+        apply: (content: string) => Promise<boolean>
+    ): Promise<boolean>;
+    selectTextFile(path: FilePath, diffResult: diff_result, remoteName: string): Promise<"A" | "B" | false>;
+    reloadPlugin(configDir: string, pluginName: string): Promise<void>;
+    askRestart(): void;
+    snapshotOperations: ApplicationSnapshotOperations;
+    catalogueOperations: ApplicationCatalogue;
+};
+
+/**
+ * Owns the Customisation Sync dialogue's compare, apply, duplicate, and
+ * delete workflows. It deliberately consumes the shared snapshot capability
+ * and catalogue owner, leaving lifecycle, event admission, and scanning in
+ * the context.
+ */
+export class ApplicationOperations {
+    constructor(private readonly dependencies: ApplicationOperationsDependencies) {}
+
+    private get configDir() {
+        return this.dependencies.getConfigDir();
+    }
+
+    private get localDatabase() {
+        return this.dependencies.getLocalDatabase();
+    }
+
+    private get storageAccess() {
+        return this.dependencies.storageAccess;
+    }
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string) {
+        this.dependencies.log(message, level, key);
+    }
+
+    async compareFileUsingDisplayData(
+        dataA: IPluginDataExDisplay,
+        dataB: IPluginDataExDisplay,
+        filename: string
+    ): Promise<boolean> {
+        const dataACopy =
+            dataA instanceof PluginDataExDisplayV2
+                ? new PluginDataExDisplayV2(dataA, this.dependencies.catalogueOperations.manifestLookup)
+                : { ...dataA };
+        const dataBCopy =
+            dataB instanceof PluginDataExDisplayV2
+                ? new PluginDataExDisplayV2(dataB, this.dependencies.catalogueOperations.manifestLookup)
+                : { ...dataB };
+        dataACopy.files = dataACopy.files.filter((file) => file.filename == filename);
+        dataBCopy.files = dataBCopy.files.filter((file) => file.filename == filename);
+        return await this.compareUsingDisplayData(dataACopy, dataBCopy, true);
+    }
+
+    async compareUsingDisplayData(dataA: IPluginDataExDisplay, dataB: IPluginDataExDisplay, compareEach = false) {
+        const loadFile = async (data: IPluginDataExDisplay) => {
+            if (data instanceof PluginDataExDisplayV2 || compareEach) {
+                return data.files[0] as LoadedEntryPluginDataExFile;
+            }
+            const loadDoc = await this.localDatabase.getDBEntry(data.documentPath);
+            if (!loadDoc) return false;
+            const pluginData = deserialize(getDocDataAsArray(loadDoc.data), {}) as PluginDataEx;
+            pluginData.documentPath = data.documentPath;
+            const file = pluginData.files[0];
+            const doc = { ...loadDoc, ...file, datatype: "newnote" } as LoadedEntryPluginDataExFile;
+            return doc;
+        };
+        const fileA = await loadFile(dataA);
+        const fileB = await loadFile(dataB);
+        this._log(`Comparing: ${dataA.documentPath} <-> ${dataB.documentPath}`, LOG_LEVEL_VERBOSE);
+        if (!fileA || !fileB) {
+            this._log(
+                `Could not load ${dataA.name} for comparison: ${!fileA ? dataA.term : ""}${!fileB ? dataB.term : ""}`,
+                LOG_LEVEL_NOTICE
+            );
+            return false;
+        }
+        const path = fileA.filename.split("/").pop() as FilePath;
+        if (path.endsWith(".json")) {
+            return serialized("config:merge-data", async () => {
+                this._log("Opening data-merging dialog", LOG_LEVEL_VERBOSE);
+                return await this.dependencies.resolveJsonConflict(path, [fileA, fileB], dataB.term, async (result) => {
+                    try {
+                        return await this.applyData(dataA, result);
+                    } catch (ex) {
+                        this._log("Could not apply merged file");
+                        this._log(ex, LOG_LEVEL_VERBOSE);
+                        return false;
+                    }
+                });
+            });
+        } else {
+            const dmp = new diff_match_patch();
+            let docAData = getDocData(fileA.data);
+            let docBData = getDocData(fileB.data);
+            if (fileA?.datatype != "plain") {
+                docAData = base64ToString(docAData);
+            }
+            if (fileB?.datatype != "plain") {
+                docBData = base64ToString(docBData);
+            }
+            const diffMap = dmp.diff_linesToChars_(docAData, docBData);
+
+            const diff = dmp.diff_main(diffMap.chars1, diffMap.chars2, false);
+            dmp.diff_charsToLines_(diff, diffMap.lineArray);
+            dmp.diff_cleanupSemantic(diff);
+            const diffResult: diff_result = {
+                left: { rev: "A", ...fileA, data: docAData },
+                right: { rev: "B", ...fileB, data: docBData },
+                diff: diff,
+            };
+            const ret = await this.dependencies.selectTextFile(path, diffResult, dataB.term);
+            if (ret === false) return false;
+            const resultContent = ret == "A" ? docAData : ret == "B" ? docBData : undefined;
+            if (resultContent) {
+                return await this.applyData(dataA, resultContent);
+            }
+            return false;
+        }
+    }
+
+    async duplicateData(data: IPluginDataExDisplay, deviceName: string): Promise<void> {
+        const path = `${this.configDir}/${data.files[0].filename}` as FilePath;
+        await this.dependencies.snapshotOperations.storeCustomizationFiles(path, deviceName);
+        await this.dependencies.catalogueOperations.updatePluginList(
+            false,
+            this.dependencies.path.filenameToUnifiedKey(path, deviceName)
+        );
+    }
+
+    async applyDataV2(data: PluginDataExDisplayV2, content?: string): Promise<boolean> {
+        const baseDir = this.configDir;
+        try {
+            if (content) {
+                // Preserve the inherited truthiness check: an explicitly empty
+                // replacement is treated as the no-content path.
+                const filename = data.files[0].filename;
+                this._log(`Applying ${filename} of ${data.displayName || data.name}..`);
+                const path = `${baseDir}/${filename}` as FilePath;
+                await this.storageAccess.ensureDir(path);
+                // If the content has applied, modified time will be updated to the current time.
+                await this.storageAccess.writeHiddenFileAuto(path, content);
+                await this.dependencies.snapshotOperations.storeCustomisationFileV2(
+                    path,
+                    this.dependencies.getDeviceAndVaultName()
+                );
+            } else {
+                const files = data.files;
+                for (const f of files) {
+                    // If files have applied, modified time will be updated to the current time.
+                    const stat = { mtime: f.mtime, ctime: f.ctime };
+                    const path = `${baseDir}/${f.filename}` as FilePath;
+                    this._log(`Applying ${f.filename} of ${data.displayName || data.name}..`);
+                    // const contentEach = createBlob(f.data);
+                    await this.storageAccess.ensureDir(path);
+
+                    if (f.datatype == "newnote") {
+                        let oldData;
+                        try {
+                            oldData = await this.storageAccess.readHiddenFileBinary(path);
+                        } catch (ex) {
+                            this._log(`Could not read the file ${f.filename}`, LOG_LEVEL_VERBOSE);
+                            this._log(ex, LOG_LEVEL_VERBOSE);
+                            oldData = new ArrayBuffer(0);
+                        }
+                        const content = base64ToArrayBuffer(f.data);
+                        if (await isDocContentSame(oldData, content)) {
+                            this._log(`The file ${f.filename} is already up-to-date`, LOG_LEVEL_VERBOSE);
+                            continue;
+                        }
+                        await this.storageAccess.writeHiddenFileAuto(path, content, stat);
+                    } else {
+                        let oldData;
+                        try {
+                            oldData = await this.storageAccess.readHiddenFileText(path);
+                        } catch (ex) {
+                            this._log(`Could not read the file ${f.filename}`, LOG_LEVEL_VERBOSE);
+                            this._log(ex, LOG_LEVEL_VERBOSE);
+                            oldData = "";
+                        }
+                        const content = getDocData(f.data);
+                        if (await isDocContentSame(oldData, content)) {
+                            this._log(`The file ${f.filename} is already up-to-date`, LOG_LEVEL_VERBOSE);
+                            continue;
+                        }
+                        await this.storageAccess.writeHiddenFileAuto(path, content, stat);
+                    }
+                    this._log(`Applied ${f.filename} of ${data.displayName || data.name}..`);
+                    await this.dependencies.snapshotOperations.storeCustomisationFileV2(
+                        path,
+                        this.dependencies.getDeviceAndVaultName()
+                    );
+                }
+            }
+        } catch (ex) {
+            this._log(`Applying ${data.displayName || data.name}.. Failed`, LOG_LEVEL_NOTICE);
+            this._log(ex, LOG_LEVEL_VERBOSE);
+            return false;
+        }
+        return true;
+    }
+
+    async applyData(data: IPluginDataExDisplay, content?: string): Promise<boolean> {
+        this._log(`Applying ${data.displayName || data.name}..`);
+
+        if (data instanceof PluginDataExDisplayV2) {
+            return this.applyDataV2(data, content);
+        }
+        return this.applyDataV1(data, content);
+    }
+
+    private async applyDataV1(data: IPluginDataExDisplay, content?: string): Promise<boolean> {
+        const baseDir = this.configDir;
+        try {
+            if (!data.documentPath) throw new LiveSyncError("InternalError: Document path not exist");
+            const dx = await this.localDatabase.getDBEntry(data.documentPath);
+            if (dx == false) {
+                throw new LiveSyncError("Not found on database");
+            }
+            const loadedData = deserialize(getDocDataAsArray(dx.data), {}) as PluginDataEx;
+            for (const f of loadedData.files) {
+                this._log(`Applying ${f.filename} of ${data.displayName || data.name}..`);
+                try {
+                    // console.dir(f);
+                    const path = `${baseDir}/${f.filename}`;
+                    await this.storageAccess.ensureDir(path);
+                    if (!content) {
+                        const dt = decodeBinary(f.data);
+                        await this.storageAccess.writeHiddenFileAuto(path, dt);
+                    } else {
+                        await this.storageAccess.writeHiddenFileAuto(path, content);
+                    }
+                    this._log(`Applying ${f.filename} of ${data.displayName || data.name}.. Done`);
+                } catch (ex) {
+                    this._log(`Applying ${f.filename} of ${data.displayName || data.name}.. Failed`);
+                    this._log(ex, LOG_LEVEL_VERBOSE);
+                }
+            }
+            const uPath = `${baseDir}/${loadedData.files[0].filename}` as FilePath;
+            await this.dependencies.snapshotOperations.storeCustomizationFiles(uPath);
+            // The inherited workflow refreshes once through persistence, then
+            // explicitly refreshes again with the dialogue's notice flag.
+            await this.dependencies.catalogueOperations.updatePluginList(true, uPath);
+            await delay(100);
+            this._log(`Config ${data.displayName || data.name} has been applied`, LOG_LEVEL_NOTICE);
+            if (data.category == "PLUGIN_DATA" || data.category == "PLUGIN_MAIN") {
+                await this.dependencies.reloadPlugin(baseDir, data.name);
+            } else if (data.category == "CONFIG") {
+                this.dependencies.askRestart();
+            }
+            return true;
+        } catch (ex) {
+            this._log(`Applying ${data.displayName || data.name}.. Failed`);
+            this._log(ex, LOG_LEVEL_VERBOSE);
+            return false;
+        }
+    }
+
+    async deleteData(data: PluginDataEx): Promise<boolean> {
+        try {
+            if (data.documentPath) {
+                const delList: FilePathWithPrefix[] = [];
+                if (this.dependencies.snapshotOperations.isV2Enabled()) {
+                    const deleteList = this.dependencies.catalogueOperations
+                        .findPlugins(data.documentPath)
+                        .filter((entry) => entry instanceof PluginDataExDisplayV2)
+                        .map((entry) => entry.files)
+                        .flat();
+                    for (const e of deleteList) {
+                        delList.push(e.path);
+                    }
+                }
+                delList.push(data.documentPath);
+                const p = delList.map(async (e) => {
+                    await this.dependencies.snapshotOperations.deleteConfigOnDatabase(e);
+                    // Preserve the inherited unconditional refresh after the
+                    // persistence wrapper, including when it emitted no refresh.
+                    await this.dependencies.catalogueOperations.updatePluginList(false, e);
+                });
+                await Promise.allSettled(p);
+                // Preserve the inherited success result even when individual
+                // deletion/refresh promises settle unsuccessfully.
+                this._log(
+                    `Deleted: ${data.category}/${data.name} of ${data.category} (${delList.length} items)`,
+                    LOG_LEVEL_NOTICE
+                );
+            }
+            return true;
+        } catch (ex) {
+            this._log(`Failed to delete: ${data.documentPath}`, LOG_LEVEL_NOTICE);
+            this._log(ex, LOG_LEVEL_VERBOSE);
+            return false;
+        }
+    }
+}

src/features/ConfigSync/applicationOperations.unit.spec.ts

@@ -0,0 +1,306 @@
+import { describe, expect, it, vi } from "vitest";
+
+const asyncHarness = vi.hoisted(() => ({
+    delay: vi.fn(async () => undefined),
+    fireAndForget: vi.fn((operation: () => unknown) => {
+        void operation();
+    }),
+}));
+
+vi.mock("@/deps.ts", () => ({
+    diff_match_patch: class DiffMatchPatch {},
+    parseYaml: vi.fn(),
+}));
+vi.mock("@/common/translation", () => ({
+    $msg: vi.fn((message: string) => message),
+}));
+vi.mock("@vrtmrz/livesync-commonlib/compat/common/utils", async (importOriginal) => {
+    const actual = await importOriginal<typeof import("@vrtmrz/livesync-commonlib/compat/common/utils")>();
+    return {
+        ...actual,
+        delay: asyncHarness.delay,
+        fireAndForget: asyncHarness.fireAndForget,
+    };
+});
+
+import type { FilePath, FilePathWithPrefix, LoadedEntry } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { PluginManifest } from "@/deps.ts";
+import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
+import { createCustomisationSyncCodec, type PluginDataEx } from "./customisationSyncCodec.ts";
+import { ApplicationOperations, type ApplicationOperationsDependencies } from "./applicationOperations.ts";
+import { PluginDataExDisplayV2 } from "./customisationSyncModel.ts";
+import type { SnapshotPersistenceResult } from "./snapshotPersistence.ts";
+import { SnapshotOperations } from "./snapshotOperations.ts";
+import type { IPluginDataExDisplay } from "./customisationSyncView.ts";
+
+const codec = createCustomisationSyncCodec({ digestHash, parseYaml: () => undefined });
+
+function createOperations() {
+    const events: string[] = [];
+    let usePluginSyncV2 = false;
+    type PersistenceResult = SnapshotPersistenceResult<true>;
+    const getDBEntry = vi.fn(async (_path: FilePathWithPrefix) => false as false | LoadedEntry);
+    const ensureDir = vi.fn(async (_path: string) => {
+        events.push("ensure-dir");
+        return true;
+    });
+    const readHiddenFileBinary = vi.fn(async (_path: string) => new ArrayBuffer(0));
+    const readHiddenFileText = vi.fn(async (_path: string) => "");
+    const writeHiddenFileAuto = vi.fn(async (_path: string, _data: string | ArrayBuffer) => {
+        events.push("write-file");
+        return true;
+    });
+    const storeCustomisationFileV2 = vi.fn(
+        async (): Promise<PersistenceResult> => ({
+            value: true,
+            status: "saved" as const,
+            refreshes: [] as const,
+        })
+    );
+    const storeCustomizationFiles = vi.fn(
+        async (): Promise<PersistenceResult> => ({
+            value: true,
+            status: "saved" as const,
+            refreshes: [] as const,
+        })
+    );
+    const deleteConfigOnDatabase = vi.fn(
+        async (): Promise<PersistenceResult> => ({
+            value: true,
+            status: "deleted" as const,
+            refreshes: [] as const,
+        })
+    );
+    const updatePluginList = vi.fn(async (showMessage: boolean, _path?: FilePathWithPrefix | FilePath) => {
+        events.push(`refresh-v1:${showMessage}`);
+    });
+    const updatePluginListV2 = vi.fn(async (_showMessage: boolean, _path: FilePathWithPrefix) => {
+        events.push("refresh-v2");
+    });
+    const findPlugins = vi.fn(() => [] as readonly IPluginDataExDisplay[]);
+    const reloadPlugin = vi.fn(async (_configDir: string, _pluginName: string) => {
+        events.push("reload-plugin");
+    });
+    const askRestart = vi.fn(() => {
+        events.push("ask-restart");
+    });
+    const catalogueOperations = {
+        findPlugins,
+        manifestLookup: new Map<string, PluginManifest>(),
+        updatePluginList,
+        updatePluginListV2,
+    };
+    const snapshotOperations = new SnapshotOperations({
+        getSettings: () => ({ usePluginSyncV2 }),
+        getDeviceAndVaultName: () => "device-a",
+        log: vi.fn(),
+        snapshotPersistence: {
+            storeCustomisationFileV2,
+            storeCustomizationFiles,
+            deleteConfigOnDatabase,
+        },
+        catalogueOperations,
+    });
+    const dependencies: ApplicationOperationsDependencies = {
+        getLocalDatabase: () => ({ getDBEntry }),
+        storageAccess: {
+            ensureDir,
+            readHiddenFileBinary,
+            readHiddenFileText,
+            writeHiddenFileAuto,
+        },
+        path: {
+            filenameToUnifiedKey: (path, term) => `ix:${term}/CONFIG/${path.split("/").pop()}.md` as FilePathWithPrefix,
+        },
+        log: vi.fn(),
+        getConfigDir: () => ".obsidian",
+        getDeviceAndVaultName: () => "device-a",
+        resolveJsonConflict: vi.fn(async () => false),
+        selectTextFile: vi.fn(async (): Promise<"A" | "B" | false> => false),
+        reloadPlugin,
+        askRestart,
+        snapshotOperations,
+        catalogueOperations,
+    };
+    return {
+        application: new ApplicationOperations(dependencies),
+        dependencies,
+        events,
+        setUseV2: (value: boolean) => {
+            usePluginSyncV2 = value;
+        },
+        getDBEntry,
+        persistence: { deleteConfigOnDatabase, storeCustomisationFileV2, storeCustomizationFiles },
+        catalogue: { findPlugins, updatePluginList, updatePluginListV2 },
+        storage: { ensureDir, readHiddenFileBinary, readHiddenFileText, writeHiddenFileAuto },
+        reloadPlugin,
+        askRestart,
+    };
+}
+
+const display = {
+    documentPath: "ix:device-a/PLUGIN_DATA/example.md" as FilePathWithPrefix,
+    category: "PLUGIN_DATA",
+    name: "example",
+    term: "device-a",
+    files: [
+        { filename: "plugins/example/data.json", data: ["a"], mtime: 1, size: 1 },
+        { filename: "plugins/example/other.json", data: ["b"], mtime: 2, size: 1 },
+    ],
+    mtime: 2,
+} satisfies IPluginDataExDisplay;
+
+describe("Customisation Sync application operations", () => {
+    it("keeps file-level comparison clones and duplication behaviour inside the owner", async () => {
+        const fixture = createOperations();
+        const compareUsingDisplayData = vi
+            .spyOn(fixture.application, "compareUsingDisplayData")
+            .mockResolvedValue(true);
+
+        await expect(
+            fixture.application.compareFileUsingDisplayData(display, display, "plugins/example/data.json")
+        ).resolves.toBe(true);
+        const [left, right, compareEach] = compareUsingDisplayData.mock.calls[0];
+        expect(left.files.map((file) => file.filename)).toEqual(["plugins/example/data.json"]);
+        expect(right.files.map((file) => file.filename)).toEqual(["plugins/example/data.json"]);
+        expect(compareEach).toBe(true);
+        expect(display.files).toHaveLength(2);
+
+        await fixture.application.duplicateData(display, "device-b");
+        expect(fixture.persistence.storeCustomizationFiles).toHaveBeenCalledWith(
+            ".obsidian/plugins/example/data.json",
+            "device-b"
+        );
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false, "ix:device-b/CONFIG/data.json.md");
+    });
+
+    it("uses the compared filename for legacy file comparisons", async () => {
+        const fixture = createOperations();
+
+        await expect(
+            fixture.application.compareFileUsingDisplayData(display, display, "plugins/example/data.json")
+        ).resolves.toBe(false);
+        expect(fixture.dependencies.resolveJsonConflict).toHaveBeenCalledWith(
+            "data.json",
+            expect.any(Array),
+            "device-a",
+            expect.any(Function)
+        );
+    });
+
+    it("awaits V1 refreshes before the explicit effect and preserves reload ordering", async () => {
+        const fixture = createOperations();
+        fixture.setUseV2(false);
+        fixture.persistence.storeCustomizationFiles.mockImplementation(async () => {
+            fixture.events.push("persist");
+            return {
+                value: true,
+                status: "saved" as const,
+                refreshes: [
+                    {
+                        mode: "v1" as const,
+                        timing: "await" as const,
+                        path: "ix:device-a/PLUGIN_MAIN/example.md" as FilePathWithPrefix,
+                    },
+                ],
+            };
+        });
+        fixture.getDBEntry.mockResolvedValue({
+            data: codec.serialize({
+                category: "PLUGIN_MAIN",
+                name: "example",
+                term: "device-a",
+                files: [{ filename: "plugins/example/main.js", data: ["source"], mtime: 1, size: 6 }],
+                mtime: 1,
+            } satisfies PluginDataEx),
+        } as LoadedEntry);
+
+        const data = { ...display, category: "PLUGIN_MAIN", name: "example" } satisfies IPluginDataExDisplay;
+        await expect(fixture.application.applyData(data, "replacement")).resolves.toBe(true);
+
+        expect(fixture.events).toEqual([
+            "ensure-dir",
+            "write-file",
+            "persist",
+            "refresh-v1:false",
+            "refresh-v1:true",
+            "reload-plugin",
+        ]);
+        expect(fixture.reloadPlugin).toHaveBeenCalledWith(".obsidian", "example");
+        expect(asyncHarness.delay).toHaveBeenCalledWith(100);
+    });
+
+    it("starts V2 catalogue refreshes without awaiting them", async () => {
+        const fixture = createOperations();
+        let releaseRefresh!: () => void;
+        const refresh = new Promise<void>((resolve) => {
+            releaseRefresh = resolve;
+        });
+        fixture.setUseV2(true);
+        fixture.persistence.storeCustomisationFileV2.mockResolvedValue({
+            value: true,
+            status: "saved",
+            refreshes: [
+                {
+                    mode: "v2",
+                    timing: "fire-and-forget",
+                    path: "ix:device-a/CONFIG/app.json%app.json" as FilePathWithPrefix,
+                },
+            ],
+        });
+        fixture.catalogue.updatePluginListV2.mockImplementation(async () => await refresh);
+        const data = new PluginDataExDisplayV2(
+            {
+                ...display,
+                files: [{ filename: "app.json", data: ["source"], mtime: 1, size: 6 }],
+            },
+            new Map()
+        );
+
+        await expect(fixture.application.applyData(data, "replacement")).resolves.toBe(true);
+        expect(fixture.catalogue.updatePluginListV2).toHaveBeenCalledWith(
+            false,
+            "ix:device-a/CONFIG/app.json%app.json"
+        );
+        releaseRefresh();
+        await refresh;
+    });
+
+    it("deletes the V2 files and binder through the direct owners", async () => {
+        const fixture = createOperations();
+        fixture.setUseV2(true);
+        const v2Path = "ix:device-a/PLUGIN_DATA/example%data.json" as FilePathWithPrefix;
+        const binderPath = "ix:device-a/PLUGIN_DATA/example.md" as FilePathWithPrefix;
+        const v2Entry = new PluginDataExDisplayV2(
+            {
+                ...display,
+                documentPath: binderPath,
+                files: [
+                    {
+                        filename: "data.json",
+                        path: v2Path,
+                        data: ["source"],
+                        mtime: 1,
+                        ctime: 1,
+                        size: 6,
+                        datatype: "plain",
+                    } as never,
+                ],
+            },
+            new Map()
+        );
+        fixture.catalogue.findPlugins.mockReturnValue([v2Entry]);
+
+        await expect(
+            fixture.application.deleteData({
+                ...display,
+                documentPath: binderPath,
+            })
+        ).resolves.toBe(true);
+
+        expect(fixture.persistence.deleteConfigOnDatabase).toHaveBeenNthCalledWith(1, v2Path, false);
+        expect(fixture.persistence.deleteConfigOnDatabase).toHaveBeenNthCalledWith(2, binderPath, false);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenNthCalledWith(1, false, v2Path);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenNthCalledWith(2, false, binderPath);
+    });
+});

src/features/ConfigSync/catalogueMigration.ts

@@ -0,0 +1,126 @@
+import { createBlob, getDocDataAsArray } from "@vrtmrz/livesync-commonlib/compat/common/utils";
+import type {
+    AnyEntry,
+    FilePathWithPrefix,
+    LOG_LEVEL,
+    SavingEntry,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_INFO, LOG_LEVEL_NOTICE, LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { IPathService } from "@vrtmrz/livesync-commonlib/compat/services/base/IService";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+
+import { ICXHeader } from "@/common/types.ts";
+import type { SnapshotPersistence } from "./snapshotPersistence.ts";
+import type { CustomisationSyncReadCodec } from "./customisationSyncReadOperations.ts";
+
+type CatalogueMigrationDatabase = Pick<LiveSyncLocalDB, "getDBEntry" | "putDBEntry">;
+
+type CatalogueMigrationCodec = Pick<CustomisationSyncReadCodec, "deserialize"> & {
+    dummyHead: string;
+    dummyEnd: string;
+};
+
+export type CatalogueMigrationDependencies = {
+    getLocalDatabase(): CatalogueMigrationDatabase;
+    path: Pick<IPathService, "path2id">;
+    log: LogFunction;
+    snapshotPersistence: Pick<SnapshotPersistence, "deleteConfigOnDatabase">;
+    refreshV1(showMessage: boolean, path: FilePathWithPrefix): Promise<void>;
+    codec: CatalogueMigrationCodec;
+};
+
+/** Bridges persisted V1 binders into the V2 per-file document format. */
+export class CatalogueMigration {
+    constructor(private readonly dependencies: CatalogueMigrationDependencies) {}
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string): void {
+        this.dependencies.log(message, level, key);
+    }
+
+    async migrateV1ToV2(showMessage: boolean, entry: AnyEntry): Promise<void> {
+        const v1Path = entry.path;
+        this._log(`Migrating ${entry.path} to V2`, showMessage ? LOG_LEVEL_NOTICE : LOG_LEVEL_INFO);
+        if (entry.deleted) {
+            this._log(`The entry ${v1Path} is already deleted`, LOG_LEVEL_VERBOSE);
+            return;
+        }
+        // Compatibility question: the inherited conjunction admits any `ix:`
+        // path or any `.md` path, although the log describes a stricter binder
+        // check. Preserve it until malformed migration candidates are covered.
+        if (!v1Path.endsWith(".md") && !v1Path.startsWith(ICXHeader)) {
+            this._log(`The entry ${v1Path} is not a customisation sync binder`, LOG_LEVEL_VERBOSE);
+            return;
+        }
+        if (v1Path.indexOf("%") !== -1) {
+            this._log(`The entry ${v1Path} is already migrated`, LOG_LEVEL_VERBOSE);
+            return;
+        }
+        const loadedEntry = await this.dependencies.getLocalDatabase().getDBEntry(v1Path);
+        if (!loadedEntry) {
+            this._log(`The entry ${v1Path} is not found`, LOG_LEVEL_VERBOSE);
+            return;
+        }
+
+        const pluginData = this.dependencies.codec.deserialize(getDocDataAsArray(loadedEntry.data), {}) as {
+            category: string;
+            files: Array<{ filename: string; data: string[] }>;
+        };
+        const prefixPath = v1Path.slice(0, -".md".length) + "%";
+        const category = pluginData.category;
+
+        for (const f of pluginData.files) {
+            const stripTable: Record<string, number> = {
+                CONFIG: 0,
+                THEME: 2,
+                SNIPPET: 1,
+                PLUGIN_MAIN: 2,
+                PLUGIN_DATA: 2,
+                PLUGIN_ETC: 2,
+            };
+            const deletePrefixCount = stripTable?.[category] ?? 1;
+            const relativeFilename = f.filename.split("/").slice(deletePrefixCount).join("/");
+            const v2Path = (prefixPath + relativeFilename) as FilePathWithPrefix;
+            this._log(`Migrating ${v1Path} / ${relativeFilename} to ${v2Path}`, LOG_LEVEL_VERBOSE);
+            const newId = await this.dependencies.path.path2id(v2Path);
+
+            const data = createBlob([
+                this.dependencies.codec.dummyHead,
+                this.dependencies.codec.dummyEnd,
+                ...getDocDataAsArray(f.data),
+            ]);
+            const saving: SavingEntry = {
+                ...loadedEntry,
+                _rev: undefined,
+                _id: newId,
+                path: v2Path,
+                data,
+                datatype: "plain",
+                type: "plain",
+                children: [],
+                eden: {},
+            };
+            const result = await this.dependencies.getLocalDatabase().putDBEntry(saving);
+            if (result && result.ok) {
+                this._log(`Migrated ${v1Path} / ${f.filename} to ${v2Path}`, LOG_LEVEL_INFO);
+                const deletion = await this.dependencies.snapshotPersistence.deleteConfigOnDatabase(v1Path);
+                const deleted = deletion.value;
+                if (deleted) {
+                    this._log(`Deleted ${v1Path} successfully`, LOG_LEVEL_INFO);
+                } else {
+                    this._log(`Failed to delete ${v1Path}`, LOG_LEVEL_NOTICE);
+                }
+                // Compatibility: the inherited migration called the context
+                // deletion wrapper, which awaited its V1 catalogue refresh.
+                // Apply that refresh explicitly now that deletion is a host-
+                // neutral persistence operation, and only when deletion emitted
+                // the same mutation outcome.
+                for (const refresh of deletion.refreshes) {
+                    if (refresh.mode == "v1" && refresh.timing == "await") {
+                        await this.dependencies.refreshV1(false, refresh.path);
+                    }
+                }
+            }
+        }
+    }
+}

src/features/ConfigSync/catalogueOperations.ts

@@ -0,0 +1,216 @@
+import { parseYaml } from "@/deps.ts";
+import { writable } from "svelte/store";
+import type {
+    AnyEntry,
+    FilePathWithPrefix,
+    LoadedEntry,
+    LOG_LEVEL,
+    ObsidianLiveSyncSettings,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { ICXHeader } from "@/common/types.ts";
+import { fireAndForget } from "@vrtmrz/livesync-commonlib/compat/common/utils";
+import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
+import { QueueProcessor } from "octagonal-wheels/concurrency/processor";
+import { reactiveSource, type ReactiveSource } from "octagonal-wheels/dataobject/reactive";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { IPathService } from "@vrtmrz/livesync-commonlib/compat/services/base/IService";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+
+import { CatalogueMigration } from "./catalogueMigration.ts";
+import { CatalogueState } from "./catalogueState.ts";
+import { CatalogueV1 } from "./catalogueV1.ts";
+import { CatalogueV2 } from "./catalogueV2.ts";
+import { createCustomisationSyncCodec } from "./customisationSyncCodec.ts";
+import type { SnapshotPersistence } from "./snapshotPersistence.ts";
+import type { IPluginDataExDisplay, LoadedEntryPluginDataExFile } from "./customisationSyncView.ts";
+
+const {
+    serialize,
+    deserialize,
+    dummyHead: DUMMY_HEAD,
+    dummyEnd: DUMMY_END,
+} = createCustomisationSyncCodec({ digestHash, parseYaml });
+const READ_CODEC = { deserialize, serialize };
+const MIGRATION_CODEC = { deserialize, dummyHead: DUMMY_HEAD, dummyEnd: DUMMY_END };
+const V2_CODEC = { dummyEnd: DUMMY_END };
+
+type CatalogueSettings = Pick<ObsidianLiveSyncSettings, "usePluginSync" | "usePluginSyncV2">;
+
+type CatalogueDatabase = Pick<LiveSyncLocalDB, "findEntries" | "getDBEntry" | "putDBEntry">;
+
+export type CatalogueOperationsDependencies = {
+    getSettings(): CatalogueSettings;
+    getLocalDatabase(): CatalogueDatabase;
+    path: Pick<IPathService, "getPath" | "path2id">;
+    log: LogFunction;
+    snapshotPersistence: Pick<SnapshotPersistence, "deleteConfigOnDatabase">;
+    publishScanCount(count: number): void;
+};
+
+/** Coordinates the shared catalogue state, scan queue, and format modules. */
+export class CatalogueOperations {
+    private readonly dependencies: CatalogueOperationsDependencies;
+    private readonly catalogueState = new CatalogueState();
+    private readonly scanProgress = reactiveSource(0);
+    private readonly pluginScanningChanged: Parameters<ReactiveSource<number>["onChanged"]>[0] = (event) => {
+        this.enumerationActive.set(event.value != 0);
+        this.dependencies.publishScanCount(event.value);
+    };
+    private readonly pluginScanProcessor: QueueProcessor<AnyEntry, AnyEntry>;
+    private readonly catalogueV1: CatalogueV1;
+    private readonly catalogueV2: CatalogueV2;
+    private readonly catalogueMigration: CatalogueMigration;
+
+    readonly enumerationActive = writable(false);
+    readonly catalogue = this.catalogueState.catalogue;
+    readonly migrationProgress = this.catalogueState.migrationProgress;
+    readonly manifests = this.catalogueState.manifests;
+
+    constructor(dependencies: CatalogueOperationsDependencies) {
+        this.dependencies = dependencies;
+
+        this.catalogueV1 = new CatalogueV1({
+            getLocalDatabase: () => this.dependencies.getLocalDatabase(),
+            path: {
+                getPath: (entry) => this.getPath(entry),
+            },
+            log: (message, level, key) => this._log(message, level, key),
+            state: this.catalogueState,
+        });
+        this.catalogueV2 = new CatalogueV2({
+            getLocalDatabase: () => this.dependencies.getLocalDatabase(),
+            log: (message, level, key) => this._log(message, level, key),
+            state: this.catalogueState,
+            codec: V2_CODEC,
+        });
+        this.catalogueMigration = new CatalogueMigration({
+            getLocalDatabase: () => this.dependencies.getLocalDatabase(),
+            path: {
+                path2id: (path) => this.path2id(path),
+            },
+            log: (message, level, key) => this._log(message, level, key),
+            snapshotPersistence: this.dependencies.snapshotPersistence,
+            refreshV1: async (showMessage, path) => await this.updatePluginList(showMessage, path),
+            codec: MIGRATION_CODEC,
+        });
+
+        this.scanProgress.onChanged(this.pluginScanningChanged);
+        // The single queue deliberately chooses V1 loading or migration when
+        // each item starts. Settings can change after enqueueing an item.
+        this.pluginScanProcessor = new QueueProcessor(
+            async (v: AnyEntry[]) => {
+                const plugin = v[0];
+                if (this.dependencies.getSettings().usePluginSyncV2) {
+                    await this.migrateV1ToV2(false, plugin);
+                    return [];
+                }
+                await this.catalogueV1.load(plugin, READ_CODEC);
+                return [];
+            },
+            {
+                suspended: false,
+                batchSize: 1,
+                concurrentLimit: 10,
+                delay: 100,
+                yieldThreshold: 10,
+                maintainDelay: false,
+                totalRemainingReactiveSource: this.scanProgress,
+            }
+        ).startPipeline();
+    }
+
+    private get settings() {
+        return this.dependencies.getSettings();
+    }
+
+    private get localDatabase() {
+        return this.dependencies.getLocalDatabase();
+    }
+
+    private getPath(entry: AnyEntry): FilePathWithPrefix {
+        return this.dependencies.path.getPath(entry);
+    }
+
+    private async path2id(filename: FilePathWithPrefix) {
+        return await this.dependencies.path.path2id(filename);
+    }
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string): void {
+        this.dependencies.log(message, level, key);
+    }
+
+    /** The current manifest lookup passed to V2 display rows. */
+    get manifestLookup() {
+        return this.catalogueState.manifestLookup;
+    }
+
+    /** Returns every row matching a document path, preserving legacy duplicates. */
+    findPlugins(documentPath: FilePathWithPrefix | string): readonly IPluginDataExDisplay[] {
+        return this.catalogueState.findPlugins(documentPath);
+    }
+
+    dispose(): void {
+        this.pluginScanProcessor.terminate();
+        this.scanProgress.offChanged(this.pluginScanningChanged);
+        this.enumerationActive.set(false);
+        this.dependencies.publishScanCount(0);
+    }
+
+    async reloadPluginList(showMessage: boolean): Promise<void> {
+        this.catalogueState.clearForReload();
+        await this.updatePluginList(showMessage);
+    }
+
+    async updatePluginList(showMessage: boolean, updatedDocumentPath?: FilePathWithPrefix): Promise<void> {
+        if (!this.settings.usePluginSync) {
+            this.pluginScanProcessor.clearQueue();
+            this.catalogueState.clearForDisabledRefresh();
+            return;
+        }
+        try {
+            this.catalogueState.beginUpdate();
+            const updatedDocumentId = updatedDocumentPath ? await this.path2id(updatedDocumentPath) : "";
+            const plugins = updatedDocumentPath
+                ? this.localDatabase.findEntries(updatedDocumentId, updatedDocumentId + "\u{10ffff}", {
+                      include_docs: true,
+                      key: updatedDocumentId,
+                      limit: 1,
+                  })
+                : this.localDatabase.findEntries(ICXHeader + "", `${ICXHeader}\u{10ffff}`, { include_docs: true });
+            for await (const v of plugins) {
+                if (v.deleted || v._deleted) continue;
+                if (v.path.indexOf("%") !== -1) {
+                    fireAndForget(() => this.updatePluginListV2(showMessage, v.path));
+                    continue;
+                }
+
+                const path = v.path || this.getPath(v);
+                if (updatedDocumentPath && updatedDocumentPath != path) continue;
+                this.pluginScanProcessor.enqueue(v);
+            }
+        } finally {
+            this.enumerationActive.set(false);
+            this.catalogueState.endUpdate();
+        }
+        this.enumerationActive.set(false);
+    }
+
+    async createPluginDataExFileV2(
+        unifiedPathV2: FilePathWithPrefix,
+        loaded?: LoadedEntry
+    ): Promise<false | LoadedEntryPluginDataExFile> {
+        return await this.catalogueV2.createPluginDataExFileV2(unifiedPathV2, loaded);
+    }
+
+    createPluginDataFromV2(unifiedPathV2: FilePathWithPrefix) {
+        return this.catalogueV2.createPluginDataFromV2(unifiedPathV2);
+    }
+
+    async updatePluginListV2(showMessage: boolean, unifiedFilenameWithKey: FilePathWithPrefix): Promise<void> {
+        await this.catalogueV2.updatePluginListV2(showMessage, unifiedFilenameWithKey);
+    }
+
+    private async migrateV1ToV2(showMessage: boolean, entry: AnyEntry): Promise<void> {
+        await this.catalogueMigration.migrateV1ToV2(showMessage, entry);
+    }
+}

src/features/ConfigSync/catalogueOperations.unit.spec.ts

@@ -0,0 +1,222 @@
+import { get } from "svelte/store";
+import { beforeEach, describe, expect, it, vi } from "vitest";
+
+const testState = vi.hoisted(() => ({
+    processors: [] as Array<{
+        clearQueue: ReturnType<typeof vi.fn>;
+        enqueue: ReturnType<typeof vi.fn>;
+        terminate: ReturnType<typeof vi.fn>;
+        startPipeline: ReturnType<typeof vi.fn>;
+        process: (entries: AnyEntry[]) => Promise<AnyEntry[]>;
+    }>,
+    reactiveSources: [] as Array<{
+        value: number;
+        onChanged: ReturnType<typeof vi.fn>;
+        offChanged: ReturnType<typeof vi.fn>;
+    }>,
+}));
+
+vi.mock("@/deps.ts", () => ({
+    parseYaml: vi.fn(),
+}));
+vi.mock("@/common/types.ts", () => ({
+    ICXHeader: "ix:",
+}));
+vi.mock("@/common/utils.ts", () => ({
+    fireAndForget: vi.fn(),
+    scheduleTask: vi.fn(),
+}));
+vi.mock("octagonal-wheels/concurrency/processor", () => ({
+    QueueProcessor: class QueueProcessor {
+        clearQueue = vi.fn();
+        enqueue = vi.fn();
+        terminate = vi.fn();
+        startPipeline = vi.fn(() => this);
+
+        process: (entries: AnyEntry[]) => Promise<AnyEntry[]>;
+
+        constructor(process: (entries: AnyEntry[]) => Promise<AnyEntry[]>) {
+            this.process = process;
+            testState.processors.push(this);
+        }
+    },
+}));
+vi.mock("octagonal-wheels/dataobject/reactive", () => ({
+    reactiveSource: vi.fn((value: number) => {
+        const source = {
+            value,
+            onChanged: vi.fn(),
+            offChanged: vi.fn(),
+        };
+        testState.reactiveSources.push(source);
+        return source;
+    }),
+}));
+
+import { scheduleTask } from "@/common/utils.ts";
+import type {
+    AnyEntry,
+    DocumentID,
+    FilePathWithPrefix,
+    LoadedEntry,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
+import { createCustomisationSyncCodec } from "./customisationSyncCodec.ts";
+import { CatalogueOperations, type CatalogueOperationsDependencies } from "./catalogueOperations.ts";
+import type { SnapshotPersistenceResult } from "./snapshotPersistence.ts";
+
+const codec = createCustomisationSyncCodec({
+    digestHash,
+    parseYaml: () => undefined,
+});
+const v2Path = "ix:device-a/PLUGIN_DATA/example%data.json" as FilePathWithPrefix;
+const v1Path = "ix:device-a/CONFIG/app.json.md" as FilePathWithPrefix;
+
+function loadedEntry(): LoadedEntry {
+    const data = `${codec.dummyHead}${codec.dummyEnd}${btoa("example data")}`;
+    return {
+        _id: "entry-id",
+        _rev: "1-a",
+        path: v2Path,
+        type: "plain",
+        datatype: "plain",
+        data,
+        ctime: 10,
+        mtime: 20,
+        size: data.length,
+        children: [],
+        eden: {},
+    } as unknown as LoadedEntry;
+}
+
+function createOperations() {
+    const settings = { usePluginSync: true, usePluginSyncV2: true };
+    const database = {
+        findEntries: vi.fn(async function* () {
+            // No refresh entries are needed by the focused V2 test.
+        }),
+        getDBEntry: vi.fn(async () => loadedEntry()),
+        putDBEntry: vi.fn(async () => ({ ok: true, id: "entry-id", rev: "2-b" })),
+    };
+    const deleteConfigOnDatabase = vi.fn(
+        async (): Promise<SnapshotPersistenceResult<boolean>> => ({
+            value: true,
+            status: "missing",
+            refreshes: [],
+        })
+    );
+    const snapshotPersistence = {
+        deleteConfigOnDatabase,
+    };
+    const dependencies: CatalogueOperationsDependencies = {
+        getSettings: () => settings,
+        getLocalDatabase: () => database,
+        path: {
+            getPath: (entry) => entry.path,
+            path2id: async (path) => path as unknown as DocumentID,
+        },
+        log: vi.fn(),
+        snapshotPersistence,
+        publishScanCount: vi.fn(),
+    };
+    return {
+        database,
+        dependencies,
+        settings,
+        operations: new CatalogueOperations(dependencies),
+        snapshotPersistence,
+    };
+}
+
+describe("Customisation Sync catalogue operations", () => {
+    beforeEach(() => {
+        testState.processors.length = 0;
+        testState.reactiveSources.length = 0;
+        vi.clearAllMocks();
+    });
+
+    it("owns and releases the active shared scan processor and its progress subscription", () => {
+        const { dependencies, operations } = createOperations();
+        operations.enumerationActive.set(true);
+
+        operations.dispose();
+
+        expect(testState.processors).toHaveLength(1);
+        expect(testState.processors[0].terminate).toHaveBeenCalledOnce();
+        expect(testState.reactiveSources[0].offChanged).toHaveBeenCalledOnce();
+        expect(get(operations.enumerationActive)).toBe(false);
+        expect(dependencies.publishScanCount).toHaveBeenCalledWith(0);
+    });
+
+    it("chooses loading or migration when queued work starts", async () => {
+        const { operations, settings } = createOperations();
+        const migrate = vi
+            .spyOn(
+                operations as unknown as { migrateV1ToV2: (showMessage: boolean, entry: AnyEntry) => Promise<void> },
+                "migrateV1ToV2"
+            )
+            .mockResolvedValue(undefined);
+        const entry = { path: v1Path, deleted: false } as AnyEntry;
+
+        settings.usePluginSyncV2 = false;
+        await testState.processors[0].process([entry]);
+        expect(migrate).not.toHaveBeenCalled();
+
+        settings.usePluginSyncV2 = true;
+        await testState.processors[0].process([entry]);
+        expect(migrate).toHaveBeenCalledOnce();
+        operations.dispose();
+    });
+
+    it("keeps V2 row publication delayed behind the process-global refresh task", async () => {
+        const { operations } = createOperations();
+
+        await operations.updatePluginListV2(false, v2Path);
+
+        expect(get(operations.catalogue)).toEqual([]);
+        expect(scheduleTask).toHaveBeenCalledWith("updatePluginListV2", 100, expect.any(Function));
+
+        const publish = vi.mocked(scheduleTask).mock.calls[0]?.[2] as (() => void) | undefined;
+        publish?.();
+
+        expect(get(operations.catalogue)).toHaveLength(1);
+        expect(get(operations.catalogue)[0]).toMatchObject({
+            documentPath: "ix:device-a/PLUGIN_DATA/example.md",
+            files: [{ filename: "plugins/example/data.json" }],
+        });
+        operations.dispose();
+    });
+
+    it("uses the persistence deletion outcome and explicitly awaits migration refresh", async () => {
+        const { database, operations, snapshotPersistence } = createOperations();
+        const loadedV1 = {
+            ...loadedEntry(),
+            path: v1Path,
+            data: codec.serialize({
+                category: "CONFIG",
+                name: "app.json",
+                term: "device-a",
+                files: [{ filename: "app.json", data: [btoa("config")], mtime: 10, size: 6 }],
+                mtime: 10,
+            }),
+        } as LoadedEntry;
+        database.getDBEntry.mockResolvedValue(loadedV1);
+        snapshotPersistence.deleteConfigOnDatabase.mockResolvedValue({
+            value: true,
+            status: "deleted",
+            refreshes: [{ mode: "v1", timing: "await", path: v1Path }],
+        });
+        const refresh = vi.spyOn(operations, "updatePluginList").mockResolvedValue(undefined);
+
+        await (
+            operations as unknown as {
+                migrateV1ToV2(showMessage: boolean, entry: LoadedEntry): Promise<void>;
+            }
+        ).migrateV1ToV2(false, { path: v1Path, deleted: false } as LoadedEntry);
+
+        expect(database.putDBEntry).toHaveBeenCalledOnce();
+        expect(snapshotPersistence.deleteConfigOnDatabase).toHaveBeenCalledWith(v1Path);
+        expect(refresh).toHaveBeenCalledWith(false, v1Path);
+        operations.dispose();
+    });
+});

src/features/ConfigSync/catalogueState.ts

@@ -9,11 +9,12 @@ import type { IPluginDataExDisplay } from "./customisationSyncView.ts";
 /**
  * Owns the transient catalogue projection used by Customisation Sync.
  *
- * The database and storage operations remain in the context. This owner only
+ * The database and storage operations remain in the catalogue modules. This
- * coordinates the in-memory rows, their reactive publications, manifest
+ * owner only coordinates the in-memory rows, their reactive publications,
- * lookup, and the update counter which is derived from those operations.
+ * manifest lookup, and the update counter which is derived from those
+ * operations.
  */
-export class CustomisationSyncCatalogueState {
+export class CatalogueState {
     private catalogueRows: IPluginDataExDisplay[] = [];
     private readonly manifestByKey = new Map<string, PluginManifest>();
     private readonly loadedManifestMTimeByKey = new Map<string, number>();
@@ -33,7 +34,7 @@ export class CustomisationSyncCatalogueState {
         return this.loadedManifestMTimeByKey;
     }
 
-    /** Returns the authoritative row for a V1 document path, when present. */
+    /** Returns the authoritative row for a document path, when present. */
     findPlugin(documentPath: FilePathWithPrefix | string): IPluginDataExDisplay | undefined {
         return this.catalogueRows.find((entry) => entry.documentPath == documentPath);
     }

src/features/ConfigSync/catalogueState.unit.spec.ts

@@ -3,7 +3,7 @@ import { describe, expect, it, vi } from "vitest";
 import type { PluginManifest } from "@/deps.ts";
 import type { FilePathWithPrefix } from "@vrtmrz/livesync-commonlib/compat/common/types";
 
-import { CustomisationSyncCatalogueState } from "./customisationSyncCatalogueState.ts";
+import { CatalogueState } from "./catalogueState.ts";
 import { PluginDataExDisplayV2 } from "./customisationSyncModel.ts";
 import type { IPluginDataExDisplay, LoadedEntryPluginDataExFile } from "./customisationSyncView.ts";
 
@@ -30,7 +30,7 @@ function file(filename: string, mtime: number): LoadedEntryPluginDataExFile {
 
 describe("Customisation Sync catalogue state", () => {
     it("publishes V1 replacement and keeps V2 replacement delayed", async () => {
-        const state = new CustomisationSyncCatalogueState();
+        const state = new CatalogueState();
         const setCatalogue = vi.spyOn(state.catalogue, "set");
         const row = display();
 
@@ -54,7 +54,7 @@ describe("Customisation Sync catalogue state", () => {
     });
 
     it("retains the first parsed manifest and records failed mtimes", () => {
-        const state = new CustomisationSyncCatalogueState();
+        const state = new CatalogueState();
         const first = { name: "First", version: "1.0.0" } as PluginManifest;
         const parseManifest = vi.fn(() => first);
 
@@ -69,7 +69,7 @@ describe("Customisation Sync catalogue state", () => {
         expect(state.loadedManifestMTime.get("device-a/plugins/example")).toBe(20);
         expect(parseManifest).toHaveBeenCalledOnce();
 
-        const failedState = new CustomisationSyncCatalogueState();
+        const failedState = new CatalogueState();
         const onParseError = vi.fn();
         const failure = new SyntaxError("invalid");
         failedState.processManifest(
@@ -88,7 +88,7 @@ describe("Customisation Sync catalogue state", () => {
     });
 
     it("clears rows and loaded mtimes on reload while retaining manifest lookup", () => {
-        const state = new CustomisationSyncCatalogueState();
+        const state = new CatalogueState();
         const key = "device-a/plugins/example";
         state.processManifest(key, 20, () => ({ name: "Example" }) as PluginManifest);
         state.replacePlugin(display());
@@ -102,7 +102,7 @@ describe("Customisation Sync catalogue state", () => {
     });
 
     it("keeps manifest caches through the narrower disabled refresh", () => {
-        const state = new CustomisationSyncCatalogueState();
+        const state = new CatalogueState();
         const key = "device-a/plugins/example";
         state.processManifest(key, 20, () => ({ name: "Example" }) as PluginManifest);
         state.replacePlugin(display());
@@ -115,7 +115,7 @@ describe("Customisation Sync catalogue state", () => {
     });
 
     it("tracks V2 updates through migration progress", () => {
-        const state = new CustomisationSyncCatalogueState();
+        const state = new CatalogueState();
 
         state.beginUpdate();
         state.beginUpdate();

src/features/ConfigSync/catalogueV1.ts

@@ -0,0 +1,50 @@
+import type { AnyEntry, LOG_LEVEL } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_NOTICE, LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { IPathService } from "@vrtmrz/livesync-commonlib/compat/services/base/IService";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+
+import { CatalogueState } from "./catalogueState.ts";
+import { loadCustomisationDisplayData, type CustomisationSyncReadCodec } from "./customisationSyncReadOperations.ts";
+
+type CatalogueV1Database = Pick<LiveSyncLocalDB, "getDBEntry" | "putDBEntry">;
+
+export type CatalogueV1Dependencies = {
+    getLocalDatabase(): CatalogueV1Database;
+    path: Pick<IPathService, "getPath">;
+    log: LogFunction;
+    state: CatalogueState;
+};
+
+/** Loads and publishes legacy V1 catalogue rows. */
+export class CatalogueV1 {
+    constructor(private readonly dependencies: CatalogueV1Dependencies) {}
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string): void {
+        this.dependencies.log(message, level, key);
+    }
+
+    async load(entry: AnyEntry, codec: CustomisationSyncReadCodec): Promise<void> {
+        const path = entry.path || this.dependencies.path.getPath(entry);
+        const oldEntry = this.dependencies.state.findPlugin(path);
+        if (oldEntry && oldEntry.mtime == entry.mtime) return;
+        try {
+            const pluginData = await loadCustomisationDisplayData(
+                {
+                    getLocalDatabase: () => this.dependencies.getLocalDatabase(),
+                    path: this.dependencies.path,
+                    log: this.dependencies.log,
+                },
+                path,
+                codec
+            );
+            if (pluginData) {
+                this.dependencies.state.replacePlugin(pluginData);
+            }
+            // Failed to load
+        } catch (ex) {
+            this._log(`Something happened at enumerating customization :${path}`, LOG_LEVEL_NOTICE);
+            this._log(ex, LOG_LEVEL_VERBOSE);
+        }
+    }
+}

src/features/ConfigSync/catalogueV2.ts

@@ -0,0 +1,123 @@
+import type { PluginManifest } from "@/deps.ts";
+import type { FilePathWithPrefix, LoadedEntry, LOG_LEVEL } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+
+import { scheduleTask } from "@/common/utils.ts";
+import { CatalogueState } from "./catalogueState.ts";
+import { PluginDataExDisplayV2 } from "./customisationSyncModel.ts";
+import { parseCustomisationSyncV2DocumentPath } from "./customisationSyncPaths.ts";
+import { decodeCustomisationSyncV2File, loadCustomisationV2Entry } from "./customisationSyncReadOperations.ts";
+import type { LoadedEntryPluginDataExFile } from "./customisationSyncView.ts";
+
+type CatalogueV2Database = Pick<LiveSyncLocalDB, "getDBEntry">;
+
+export type CatalogueV2Dependencies = {
+    getLocalDatabase(): CatalogueV2Database;
+    log: LogFunction;
+    state: CatalogueState;
+    codec: { dummyEnd: string };
+};
+
+/** Builds, updates, and publishes V2 catalogue rows and manifests. */
+export class CatalogueV2 {
+    constructor(private readonly dependencies: CatalogueV2Dependencies) {}
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string): void {
+        this.dependencies.log(message, level, key);
+    }
+
+    get manifestLookup() {
+        return this.dependencies.state.manifestLookup;
+    }
+
+    async createPluginDataExFileV2(
+        unifiedPathV2: FilePathWithPrefix,
+        loaded?: LoadedEntry
+    ): Promise<false | LoadedEntryPluginDataExFile> {
+        // Compatibility: a caller-supplied entry bypasses the database lookup
+        // and the isLoadedEntry check performed by loadCustomisationV2Entry.
+        const loadedEntry =
+            loaded ??
+            (await loadCustomisationV2Entry(
+                {
+                    getLocalDatabase: () => this.dependencies.getLocalDatabase(),
+                    log: this.dependencies.log,
+                },
+                unifiedPathV2
+            ));
+        if (!loadedEntry) return false;
+        const { confKey, file, isManifest } = decodeCustomisationSyncV2File(
+            unifiedPathV2,
+            loadedEntry,
+            this.dependencies.codec.dummyEnd
+        );
+        if (isManifest) {
+            this.dependencies.state.processManifest(
+                confKey,
+                file.mtime,
+                () => JSON.parse(file.data[0]) as PluginManifest,
+                (error) => {
+                    this._log(
+                        `The file ${loadedEntry.path} seems to manifest, but could not be decoded as JSON`,
+                        LOG_LEVEL_VERBOSE
+                    );
+                    this._log(error, LOG_LEVEL_VERBOSE);
+                }
+            );
+        }
+        return file;
+    }
+
+    createPluginDataFromV2(unifiedPathV2: FilePathWithPrefix): PluginDataExDisplayV2 | undefined {
+        const { category, device, key, pathV1 } = parseCustomisationSyncV2DocumentPath(unifiedPathV2);
+        if (category == "") return;
+
+        return new PluginDataExDisplayV2(
+            {
+                documentPath: pathV1,
+                category,
+                name: key,
+                term: `${device}`,
+                files: [],
+                mtime: 0,
+            },
+            this.dependencies.state.manifestLookup
+        );
+    }
+
+    async updatePluginListV2(showMessage: boolean, unifiedFilenameWithKey: FilePathWithPrefix): Promise<void> {
+        // The public parameter is retained for the established catalogue
+        // signature; V2 publication has never used it.
+        void showMessage;
+        try {
+            this.dependencies.state.beginUpdate();
+            const { pathV1 } = parseCustomisationSyncV2DocumentPath(unifiedFilenameWithKey);
+
+            const oldEntry = this.dependencies.state.findPlugin(pathV1);
+            let entry: PluginDataExDisplayV2 | undefined;
+            // Compatibility question: when a V1 row is found first for this
+            // logical path, the inherited implementation constructs a fresh
+            // V2 row rather than looking for another existing V2 row. Preserve
+            // that selection until mixed-format catalogue races are covered.
+            if (!oldEntry || !(oldEntry instanceof PluginDataExDisplayV2)) {
+                entry = this.createPluginDataFromV2(unifiedFilenameWithKey);
+            } else {
+                entry = oldEntry;
+            }
+            if (!entry) return;
+
+            const file = await this.createPluginDataExFileV2(unifiedFilenameWithKey);
+            // Compatibility: the inherited update always re-adds an empty V2
+            // row after deleting its final file.
+            await this.dependencies.state.updateV2Plugin(entry, file, unifiedFilenameWithKey);
+
+            scheduleTask("updatePluginListV2", 100, () => {
+                this.dependencies.state.publishCatalogue();
+            });
+        } finally {
+            this.dependencies.state.endUpdate();
+        }
+    }
+}

src/features/ConfigSync/customisationSyncContext.command.unit.spec.ts

@@ -64,27 +64,17 @@ describe("CustomisationSyncContext commands", () => {
         expect(updatePluginList).toHaveBeenCalledWith(false, "ix:example");
     });
 
-    it("releases every owned processor and reactive subscription", () => {
+    it("delegates catalogue resource release during disposal", () => {
         const hideConfigurationNotice = vi.fn();
-        const publishScanCount = vi.fn();
         const periodicPluginSweepProcessor = { disable: vi.fn() };
-        const pluginScanProcessor = { terminate: vi.fn() };
+        const catalogueOperations = { dispose: vi.fn() };
-        const pluginScanProcessorV2 = { terminate: vi.fn() };
-        const pluginScanningChanged = vi.fn();
-        const offChanged = vi.fn();
-        const setEnumerationActive = vi.fn();
         const configSync = Object.create(CustomisationSyncContext.prototype) as CustomisationSyncContext;
         Object.assign(configSync, {
             dependencies: createCustomisationSyncTestDependencies({
                 hideConfigurationNotice,
-                publishScanCount,
             }),
             periodicPluginSweepProcessor,
-            pluginScanProcessor,
+            catalogueOperations,
-            pluginScanProcessorV2,
-            pluginScanningChanged,
-            scanProgress: { offChanged },
-            enumerationActive: { set: setEnumerationActive },
         });
 
         configSync.dispose();
@@ -92,11 +82,7 @@ describe("CustomisationSyncContext commands", () => {
         expect(cancelTask).toHaveBeenCalledWith("config-sync:updated-configuration");
         expect(hideConfigurationNotice).toHaveBeenCalledOnce();
         expect(periodicPluginSweepProcessor.disable).toHaveBeenCalledOnce();
-        expect(pluginScanProcessor.terminate).toHaveBeenCalledOnce();
+        expect(catalogueOperations.dispose).toHaveBeenCalledOnce();
-        expect(pluginScanProcessorV2.terminate).toHaveBeenCalledOnce();
-        expect(offChanged).toHaveBeenCalledWith(pluginScanningChanged);
-        expect(setEnumerationActive).toHaveBeenCalledWith(false);
-        expect(publishScanCount).toHaveBeenCalledWith(0);
     });
 
     it("characterises the inherited setting-realisation gates pending separate review", async () => {

src/features/ConfigSync/customisationSyncContext.routing.unit.spec.ts

@@ -90,9 +90,9 @@ describe("Customisation Sync raw-event admission", () => {
     it("rejects a path outside the recognised Customisation Sync categories", async () => {
         const { configSync, ownsLocalFile } = createConfigSync();
 
-        await expect(configSync.serviceHandlers.processOptionalFileEvent(".obsidian/workspace" as FilePath)).resolves.toBe(
+        await expect(
-            false
+            configSync.serviceHandlers.processOptionalFileEvent(".obsidian/workspace" as FilePath)
-        );
+        ).resolves.toBe(false);
         expect(ownsLocalFile).not.toHaveBeenCalled();
         expect(scheduleTask).not.toHaveBeenCalled();
     });

src/features/ConfigSync/customisationSyncContext.scan-routing.unit.spec.ts

@@ -1,5 +1,4 @@
 import { describe, expect, it, vi } from "vitest";
-import type { FilePath, FilePathWithPrefix } from "@vrtmrz/livesync-commonlib/compat/common/types";
 
 vi.mock("@/deps.ts", () => ({
     diff_match_patch: class DiffMatchPatch {},
@@ -18,116 +17,21 @@ vi.mock("@/common/utils.ts", () => ({
     isPluginMetadata: vi.fn(),
     scheduleTask: vi.fn(),
 }));
-vi.mock("@/common/PeriodicProcessor.ts", () => ({
-    PeriodicProcessor: class PeriodicProcessor {},
-}));
 vi.mock("@/common/translation", () => ({
     $msg: vi.fn((message: string) => message),
 }));
-vi.mock("@/common/obsidianCommunityPlugins.ts", () => ({
-    getObsidianCommunityPluginManager: vi.fn(),
-}));
 
 import { CustomisationSyncContext } from "./customisationSyncContext.ts";
-import { createCustomisationSyncTestDependencies } from "./customisationSyncContext.unit.fixture.ts";
 
-const PATH = ".obsidian/plugins/example/data.json" as FilePath;
+describe("Customisation Sync scan delegation", () => {
-const V1_PATH = "ix:device-a/PLUGIN_DATA/example.md" as FilePathWithPrefix;
+    it("preserves the public scan argument and result through the focused owner", async () => {
-const V2_PATH = "ix:device-a/PLUGIN_DATA/example%data.json" as FilePathWithPrefix;
+        const scanAllConfigFiles = vi.fn(async (_showMessage: boolean) => undefined);
+        const context = Object.create(CustomisationSyncContext.prototype) as CustomisationSyncContext;
+        Object.assign(context, { scanOperations: { scanAllConfigFiles } });
 
-function asyncEntries(entries: object[]) {
+        await expect(context.scanAllConfigFiles(true)).resolves.toBeUndefined();
-    return {
-        async *[Symbol.asyncIterator]() {
-            yield* entries;
-        },
-    };
-}
 
-function createConfigSync(options: {
+        expect(scanAllConfigFiles).toHaveBeenCalledOnce();
-    useV2: boolean;
+        expect(scanAllConfigFiles).toHaveBeenCalledWith(true);
-    localFiles?: FilePath[];
-    databasePaths?: FilePathWithPrefix[];
-    ownsLocalFile?: boolean;
-    ownsLocalDocument?: boolean;
-}) {
-    const storeCustomizationFiles = vi.fn(async () => true);
-    const storeCustomisationFileV2 = vi.fn(async () => true);
-    const deleteConfigOnDatabase = vi.fn(async () => true);
-    const ownsLocalFile = vi.fn(() => options.ownsLocalFile ?? true);
-    const ownsLocalDocument = vi.fn(() => options.ownsLocalDocument ?? true);
-    const databaseEntries = (options.databasePaths ?? []).map((path) => ({ _id: path, path }));
-    const localDatabase = {
-        findEntries: vi.fn(() => asyncEntries(databaseEntries)),
-        allDocsRaw: vi.fn(async () => ({
-            rows: databaseEntries.map((doc) => ({ doc: { ...doc, deleted: false } })),
-        })),
-    };
-    const configSync = Object.create(CustomisationSyncContext.prototype) as CustomisationSyncContext;
-    Object.assign(configSync, {
-        dependencies: createCustomisationSyncTestDependencies({
-            getConfigDir: () => ".obsidian",
-            getSettings: () => ({
-                usePluginSync: true,
-                usePluginSyncV2: options.useV2,
-                usePluginEtc: true,
-                pluginSyncExtendedSetting: {},
-                autoSweepPlugins: false,
-                autoSweepPluginsPeriodic: false,
-                watchInternalFileChanges: false,
-                notifyPluginOrSettingUpdated: false,
-            }),
-            getLocalDatabase: () => localDatabase as never,
-            ownsLocalFile,
-            ownsLocalDocument,
-        }),
-        scanInternalFiles: vi.fn(async () => options.localFiles ?? []),
-        pathOperations: {
-            isTargetPath: vi.fn(() => true),
-            filenameToUnifiedKey: vi.fn(() => V1_PATH),
-            filenameWithUnifiedKey: vi.fn(() => V2_PATH),
-            unifiedKeyPrefixOfTerminal: vi.fn(() => "ix:device-a/"),
-        },
-        getPath: vi.fn((entry: { path: FilePathWithPrefix }) => entry.path),
-        storeCustomizationFiles,
-        storeCustomisationFileV2,
-        deleteConfigOnDatabase,
-        updatePluginList: vi.fn(async () => undefined),
-        _log: vi.fn(),
-    });
-    return {
-        configSync,
-        deleteConfigOnDatabase,
-        ownsLocalDocument,
-        ownsLocalFile,
-        storeCustomisationFileV2,
-        storeCustomizationFiles,
-    };
-}
-
-describe("Customisation Sync scan ownership", () => {
-    it.each([
-        ["V1", false],
-        ["V2", true],
-    ] as const)("does not store a %s local file assigned to another owner", async (_label, useV2) => {
-        const fixture = createConfigSync({ useV2, localFiles: [PATH], ownsLocalFile: false });
-
-        await fixture.configSync.scanAllConfigFiles(false);
-
-        expect(fixture.ownsLocalFile).toHaveBeenCalledWith(PATH);
-        expect(fixture.storeCustomizationFiles).not.toHaveBeenCalled();
-        expect(fixture.storeCustomisationFileV2).not.toHaveBeenCalled();
-    });
-
-    it("does not create a deletion for an existing V1 document which is no longer locally owned", async () => {
-        const fixture = createConfigSync({
-            useV2: false,
-            databasePaths: [V1_PATH],
-            ownsLocalDocument: false,
-        });
-
-        await fixture.configSync.scanAllConfigFiles(false);
-
-        expect(fixture.ownsLocalDocument).toHaveBeenCalledWith(V1_PATH);
-        expect(fixture.deleteConfigOnDatabase).not.toHaveBeenCalled();
     });
 });

src/features/ConfigSync/customisationSyncContext.v2Manifest.unit.spec.ts

@@ -26,6 +26,16 @@ vi.mock("@/common/translation", () => ({
 vi.mock("@/common/obsidianCommunityPlugins.ts", () => ({
     getObsidianCommunityPluginManager: vi.fn(),
 }));
+vi.mock("octagonal-wheels/concurrency/processor", () => ({
+    QueueProcessor: class QueueProcessor {
+        clearQueue = vi.fn();
+        enqueue = vi.fn();
+        terminate = vi.fn();
+        startPipeline() {
+            return this;
+        }
+    },
+}));
 
 import {
     LOG_LEVEL_VERBOSE,
@@ -34,7 +44,7 @@ import {
 } from "@vrtmrz/livesync-commonlib/compat/common/types";
 import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
 import { createCustomisationSyncCodec } from "./customisationSyncCodec.ts";
-import { CustomisationSyncCatalogueState } from "./customisationSyncCatalogueState.ts";
+import { CatalogueOperations } from "./catalogueOperations.ts";
 import { CustomisationSyncContext } from "./customisationSyncContext.ts";
 import { createCustomisationSyncTestDependencies } from "./customisationSyncContext.unit.fixture.ts";
 
@@ -64,22 +74,31 @@ function loadedManifest(manifestSource: string, mtime: number): LoadedEntry {
 
 function createContext() {
     const log = vi.fn();
-    const catalogueState = new CustomisationSyncCatalogueState();
+    const snapshotPersistence = {
-    const pluginManifests = catalogueState.manifestLookup;
+        deleteConfigOnDatabase: vi.fn(async () => ({ value: true, status: "missing" as const, refreshes: [] })),
-    const loadedManifest_mTime = catalogueState.loadedManifestMTime;
+    };
-    const setManifests = vi.spyOn(catalogueState.manifests, "set");
+    const catalogueOperations = new CatalogueOperations({
-    const setCatalogue = vi.spyOn(catalogueState.catalogue, "set");
+        ...createCustomisationSyncTestDependencies({
+            log,
+            getLocalDatabase: () => ({ getDBEntry: async () => false }) as never,
+        }),
+        snapshotPersistence,
+        publishScanCount: vi.fn(),
+    });
+    const pluginManifests = catalogueOperations.manifestLookup;
+    const setManifests = vi.spyOn(catalogueOperations.manifests, "set");
+    const setCatalogue = vi.spyOn(catalogueOperations.catalogue, "set");
     const context = Object.create(CustomisationSyncContext.prototype) as CustomisationSyncContext;
     Object.assign(context, {
         dependencies: createCustomisationSyncTestDependencies({
             log,
             getLocalDatabase: () => ({ getDBEntry: async () => false }) as never,
         }),
-        catalogueState,
+        catalogueOperations,
     });
     return {
+        catalogueOperations,
         context,
-        loadedManifest_mTime,
         log,
         pluginManifests,
         setCatalogue,
@@ -89,7 +108,7 @@ function createContext() {
 
 describe("compatibility: Customisation Sync V2 manifest state", () => {
     it("keeps the first parsed manifest when a later file has a different mtime", async () => {
-        const { context, loadedManifest_mTime, pluginManifests, setManifests } = createContext();
+        const { catalogueOperations, context, pluginManifests, setManifests } = createContext();
 
         await context.testing.createPluginDataExFileV2(
             path,
@@ -101,12 +120,12 @@ describe("compatibility: Customisation Sync V2 manifest state", () => {
         );
 
         expect(pluginManifests.get(confKey)).toMatchObject({ name: "First", version: "1.0.0" });
-        expect(loadedManifest_mTime.get(confKey)).toBe(20);
         expect(setManifests).toHaveBeenCalledOnce();
+        catalogueOperations.dispose();
     });
 
     it("records a failed manifest mtime and does not retry the same revision", async () => {
-        const { context, loadedManifest_mTime, log, pluginManifests, setCatalogue } = createContext();
+        const { catalogueOperations, context, log, pluginManifests, setCatalogue } = createContext();
         const invalid = loadedManifest("{invalid", 20);
 
         await expect(context.testing.createPluginDataExFileV2(path, invalid)).resolves.toMatchObject({
@@ -115,7 +134,6 @@ describe("compatibility: Customisation Sync V2 manifest state", () => {
         await context.testing.createPluginDataExFileV2(path, invalid);
 
         expect(pluginManifests.has(confKey)).toBe(false);
-        expect(loadedManifest_mTime.get(confKey)).toBe(20);
         expect(log).toHaveBeenCalledTimes(2);
         expect(log).toHaveBeenNthCalledWith(
             1,
@@ -125,5 +143,6 @@ describe("compatibility: Customisation Sync V2 manifest state", () => {
         );
         expect(log).toHaveBeenNthCalledWith(2, expect.any(SyntaxError), LOG_LEVEL_VERBOSE, undefined);
         expect(setCatalogue).toHaveBeenCalledOnce();
+        catalogueOperations.dispose();
     });
 });

src/features/ConfigSync/customisationSyncContext.view.unit.spec.ts

@@ -121,31 +121,18 @@ describe("CustomisationSyncContext dialogue view", () => {
         expect(askString).toHaveBeenCalledWith("Duplicate", "device name", "");
     });
 
-    it("keeps file-level comparison clones and duplication inside the view boundary", async () => {
+    it("delegates file-level comparison and duplication to the application owner", async () => {
         const { configSync } = createConfigSync();
-        const compareUsingDisplayData = vi.fn<
+        const compareFileUsingDisplayData = vi.fn(async () => true);
-            (dataA: IPluginDataExDisplay, dataB: IPluginDataExDisplay, compareEach?: boolean) => Promise<boolean>
+        const duplicateData = vi.fn(async () => undefined);
-        >(async () => true);
-        const storeCustomizationFiles = vi.fn(async () => true);
-        const updatePluginList = vi.fn(async () => undefined);
         Object.assign(configSync, {
-            compareUsingDisplayData,
+            applicationOperations: { compareFileUsingDisplayData, duplicateData },
-            pathOperations: {
-                filenameToUnifiedKey: vi.fn(() => "ix:device-b/PLUGIN_DATA/example.md"),
-            },
-            storeCustomizationFiles,
-            updatePluginList,
         });
 
         await expect(configSync.compareFileUsingDisplayData(display, display, "data.json")).resolves.toBe(true);
-        const [left, right, compareEach] = compareUsingDisplayData.mock.calls[0];
+        expect(compareFileUsingDisplayData).toHaveBeenCalledWith(display, display, "data.json");
-        expect(left.files.map((file) => file.filename)).toEqual(["data.json"]);
-        expect(right.files.map((file) => file.filename)).toEqual(["data.json"]);
-        expect(compareEach).toBe(true);
-        expect(display.files).toHaveLength(2);
 
         await configSync.duplicateData(display, "device-b");
-        expect(storeCustomizationFiles).toHaveBeenCalledWith(".obsidian/data.json", "device-b");
+        expect(duplicateData).toHaveBeenCalledWith(display, "device-b");
-        expect(updatePluginList).toHaveBeenCalledWith(false, "ix:device-b/PLUGIN_DATA/example.md");
     });
 });

src/features/ConfigSync/scanOperations.ts

@@ -0,0 +1,197 @@
+import type {
+    AnyEntry,
+    FilePath,
+    FilePathWithPrefix,
+    InternalFileEntry,
+    LOG_LEVEL,
+    ObsidianLiveSyncSettings,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_INFO, LOG_LEVEL_NOTICE, LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { fireAndForget } from "@vrtmrz/livesync-commonlib/compat/common/utils";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+import { shareRunningResult } from "octagonal-wheels/concurrency/lock";
+import { Semaphore } from "octagonal-wheels/concurrency/semaphore";
+
+import { $msg } from "@/common/translation";
+import { ICXHeader } from "@/common/types.ts";
+import {
+    collectOptionalFileSyncFiles,
+    type OptionalFileSyncFileTreeDependencies,
+} from "@/features/optionalFileSyncFileTree.ts";
+import type { CatalogueOperations } from "./catalogueOperations.ts";
+import type { CustomisationSyncPathOperations } from "./customisationSyncPathOperations.ts";
+import type { SnapshotOperations } from "./snapshotOperations.ts";
+
+type ScanSettings = Pick<ObsidianLiveSyncSettings, "usePluginSyncV2">;
+type ScanDatabase = Pick<LiveSyncLocalDB, "allDocsRaw" | "findEntries">;
+type ScanPathOperations = Pick<
+    CustomisationSyncPathOperations,
+    "isTargetPath" | "filenameToUnifiedKey" | "filenameWithUnifiedKey" | "unifiedKeyPrefixOfTerminal"
+> & {
+    getPath(entry: AnyEntry): FilePathWithPrefix;
+};
+type ScanSnapshotOperations = Pick<
+    SnapshotOperations,
+    "storeCustomisationFileV2" | "storeCustomizationFiles" | "deleteConfigOnDatabase"
+>;
+type ScanCatalogueOperations = Pick<CatalogueOperations, "updatePluginList">;
+
+export type ScanOperationsDependencies = OptionalFileSyncFileTreeDependencies & {
+    getSettings(): ScanSettings;
+    getLocalDatabase(): ScanDatabase;
+    path: ScanPathOperations;
+    log: LogFunction;
+    getConfigDir(): string;
+    getDeviceAndVaultName(): string;
+    ownsLocalFile(path: FilePath): boolean;
+    ownsLocalDocument(path: FilePathWithPrefix): boolean;
+    snapshotOperations: ScanSnapshotOperations;
+    catalogueOperations: ScanCatalogueOperations;
+};
+
+/**
+ * Owns Customisation Sync file enumeration and reconciliation with the local
+ * database. Snapshot writes and catalogue publication remain explicit ports so
+ * scans do not depend on the context or its lifecycle.
+ */
+export class ScanOperations {
+    constructor(private readonly dependencies: ScanOperationsDependencies) {}
+
+    private get localDatabase() {
+        return this.dependencies.getLocalDatabase();
+    }
+
+    private getPath(entry: AnyEntry): FilePathWithPrefix {
+        return this.dependencies.path.getPath(entry);
+    }
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string) {
+        this.dependencies.log(message, level, key);
+    }
+
+    async scanInternalFiles(): Promise<FilePath[]> {
+        const filenames = (
+            await collectOptionalFileSyncFiles(this.dependencies, this.dependencies.getConfigDir(), {
+                maxDepth: 2,
+                onError: (path, error) => {
+                    this._log(`Could not traverse(CustomisationSync):${path}`, LOG_LEVEL_INFO);
+                    this._log(error, LOG_LEVEL_VERBOSE);
+                },
+            })
+        )
+            .filter((e) => e.startsWith("."))
+            .filter((e) => !e.startsWith(".trash"));
+        return filenames as FilePath[];
+    }
+
+    async scanAllConfigFiles(showMessage: boolean): Promise<void> {
+        await shareRunningResult("scanAllConfigFiles", async () => {
+            const logLevel = showMessage ? LOG_LEVEL_NOTICE : LOG_LEVEL_INFO;
+            this._log("Scanning customizing files.", logLevel, "scan-all-config");
+            const term = this.dependencies.getDeviceAndVaultName();
+            if (term == "") {
+                this._log($msg("We have to configure the device name"), LOG_LEVEL_NOTICE);
+                return;
+            }
+            const filesAll = await this.scanInternalFiles();
+            if (this.dependencies.getSettings().usePluginSyncV2) {
+                await this.scanV2ConfigFiles(filesAll, term);
+            } else {
+                await this.scanV1ConfigFiles(filesAll, term);
+            }
+        });
+    }
+
+    private async scanV2ConfigFiles(filesAll: readonly FilePath[], term: string): Promise<void> {
+        const filesAllUnified = filesAll
+            .filter((e) => this.dependencies.path.isTargetPath(e))
+            .map((e) => [this.dependencies.path.filenameWithUnifiedKey(e, term), e] as [FilePathWithPrefix, FilePath]);
+        const localFileMap = new Map(filesAllUnified.map((e) => [e[0], e[1]]));
+        const prefix = this.dependencies.path.unifiedKeyPrefixOfTerminal(term);
+        const entries = this.localDatabase.findEntries(prefix + "", `${prefix}\u{10ffff}`, {
+            include_docs: true,
+        });
+        const tasks = [] as (() => Promise<void>)[];
+        const concurrency = 10;
+        const semaphore = Semaphore(concurrency);
+        for await (const item of entries) {
+            if (item.path.indexOf("%") !== -1) {
+                continue;
+            }
+            tasks.push(async () => {
+                const releaser = await semaphore.acquire();
+                try {
+                    const unifiedFilenameWithKey = `${item._id}` as FilePathWithPrefix;
+                    const localPath = localFileMap.get(unifiedFilenameWithKey);
+                    if (localPath) {
+                        if (this.dependencies.ownsLocalFile(localPath)) {
+                            await this.dependencies.snapshotOperations.storeCustomisationFileV2(localPath, term);
+                        }
+                        localFileMap.delete(unifiedFilenameWithKey);
+                    } else if (this.dependencies.ownsLocalDocument(this.getPath(item))) {
+                        await this.dependencies.snapshotOperations.deleteConfigOnDatabase(unifiedFilenameWithKey);
+                    }
+                } catch (ex) {
+                    this._log(`scanAllConfigFiles - Error: ${item._id}`, LOG_LEVEL_VERBOSE);
+                    this._log(ex, LOG_LEVEL_VERBOSE);
+                } finally {
+                    releaser();
+                }
+            });
+        }
+        await Promise.all(tasks.map((e) => e()));
+        // Extra files
+        const taskExtra = [] as (() => Promise<void>)[];
+        for (const [, filePath] of localFileMap) {
+            if (!this.dependencies.ownsLocalFile(filePath)) continue;
+            taskExtra.push(async () => {
+                const releaser = await semaphore.acquire();
+                try {
+                    await this.dependencies.snapshotOperations.storeCustomisationFileV2(filePath, term);
+                } catch (ex) {
+                    this._log(`scanAllConfigFiles - Error: ${filePath}`, LOG_LEVEL_VERBOSE);
+                    this._log(ex, LOG_LEVEL_VERBOSE);
+                } finally {
+                    releaser();
+                }
+            });
+        }
+        await Promise.all(taskExtra.map((e) => e()));
+        fireAndForget(() => this.dependencies.catalogueOperations.updatePluginList(false));
+    }
+
+    private async scanV1ConfigFiles(filesAll: readonly FilePath[], term: string): Promise<void> {
+        const files = filesAll
+            .filter((e) => this.dependencies.path.isTargetPath(e))
+            .map((e) => ({ key: this.dependencies.path.filenameToUnifiedKey(e), file: e }));
+        const virtualPathsOfLocalFiles = [...new Set(files.map((e) => e.key))];
+        const filesOnDB = (
+            (
+                await this.localDatabase.allDocsRaw({
+                    startkey: ICXHeader + "",
+                    endkey: `${ICXHeader}\u{10ffff}`,
+                    include_docs: true,
+                })
+            ).rows.map((e) => e.doc) as InternalFileEntry[]
+        ).filter((e) => !e.deleted);
+        let deleteCandidate = filesOnDB.map((e) => this.getPath(e)).filter((e) => e.startsWith(`${ICXHeader}${term}/`));
+        for (const vp of virtualPathsOfLocalFiles) {
+            const p = files.find((e) => e.key == vp)?.file;
+            if (!p) {
+                this._log(`scanAllConfigFiles - File not found: ${vp}`, LOG_LEVEL_VERBOSE);
+                continue;
+            }
+            if (this.dependencies.ownsLocalFile(p)) {
+                await this.dependencies.snapshotOperations.storeCustomizationFiles(p);
+            }
+            deleteCandidate = deleteCandidate.filter((e) => e != vp);
+        }
+        for (const vp of deleteCandidate) {
+            if (this.dependencies.ownsLocalDocument(vp)) {
+                await this.dependencies.snapshotOperations.deleteConfigOnDatabase(vp);
+            }
+        }
+        fireAndForget(() => this.dependencies.catalogueOperations.updatePluginList(false));
+    }
+}

src/features/ConfigSync/scanOperations.unit.spec.ts

@@ -0,0 +1,327 @@
+import { beforeEach, describe, expect, it, vi } from "vitest";
+import {
+    LOG_LEVEL_INFO,
+    LOG_LEVEL_NOTICE,
+    LOG_LEVEL_VERBOSE,
+    type FilePath,
+    type FilePathWithPrefix,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+
+const asyncHarness = vi.hoisted(() => ({
+    fireAndForget: vi.fn((operation: () => unknown) => {
+        void operation();
+    }),
+}));
+
+vi.mock("@/common/translation", () => ({
+    $msg: vi.fn((message: string) => message),
+}));
+vi.mock("@vrtmrz/livesync-commonlib/compat/common/utils", async (importOriginal) => {
+    const actual = await importOriginal<typeof import("@vrtmrz/livesync-commonlib/compat/common/utils")>();
+    return {
+        ...actual,
+        fireAndForget: asyncHarness.fireAndForget,
+    };
+});
+
+import { ScanOperations, type ScanOperationsDependencies } from "./scanOperations.ts";
+
+type ScanEntry = {
+    _id: FilePathWithPrefix;
+    path: FilePathWithPrefix;
+    deleted?: boolean;
+};
+
+type FixtureOptions = {
+    useV2?: boolean;
+    usePluginSync?: boolean;
+    term?: string;
+    files?: FilePath[];
+    targetFiles?: FilePath[];
+    databaseEntries?: ScanEntry[];
+    v1Paths?: Record<string, FilePathWithPrefix>;
+    v2Paths?: Record<string, FilePathWithPrefix>;
+    ownsLocalFile?: (path: FilePath) => boolean;
+    ownsLocalDocument?: (path: FilePathWithPrefix) => boolean;
+    listFiles?: (path: string) => Promise<{ files: readonly string[]; folders: readonly string[] }>;
+};
+
+function asyncEntries<T>(entries: readonly T[]) {
+    return {
+        async *[Symbol.asyncIterator]() {
+            yield* entries;
+        },
+    };
+}
+
+function createFixture(options: FixtureOptions = {}) {
+    const files = options.files ?? [];
+    const term = options.term ?? "device-a";
+    const databaseEntries = options.databaseEntries ?? [];
+    const v1Paths = options.v1Paths ?? {};
+    const v2Paths = options.v2Paths ?? {};
+    const log = vi.fn();
+    const allDocsRaw = vi.fn(async () => ({
+        rows: databaseEntries.map((doc) => ({ id: doc._id, doc })),
+    }));
+    const findEntries = vi.fn(() => asyncEntries(databaseEntries));
+    const storeCustomisationFileV2 = vi.fn(async (_path: FilePath, _term: string) => true);
+    const storeCustomizationFiles = vi.fn(async (_path: FilePath) => true);
+    const deleteConfigOnDatabase = vi.fn(async (_path: FilePathWithPrefix) => true);
+    const updatePluginList = vi.fn(async (_showMessage: boolean) => undefined);
+    const listFiles = vi.fn(
+        options.listFiles ??
+            (async () => ({ files, folders: [] }) as { files: readonly string[]; folders: readonly string[] })
+    );
+    const dependencies = {
+        listFiles,
+        getSettings: () => ({ usePluginSyncV2: options.useV2 ?? false, usePluginSync: options.usePluginSync ?? true }),
+        getLocalDatabase: () => ({ allDocsRaw, findEntries }),
+        path: {
+            isTargetPath: (path: string) => options.targetFiles?.includes(path as FilePath) ?? true,
+            filenameToUnifiedKey: (path: string) =>
+                v1Paths[path] ?? (`ix:${term}/CONFIG/${path.split("/").pop()}.md` as FilePathWithPrefix),
+            filenameWithUnifiedKey: (path: string) =>
+                v2Paths[path] ??
+                (`ix:${term}/CONFIG/${path.split("/").pop()}%${path.split("/").pop()}` as FilePathWithPrefix),
+            unifiedKeyPrefixOfTerminal: (termOverride?: string) => `ix:${termOverride ?? term}/` as FilePathWithPrefix,
+            getPath: (entry: ScanEntry) => entry.path,
+        },
+        log,
+        getConfigDir: () => ".obsidian",
+        getDeviceAndVaultName: () => term,
+        ownsLocalFile: options.ownsLocalFile ?? (() => true),
+        ownsLocalDocument: options.ownsLocalDocument ?? (() => true),
+        snapshotOperations: {
+            storeCustomisationFileV2,
+            storeCustomizationFiles,
+            deleteConfigOnDatabase,
+        },
+        catalogueOperations: { updatePluginList },
+    } as unknown as ScanOperationsDependencies;
+    return {
+        operations: new ScanOperations(dependencies),
+        dependencies,
+        listFiles,
+        log,
+        allDocsRaw,
+        findEntries,
+        snapshot: { storeCustomisationFileV2, storeCustomizationFiles, deleteConfigOnDatabase },
+        catalogue: { updatePluginList },
+    };
+}
+
+describe("ScanOperations", () => {
+    beforeEach(() => {
+        asyncHarness.fireAndForget.mockClear();
+    });
+
+    it("filters the bounded file tree and logs traversal errors", async () => {
+        const traversalError = new Error("cannot read folder");
+        const listFiles = vi.fn(async (path: string) => {
+            switch (path) {
+                case ".obsidian":
+                    return {
+                        files: [".obsidian/app.json", "settings.json", ".trash/root.json"],
+                        folders: [".obsidian/plugins", ".trash", ".obsidian/unreadable"],
+                    };
+                case ".obsidian/plugins":
+                    return {
+                        files: [".obsidian/plugins/example/data.json"],
+                        folders: [".obsidian/plugins/example"],
+                    };
+                case ".obsidian/plugins/example":
+                    return {
+                        files: [".obsidian/plugins/example/manifest.json"],
+                        folders: [".obsidian/plugins/example/deeper"],
+                    };
+                case ".trash":
+                    return { files: [".trash/ignored.json"], folders: [] };
+                case ".obsidian/unreadable":
+                    throw traversalError;
+                default:
+                    throw new Error(`unexpected traversal: ${path}`);
+            }
+        });
+        const fixture = createFixture({ listFiles });
+
+        await expect(fixture.operations.scanInternalFiles()).resolves.toEqual([
+            ".obsidian/app.json",
+            ".obsidian/plugins/example/data.json",
+            ".obsidian/plugins/example/manifest.json",
+        ]);
+
+        expect(listFiles).not.toHaveBeenCalledWith(".obsidian/plugins/example/deeper");
+        expect(fixture.log).toHaveBeenCalledWith(
+            "Could not traverse(CustomisationSync):.obsidian/unreadable",
+            LOG_LEVEL_INFO,
+            undefined
+        );
+        expect(fixture.log).toHaveBeenCalledWith(traversalError, LOG_LEVEL_VERBOSE, undefined);
+    });
+
+    it("stops before traversal when the device term is empty", async () => {
+        const fixture = createFixture({ term: "", usePluginSync: false, files: [".obsidian/app.json"] as FilePath[] });
+
+        await fixture.operations.scanAllConfigFiles(true);
+
+        expect(fixture.listFiles).not.toHaveBeenCalled();
+        expect(fixture.allDocsRaw).not.toHaveBeenCalled();
+        expect(fixture.findEntries).not.toHaveBeenCalled();
+        expect(fixture.snapshot.storeCustomizationFiles).not.toHaveBeenCalled();
+        expect(fixture.snapshot.storeCustomisationFileV2).not.toHaveBeenCalled();
+        expect(fixture.snapshot.deleteConfigOnDatabase).not.toHaveBeenCalled();
+        expect(fixture.catalogue.updatePluginList).not.toHaveBeenCalled();
+        expect(fixture.log).toHaveBeenCalledWith("Scanning customizing files.", LOG_LEVEL_NOTICE, "scan-all-config");
+        expect(fixture.log).toHaveBeenCalledWith("We have to configure the device name", LOG_LEVEL_NOTICE, undefined);
+    });
+
+    it("dispatches according to the current V1/V2 setting on each scan", async () => {
+        const path = ".obsidian/app.json" as FilePath;
+        const fixture = createFixture({ files: [path], useV2: false });
+        let useV2 = false;
+        fixture.dependencies.getSettings = () => ({ usePluginSyncV2: useV2 });
+
+        await fixture.operations.scanAllConfigFiles(false);
+        useV2 = true;
+        await fixture.operations.scanAllConfigFiles(false);
+
+        expect(fixture.snapshot.storeCustomizationFiles).toHaveBeenCalledWith(path);
+        expect(fixture.snapshot.storeCustomizationFiles).toHaveBeenCalledTimes(1);
+        expect(fixture.snapshot.storeCustomisationFileV2).toHaveBeenCalledWith(path, "device-a");
+        expect(fixture.snapshot.storeCustomisationFileV2).toHaveBeenCalledTimes(1);
+    });
+
+    it("routes V1 ownership and deletes only stale owned documents", async () => {
+        const ownedPath = ".obsidian/app.json" as FilePath;
+        const unownedPath = ".obsidian/appearance.json" as FilePath;
+        const ownedDocument = "ix:device-a/CONFIG/app.json.md" as FilePathWithPrefix;
+        const unownedDocument = "ix:device-a/CONFIG/appearance.json.md" as FilePathWithPrefix;
+        const staleDocument = "ix:device-a/CONFIG/stale.json.md" as FilePathWithPrefix;
+        const fixture = createFixture({
+            useV2: false,
+            usePluginSync: false,
+            files: [ownedPath, unownedPath],
+            v1Paths: {
+                [ownedPath]: ownedDocument,
+                [unownedPath]: unownedDocument,
+            },
+            databaseEntries: [
+                { _id: ownedDocument, path: ownedDocument },
+                { _id: unownedDocument, path: unownedDocument },
+                { _id: staleDocument, path: staleDocument },
+            ],
+            ownsLocalFile: (path) => path == ownedPath,
+        });
+
+        await fixture.operations.scanAllConfigFiles(false);
+
+        expect(fixture.snapshot.storeCustomizationFiles).toHaveBeenCalledWith(ownedPath);
+        expect(fixture.snapshot.storeCustomizationFiles).toHaveBeenCalledTimes(1);
+        expect(fixture.snapshot.deleteConfigOnDatabase).toHaveBeenCalledWith(staleDocument);
+        expect(fixture.snapshot.deleteConfigOnDatabase).toHaveBeenCalledTimes(1);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledTimes(1);
+        expect(fixture.allDocsRaw).toHaveBeenCalledWith({
+            startkey: "ix:",
+            endkey: "ix:\u{10ffff}",
+            include_docs: true,
+        });
+    });
+
+    it("propagates V1 snapshot failures without publishing a final refresh", async () => {
+        const path = ".obsidian/app.json" as FilePath;
+        const failure = new Error("V1 write failed");
+        const fixture = createFixture({ files: [path] });
+        fixture.snapshot.storeCustomizationFiles.mockRejectedValueOnce(failure);
+
+        await expect(fixture.operations.scanAllConfigFiles(false)).rejects.toBe(failure);
+
+        expect(fixture.catalogue.updatePluginList).not.toHaveBeenCalled();
+    });
+
+    it("routes V2 ownership, removes matched keys, and deletes stale documents", async () => {
+        const ownedPath = ".obsidian/app.json" as FilePath;
+        const unownedPath = ".obsidian/appearance.json" as FilePath;
+        const extraPath = ".obsidian/plugins/example/main.js" as FilePath;
+        const ownedDocument = "ix:device-a/CONFIG/app.json%app.json" as FilePathWithPrefix;
+        const unownedDocument = "ix:device-a/CONFIG/appearance.json%appearance.json" as FilePathWithPrefix;
+        const staleDocument = "ix:device-a/CONFIG/stale.json" as FilePathWithPrefix;
+        const skippedDocument = "ix:device-a/CONFIG/skipped%app.json" as FilePathWithPrefix;
+        const owned = new Set([ownedPath, extraPath]);
+        const fixture = createFixture({
+            useV2: true,
+            files: [ownedPath, unownedPath, extraPath],
+            v2Paths: {
+                [ownedPath]: ownedDocument,
+                [unownedPath]: unownedDocument,
+                [extraPath]: "ix:device-a/PLUGIN_MAIN/example%main.js" as FilePathWithPrefix,
+            },
+            databaseEntries: [
+                { _id: ownedDocument, path: "ix:device-a/CONFIG/app.json.md" as FilePathWithPrefix },
+                { _id: unownedDocument, path: "ix:device-a/CONFIG/appearance.json.md" as FilePathWithPrefix },
+                { _id: staleDocument, path: staleDocument },
+                { _id: skippedDocument, path: skippedDocument },
+            ],
+            ownsLocalFile: (path) => owned.has(path),
+        });
+
+        await fixture.operations.scanAllConfigFiles(false);
+
+        expect(fixture.snapshot.storeCustomisationFileV2).toHaveBeenCalledWith(ownedPath, "device-a");
+        expect(fixture.snapshot.storeCustomisationFileV2).toHaveBeenCalledWith(extraPath, "device-a");
+        expect(fixture.snapshot.storeCustomisationFileV2).toHaveBeenCalledTimes(2);
+        expect(fixture.snapshot.storeCustomisationFileV2).not.toHaveBeenCalledWith(unownedPath, "device-a");
+        expect(fixture.snapshot.deleteConfigOnDatabase).toHaveBeenCalledWith(staleDocument);
+        expect(fixture.snapshot.deleteConfigOnDatabase).toHaveBeenCalledTimes(1);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false);
+        expect(fixture.findEntries).toHaveBeenCalledWith("ix:device-a/", "ix:device-a/\u{10ffff}", {
+            include_docs: true,
+        });
+    });
+
+    it("catches and logs each V2 entry failure before publishing the refresh", async () => {
+        const path = ".obsidian/app.json" as FilePath;
+        const document = "ix:device-a/CONFIG/app.json%app.json" as FilePathWithPrefix;
+        const failure = new Error("V2 write failed");
+        const fixture = createFixture({
+            useV2: true,
+            files: [path],
+            v2Paths: { [path]: document },
+            databaseEntries: [{ _id: document, path: "ix:device-a/CONFIG/app.json.md" as FilePathWithPrefix }],
+        });
+        fixture.snapshot.storeCustomisationFileV2.mockRejectedValueOnce(failure);
+
+        await fixture.operations.scanAllConfigFiles(false);
+
+        expect(fixture.log).toHaveBeenCalledWith(
+            `scanAllConfigFiles - Error: ${document}`,
+            LOG_LEVEL_VERBOSE,
+            undefined
+        );
+        expect(fixture.log).toHaveBeenCalledWith(failure, LOG_LEVEL_VERBOSE, undefined);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false);
+    });
+
+    it("starts the final catalogue refresh without awaiting it", async () => {
+        const path = ".obsidian/app.json" as FilePath;
+        const fixture = createFixture({ files: [path] });
+        let releaseRefresh!: () => void;
+        const refresh = new Promise<void>((resolve) => {
+            releaseRefresh = resolve;
+        });
+        const refreshStarted = vi.fn();
+        fixture.catalogue.updatePluginList.mockImplementation(async () => {
+            refreshStarted();
+            await refresh;
+        });
+
+        await fixture.operations.scanAllConfigFiles(false);
+
+        expect(asyncHarness.fireAndForget).toHaveBeenCalledOnce();
+        expect(refreshStarted).toHaveBeenCalledOnce();
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false);
+        releaseRefresh();
+        await refresh;
+    });
+});

src/features/ConfigSync/snapshotOperations.ts

@@ -0,0 +1,82 @@
+import type {
+    FilePath,
+    FilePathWithPrefix,
+    LOG_LEVEL,
+    ObsidianLiveSyncSettings,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_NOTICE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { fireAndForget } from "@vrtmrz/livesync-commonlib/compat/common/utils";
+
+import { $msg } from "@/common/translation";
+import type { CatalogueOperations } from "./catalogueOperations.ts";
+import type { SnapshotPersistence, SnapshotRefresh } from "./snapshotPersistence.ts";
+
+type SnapshotSettings = Pick<ObsidianLiveSyncSettings, "usePluginSyncV2">;
+type SnapshotPersistencePort = Pick<
+    SnapshotPersistence,
+    "storeCustomisationFileV2" | "storeCustomizationFiles" | "deleteConfigOnDatabase"
+>;
+type SnapshotCatalogue = Pick<CatalogueOperations, "updatePluginList" | "updatePluginListV2">;
+
+export type SnapshotOperationsDependencies = {
+    getSettings(): SnapshotSettings;
+    getDeviceAndVaultName(): string;
+    log(message: unknown, level?: LOG_LEVEL, key?: string): void;
+    snapshotPersistence: SnapshotPersistencePort;
+    catalogueOperations: SnapshotCatalogue;
+};
+
+/**
+ * Adapts host-neutral Customisation Sync snapshot mutations to catalogue
+ * refreshes. Current-term selection and the inherited refresh timing live in
+ * this owner so scan, dialogue, and testing callers share one policy.
+ */
+export class SnapshotOperations {
+    constructor(private readonly dependencies: SnapshotOperationsDependencies) {}
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string) {
+        this.dependencies.log(message, level, key);
+    }
+
+    isV2Enabled(): boolean {
+        return this.dependencies.getSettings().usePluginSyncV2;
+    }
+
+    private async applyPersistenceRefreshes(refreshes: readonly SnapshotRefresh[]) {
+        for (const refresh of refreshes) {
+            if (refresh.mode == "v2" && refresh.timing == "fire-and-forget") {
+                fireAndForget(() => this.dependencies.catalogueOperations.updatePluginListV2(false, refresh.path));
+            } else if (refresh.mode == "v1" && refresh.timing == "await") {
+                await this.dependencies.catalogueOperations.updatePluginList(false, refresh.path);
+            }
+        }
+    }
+
+    async storeCustomisationFileV2(path: FilePath, term: string, force = false) {
+        const persistence = await this.dependencies.snapshotPersistence.storeCustomisationFileV2(path, term, force);
+        await this.applyPersistenceRefreshes(persistence.refreshes);
+        return persistence.value;
+    }
+
+    async storeCustomizationFiles(path: FilePath, termOverride?: string) {
+        const term = termOverride || this.dependencies.getDeviceAndVaultName();
+        if (term == "") {
+            this._log($msg("We have to configure the device name"), LOG_LEVEL_NOTICE);
+            return;
+        }
+        const persistence = this.isV2Enabled()
+            ? await this.dependencies.snapshotPersistence.storeCustomisationFileV2(path, term)
+            : await this.dependencies.snapshotPersistence.storeCustomizationFiles(path, term);
+        await this.applyPersistenceRefreshes(persistence.refreshes);
+        return persistence.value;
+    }
+
+    async deleteConfigOnDatabase(prefixedFileName: FilePathWithPrefix, forceWrite = false): Promise<boolean> {
+        const persistence = await this.dependencies.snapshotPersistence.deleteConfigOnDatabase(
+            prefixedFileName,
+            forceWrite
+        );
+        await this.applyPersistenceRefreshes(persistence.refreshes);
+        return persistence.value;
+    }
+}

src/features/ConfigSync/snapshotOperations.unit.spec.ts

@@ -0,0 +1,137 @@
+import { describe, expect, it, vi } from "vitest";
+
+const asyncHarness = vi.hoisted(() => ({
+    fireAndForget: vi.fn((operation: () => unknown) => {
+        void operation();
+    }),
+}));
+
+vi.mock("@/common/translation", () => ({
+    $msg: vi.fn((message: string) => message),
+}));
+vi.mock("@vrtmrz/livesync-commonlib/compat/common/utils", async (importOriginal) => {
+    const actual = await importOriginal<typeof import("@vrtmrz/livesync-commonlib/compat/common/utils")>();
+    return {
+        ...actual,
+        fireAndForget: asyncHarness.fireAndForget,
+    };
+});
+
+import type { FilePath, FilePathWithPrefix } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { SnapshotPersistenceResult } from "./snapshotPersistence.ts";
+import { SnapshotOperations, type SnapshotOperationsDependencies } from "./snapshotOperations.ts";
+
+const CONFIG_PATH = ".obsidian/app.json" as FilePath;
+const V1_PATH = "ix:device-b/CONFIG/app.json.md" as FilePathWithPrefix;
+const V2_PATH = "ix:device-a/CONFIG/app.json%app.json" as FilePathWithPrefix;
+
+function createOperations(usePluginSyncV2: boolean) {
+    const events: string[] = [];
+    type PersistenceResult = SnapshotPersistenceResult<true>;
+    const storeCustomisationFileV2 = vi.fn(
+        async (_path: FilePath, _term: string, _force?: boolean): Promise<PersistenceResult> => ({
+            value: true,
+            status: "saved",
+            refreshes: [],
+        })
+    );
+    const storeCustomizationFiles = vi.fn(
+        async (_path: FilePath, _term: string): Promise<PersistenceResult> => ({
+            value: true,
+            status: "saved",
+            refreshes: [],
+        })
+    );
+    const deleteConfigOnDatabase = vi.fn(
+        async (_path: FilePathWithPrefix, _force?: boolean): Promise<PersistenceResult> => ({
+            value: true,
+            status: "deleted",
+            refreshes: [],
+        })
+    );
+    const updatePluginList = vi.fn(async () => {
+        events.push("refresh-v1");
+    });
+    const updatePluginListV2 = vi.fn(async () => {
+        events.push("refresh-v2");
+    });
+    const dependencies: SnapshotOperationsDependencies = {
+        getSettings: () => ({ usePluginSyncV2 }),
+        getDeviceAndVaultName: () => "device-a",
+        log: vi.fn(),
+        snapshotPersistence: {
+            storeCustomisationFileV2,
+            storeCustomizationFiles,
+            deleteConfigOnDatabase,
+        },
+        catalogueOperations: { updatePluginList, updatePluginListV2 },
+    };
+    return {
+        operations: new SnapshotOperations(dependencies),
+        events,
+        persistence: { storeCustomisationFileV2, storeCustomizationFiles, deleteConfigOnDatabase },
+        catalogue: { updatePluginList, updatePluginListV2 },
+    };
+}
+
+describe("Snapshot Operations", () => {
+    it("selects V1 persistence with an override term and awaits its refresh", async () => {
+        const fixture = createOperations(false);
+        fixture.persistence.storeCustomizationFiles.mockImplementation(async (_path: FilePath, term: string) => {
+            fixture.events.push(`persist:${term}`);
+            return {
+                value: true,
+                status: "saved",
+                refreshes: [{ mode: "v1", timing: "await", path: V1_PATH }],
+            };
+        });
+
+        await expect(fixture.operations.storeCustomizationFiles(CONFIG_PATH, "device-b")).resolves.toBe(true);
+
+        expect(fixture.persistence.storeCustomizationFiles).toHaveBeenCalledWith(CONFIG_PATH, "device-b");
+        expect(fixture.events).toEqual(["persist:device-b", "refresh-v1"]);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false, V1_PATH);
+    });
+
+    it("selects V2 persistence with the current term and does not await its refresh", async () => {
+        const fixture = createOperations(true);
+        let releaseRefresh!: () => void;
+        const refresh = new Promise<void>((resolve) => {
+            releaseRefresh = resolve;
+        });
+        fixture.persistence.storeCustomisationFileV2.mockImplementation(async (_path: FilePath, term: string) => {
+            fixture.events.push(`persist:${term}`);
+            return {
+                value: true,
+                status: "saved",
+                refreshes: [{ mode: "v2", timing: "fire-and-forget", path: V2_PATH }],
+            };
+        });
+        fixture.catalogue.updatePluginListV2.mockImplementation(async () => {
+            fixture.events.push("refresh-v2-start");
+            await refresh;
+            fixture.events.push("refresh-v2-end");
+        });
+
+        await expect(fixture.operations.storeCustomizationFiles(CONFIG_PATH)).resolves.toBe(true);
+
+        expect(fixture.events).toEqual(["persist:device-a", "refresh-v2-start"]);
+        releaseRefresh();
+        await refresh;
+        expect(fixture.events).toEqual(["persist:device-a", "refresh-v2-start", "refresh-v2-end"]);
+    });
+
+    it("returns the persistence result after applying deletion refreshes", async () => {
+        const fixture = createOperations(false);
+        fixture.persistence.deleteConfigOnDatabase.mockImplementation(async () => ({
+            value: true,
+            status: "deleted",
+            refreshes: [{ mode: "v1", timing: "await", path: V1_PATH }],
+        }));
+
+        await expect(fixture.operations.deleteConfigOnDatabase(V1_PATH)).resolves.toBe(true);
+
+        expect(fixture.persistence.deleteConfigOnDatabase).toHaveBeenCalledWith(V1_PATH, false);
+        expect(fixture.catalogue.updatePluginList).toHaveBeenCalledWith(false, V1_PATH);
+    });
+});

src/features/ConfigSync/snapshotPersistence.ts

@@ -0,0 +1,402 @@
+import { parseYaml } from "@/deps.ts";
+import type {
+    FilePath,
+    FilePathWithPrefix,
+    InternalFileEntry,
+    LOG_LEVEL,
+    SavingEntry,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { LOG_LEVEL_DEBUG, LOG_LEVEL_VERBOSE } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import {
+    createBlob,
+    createTextBlob,
+    getDocData,
+    getDocDataAsArray,
+    isDocContentSame,
+} from "@vrtmrz/livesync-commonlib/compat/common/utils";
+import { EVEN } from "@vrtmrz/livesync-commonlib/compat/common/models/shared.const.symbols";
+import { digestHash } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/hash";
+import { arrayBufferToBase64 } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/convert";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { StorageAccess } from "@vrtmrz/livesync-commonlib/compat/interfaces/StorageAccess";
+import type { IPathService } from "@vrtmrz/livesync-commonlib/compat/services/base/IService";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+import { base64ToArrayBuffer } from "octagonal-wheels/binary/base64";
+import { serialized } from "octagonal-wheels/concurrency/lock";
+import { LiveSyncError } from "@vrtmrz/livesync-commonlib/compat/common/LSError";
+
+import { createCustomisationSyncCodec, type PluginDataEx } from "./customisationSyncCodec.ts";
+import type { CustomisationSyncPathOperations } from "./customisationSyncPathOperations.ts";
+import { readCustomisationFile } from "./customisationSyncReadOperations.ts";
+
+const {
+    serialize,
+    deserialize,
+    dummyHead: DUMMY_HEAD,
+    dummyEnd: DUMMY_END,
+} = createCustomisationSyncCodec({ digestHash, parseYaml });
+
+type SnapshotPersistenceDatabase = Pick<
+    LiveSyncLocalDB,
+    "getDBEntryFromMeta" | "getDBEntryMeta" | "putDBEntry" | "putRaw"
+>;
+
+type SnapshotPersistenceStorage = Pick<StorageAccess, "readHiddenFileBinary" | "statHidden">;
+
+type SnapshotPersistencePath = Pick<
+    CustomisationSyncPathOperations,
+    "getFileCategory" | "filenameToUnifiedKey" | "filenameWithUnifiedKey"
+> &
+    Pick<IPathService, "isMarkedAsSameChanges" | "markChangesAreSame" | "path2id">;
+
+export type SnapshotPersistenceDependencies = {
+    getLocalDatabase(): SnapshotPersistenceDatabase;
+    storageAccess: SnapshotPersistenceStorage;
+    path: SnapshotPersistencePath;
+    log: LogFunction;
+    getConfigDir(): string;
+};
+
+export type SnapshotRefresh = {
+    mode: "v1" | "v2";
+    timing: "await" | "fire-and-forget";
+    path: FilePathWithPrefix;
+};
+
+export type SnapshotPersistenceStatus = "saved" | "skipped" | "missing" | "deleted" | "already-deleted" | "failed";
+
+export type SnapshotPersistenceResult<Value> = {
+    value: Value;
+    status: SnapshotPersistenceStatus;
+    refreshes: readonly SnapshotRefresh[];
+};
+
+type DatabaseSaveResult = Awaited<ReturnType<SnapshotPersistenceDatabase["putDBEntry"]>>;
+type StoreResultValue = DatabaseSaveResult | true | undefined;
+
+function result<Value>(
+    value: Value,
+    status: SnapshotPersistenceStatus,
+    refreshes: readonly SnapshotRefresh[] = []
+): SnapshotPersistenceResult<Value> {
+    return { value, status, refreshes };
+}
+
+/**
+ * Persists local Customisation Sync snapshots without owning catalogue state,
+ * lifecycle, replication, or user-interface behaviour.
+ */
+export class SnapshotPersistence {
+    private readonly dependencies: SnapshotPersistenceDependencies;
+
+    constructor(dependencies: SnapshotPersistenceDependencies) {
+        this.dependencies = dependencies;
+    }
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string) {
+        this.dependencies.log(message, level, key);
+    }
+
+    private async readFile(path: FilePath) {
+        return await readCustomisationFile(
+            {
+                storageAccess: this.dependencies.storageAccess,
+                log: this.dependencies.log,
+            },
+            path,
+            this.dependencies.getConfigDir()
+        );
+    }
+
+    // Compatibility question: the inherited force parameter is not read.
+    // Preserve it until its intended write-bypass semantics are decided.
+    async storeCustomisationFileV2(
+        path: FilePath,
+        term: string,
+        force = false
+    ): Promise<SnapshotPersistenceResult<StoreResultValue>> {
+        void force;
+        const vf = this.dependencies.path.filenameWithUnifiedKey(path, term);
+        return await serialized(`plugin-${vf}`, async () => {
+            const prefixedFileName = vf;
+
+            const id = await this.dependencies.path.path2id(prefixedFileName);
+            const stat = await this.dependencies.storageAccess.statHidden(path);
+            if (!stat) {
+                return result(false, "missing");
+            }
+            const mtime = stat.mtime;
+            const content = await this.dependencies.storageAccess.readHiddenFileBinary(path);
+            const contentBlob = createBlob([DUMMY_HEAD, DUMMY_END, ...(await arrayBufferToBase64(content))]);
+            // const contentBlob = createBlob(content);
+            try {
+                const old = await this.dependencies
+                    .getLocalDatabase()
+                    .getDBEntryMeta(prefixedFileName, undefined, false);
+                let saveData: SavingEntry;
+                if (old === false) {
+                    saveData = {
+                        _id: id,
+                        path: prefixedFileName,
+                        data: contentBlob,
+                        mtime,
+                        ctime: mtime,
+                        datatype: "plain",
+                        size: contentBlob.size,
+                        children: [],
+                        deleted: false,
+                        type: "plain",
+                        eden: {},
+                    };
+                } else {
+                    // Compatibility question: this inherited marker check
+                    // precedes loading the old document and can suppress a
+                    // content comparison. Preserve that event-suppression
+                    // ordering until its scan contract is reviewed.
+                    if (
+                        this.dependencies.path.isMarkedAsSameChanges(prefixedFileName, [old.mtime, mtime + 1]) == EVEN
+                    ) {
+                        this._log(
+                            `STORAGE --> DB:${prefixedFileName}: (config) Skipped (Already checked the same)`,
+                            LOG_LEVEL_DEBUG
+                        );
+                        return result(undefined, "skipped");
+                    }
+                    const docXDoc = await this.dependencies.getLocalDatabase().getDBEntryFromMeta(old, false, false);
+                    if (docXDoc == false) {
+                        throw new LiveSyncError("Could not load the document");
+                    }
+                    const dataSrc = getDocData(docXDoc.data);
+                    const dataStart = dataSrc.indexOf(DUMMY_END);
+                    const oldContent = dataSrc.substring(dataStart + DUMMY_END.length);
+                    const oldContentArray = base64ToArrayBuffer(oldContent);
+                    if (await isDocContentSame(oldContentArray, content)) {
+                        this._log(
+                            `STORAGE --> DB:${prefixedFileName}: (config) Skipped (the same content)`,
+                            LOG_LEVEL_VERBOSE
+                        );
+                        this.dependencies.path.markChangesAreSame(prefixedFileName, old.mtime, mtime + 1);
+                        return result(true, "skipped");
+                    }
+                    saveData = {
+                        ...old,
+                        data: contentBlob,
+                        mtime,
+                        size: contentBlob.size,
+                        datatype: "plain",
+                        children: [],
+                        deleted: false,
+                        type: "plain",
+                    };
+                }
+                const ret = await this.dependencies.getLocalDatabase().putDBEntry(saveData);
+                this._log(`STORAGE --> DB:${prefixedFileName}: (config) Done`);
+                // Compatibility question: the inherited refresh path omits the
+                // explicit term override and therefore uses the current term.
+                // Preserve that path until its cross-device semantics are reviewed.
+                return result(ret, "saved", [
+                    {
+                        mode: "v2",
+                        timing: "fire-and-forget",
+                        path: this.dependencies.path.filenameWithUnifiedKey(path),
+                    },
+                ]);
+            } catch (ex) {
+                this._log(`STORAGE --> DB:${prefixedFileName}: (config) Failed`);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+                return result(false, "failed");
+            }
+        });
+    }
+
+    async storeCustomizationFiles(path: FilePath, term: string): Promise<SnapshotPersistenceResult<StoreResultValue>> {
+        const vf = this.dependencies.path.filenameToUnifiedKey(path, term);
+        // console.warn(`Storing ${path} to ${bareVF} :--> ${keyedVF}`);
+
+        return await serialized(`plugin-${vf}`, async () => {
+            const category = this.dependencies.path.getFileCategory(path);
+            let mtime = 0;
+            let fileTargets = [] as FilePath[];
+            // let savePath = "";
+            const name =
+                category == "CONFIG" || category == "SNIPPET"
+                    ? path.split("/").reverse()[0]
+                    : path.split("/").reverse()[1];
+            const parentPath = path.split("/").slice(0, -1).join("/");
+            const prefixedFileName = this.dependencies.path.filenameToUnifiedKey(path, term);
+            const id = await this.dependencies.path.path2id(prefixedFileName);
+            const dt: PluginDataEx = {
+                category: category,
+                files: [],
+                name: name,
+                mtime: 0,
+                term: term,
+            };
+            // let scheduleKey = "";
+            if (
+                category == "CONFIG" ||
+                category == "SNIPPET" ||
+                category == "PLUGIN_ETC" ||
+                category == "PLUGIN_DATA"
+            ) {
+                fileTargets = [path];
+                if (category == "PLUGIN_ETC") {
+                    dt.displayName = path.split("/").slice(-1).join("/");
+                }
+            } else if (category == "PLUGIN_MAIN") {
+                fileTargets = ["manifest.json", "main.js", "styles.css"].map((e) => `${parentPath}/${e}` as FilePath);
+            } else if (category == "THEME") {
+                fileTargets = ["manifest.json", "theme.css"].map((e) => `${parentPath}/${e}` as FilePath);
+            }
+            for (const target of fileTargets) {
+                const data = await this.readFile(target);
+                if (data == false) {
+                    this._log(`Config: skipped (Possibly is not exist): ${target} `, LOG_LEVEL_VERBOSE);
+                    continue;
+                }
+                if (data.version) {
+                    dt.version = data.version;
+                }
+                if (data.displayName) {
+                    dt.displayName = data.displayName;
+                }
+                // Compatibility question: the inherited aggregation uses an
+                // average rather than the newest member mtime. Preserve that
+                // scan behaviour until its timestamp policy is reviewed.
+                mtime = mtime == 0 ? data.mtime : (data.mtime + mtime) / 2;
+                dt.files.push(data);
+            }
+            dt.mtime = mtime;
+
+            // Compatibility question: the inherited empty-file path performs a
+            // deletion refresh and then an unconditional explicit refresh. Keep
+            // both outcomes, including the extra refresh when deletion succeeds.
+            if (dt.files.length == 0) {
+                this._log(`Nothing left: deleting.. ${path}`);
+                const deletion = await this.deleteConfigOnDatabase(prefixedFileName);
+                return result(undefined, deletion.status, [
+                    ...deletion.refreshes,
+                    { mode: "v1", timing: "await", path: prefixedFileName },
+                ]);
+            }
+
+            const content = createTextBlob(serialize(dt));
+            try {
+                const old = await this.dependencies
+                    .getLocalDatabase()
+                    .getDBEntryMeta(prefixedFileName, undefined, false);
+                let saveData: SavingEntry;
+                if (old === false) {
+                    saveData = {
+                        _id: id,
+                        path: prefixedFileName,
+                        data: content,
+                        mtime,
+                        ctime: mtime,
+                        datatype: "newnote",
+                        size: content.size,
+                        children: [],
+                        deleted: false,
+                        type: "newnote",
+                        eden: {},
+                    };
+                } else {
+                    if (old.mtime == mtime) {
+                        // this._log(`STORAGE --> DB:${prefixedFileName}: (config) Skipped (Same time)`, LOG_LEVEL_VERBOSE);
+                        return result(true, "skipped");
+                    }
+                    const oldC = await this.dependencies.getLocalDatabase().getDBEntryFromMeta(old, false, false);
+                    if (oldC) {
+                        const d = deserialize(getDocDataAsArray(oldC.data), {}) as PluginDataEx;
+                        if (d.files.length == dt.files.length) {
+                            // Compatibility question: the inherited comparison
+                            // looks up each current file by the previous filename
+                            // and compares a missing lookup as empty content.
+                            // Preserve this rename/empty-file behaviour for now.
+                            const diffs = d.files
+                                .map((previous) => ({
+                                    prev: previous,
+                                    curr: dt.files.find((e) => e.filename == previous.filename),
+                                }))
+                                .map(async (e) => {
+                                    try {
+                                        return await isDocContentSame(e.curr?.data ?? [], e.prev.data);
+                                    } catch {
+                                        return false;
+                                    }
+                                });
+                            const isSame = (await Promise.all(diffs)).every((e) => e == true);
+                            if (isSame) {
+                                this._log(
+                                    `STORAGE --> DB:${prefixedFileName}: (config) Skipped (Same content)`,
+                                    LOG_LEVEL_VERBOSE
+                                );
+                                return result(true, "skipped");
+                            }
+                        }
+                    }
+                    saveData = {
+                        ...old,
+                        data: content,
+                        mtime,
+                        size: content.size,
+                        datatype: "newnote",
+                        children: [],
+                        deleted: false,
+                        type: "newnote",
+                    };
+                }
+                const ret = await this.dependencies.getLocalDatabase().putDBEntry(saveData);
+                this._log(`STORAGE --> DB:${prefixedFileName}: (config) Done`);
+                return result(ret, "saved", [{ mode: "v1", timing: "await", path: saveData.path }]);
+            } catch (ex) {
+                this._log(`STORAGE --> DB:${prefixedFileName}: (config) Failed`);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+                return result(false, "failed");
+            }
+        });
+    }
+
+    // Compatibility question: the inherited forceWrite parameter is not read.
+    // Preserve it until callers define whether deletion should bypass a marker.
+    async deleteConfigOnDatabase(
+        prefixedFileName: FilePathWithPrefix,
+        forceWrite = false
+    ): Promise<SnapshotPersistenceResult<boolean>> {
+        void forceWrite;
+        // const id = await this.path2id(prefixedFileName);
+        const mtime = new Date().getTime();
+        return await serialized("file-x-" + prefixedFileName, async () => {
+            try {
+                const old = (await this.dependencies
+                    .getLocalDatabase()
+                    .getDBEntryMeta(prefixedFileName, undefined, false)) as InternalFileEntry | false;
+                let saveData: InternalFileEntry;
+                if (old === false) {
+                    this._log(`STORAGE -x> DB:${prefixedFileName}: (config) already deleted (Not found on database)`);
+                    return result(true, "missing");
+                } else {
+                    if (old.deleted) {
+                        this._log(`STORAGE -x> DB:${prefixedFileName}: (config) already deleted`);
+                        return result(true, "already-deleted");
+                    }
+                    saveData = {
+                        ...old,
+                        mtime,
+                        size: 0,
+                        children: [],
+                        deleted: true,
+                        type: "newnote",
+                    };
+                }
+                await this.dependencies.getLocalDatabase().putRaw(saveData);
+                this._log(`STORAGE -x> DB:${prefixedFileName}: (config) Done`);
+                return result(true, "deleted", [{ mode: "v1", timing: "await", path: prefixedFileName }]);
+            } catch (ex) {
+                this._log(`STORAGE -x> DB:${prefixedFileName}: (config) Failed`);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+                return result(false, "failed");
+            }
+        });
+    }
+}

src/features/ConfigSync/snapshotPersistence.unit.spec.ts

@@ -0,0 +1,219 @@
+import { describe, expect, it, vi } from "vitest";
+
+vi.mock("@/deps.ts", () => ({
+    diff_match_patch: class DiffMatchPatch {},
+    normalizePath: vi.fn((path: string) => path),
+    parseYaml: vi.fn(),
+}));
+vi.mock("@/common/utils.ts", () => ({
+    EVEN: Symbol("even"),
+    cancelTask: vi.fn(),
+    fireAndForget: vi.fn(),
+    scheduleTask: vi.fn(),
+}));
+vi.mock("@/common/types.ts", () => ({
+    ICXHeader: "ix:",
+    PERIODIC_PLUGIN_SWEEP: 60,
+}));
+vi.mock("@/common/translation", () => ({
+    $msg: vi.fn((message: string) => message),
+}));
+vi.mock("@/common/obsidianCommunityPlugins.ts", () => ({
+    getObsidianCommunityPluginManager: vi.fn(),
+}));
+vi.mock("@/features/optionalFileSyncFileTree.ts", () => ({
+    collectOptionalFileSyncFiles: vi.fn(),
+}));
+
+import type { FilePath, FilePathWithPrefix, LoadedEntry, UXStat } from "@vrtmrz/livesync-commonlib/compat/common/types";
+import { EVEN } from "@vrtmrz/livesync-commonlib/compat/common/models/shared.const.symbols";
+import { createCustomisationSyncCodec } from "./customisationSyncCodec.ts";
+import { SnapshotPersistence, type SnapshotPersistenceDependencies } from "./snapshotPersistence.ts";
+
+const CONFIG_PATH = ".obsidian/app.json" as FilePath;
+const V1_PATH = "ix:device-a/CONFIG/app.json.md" as FilePathWithPrefix;
+const V2_PATH = "ix:device-a/CONFIG/app.json%app.json" as FilePathWithPrefix;
+const codec = createCustomisationSyncCodec({
+    digestHash: (source) => source.join(""),
+    parseYaml: () => undefined,
+});
+
+function loadedV2Entry(source: string, mtime = 10): LoadedEntry {
+    const data = `${codec.dummyHead}${codec.dummyEnd}${btoa(source)}`;
+    return {
+        _id: "entry-id",
+        _rev: "1-a",
+        path: V2_PATH,
+        type: "plain",
+        datatype: "plain",
+        data,
+        ctime: mtime,
+        mtime,
+        size: data.length,
+        children: [],
+        eden: {},
+    } as unknown as LoadedEntry;
+}
+
+function createPersistence(
+    options: {
+        category?: "CONFIG" | "PLUGIN_MAIN";
+        old?: false | LoadedEntry;
+        stat?: UXStat | null;
+        content?: string;
+        currentTerm?: string;
+    } = {}
+) {
+    const currentTerm = options.currentTerm ?? "device-a";
+    const statHidden = vi.fn(
+        async (_path: string): Promise<UXStat | null> =>
+            options.stat === undefined ? { type: "file", ctime: 10, mtime: 10, size: 5 } : options.stat
+    );
+    const readHiddenFileBinary = vi.fn(
+        async (_path: string) => new TextEncoder().encode(options.content ?? "hello").buffer
+    );
+    const getDBEntryMeta = vi.fn(async () => options.old ?? false);
+    const getDBEntryFromMeta = vi.fn(async (entry: LoadedEntry) => entry);
+    const putDBEntry = vi.fn(async () => ({ ok: true, id: "entry-id", rev: "2-b" }));
+    const putRaw = vi.fn(async () => ({ ok: true, id: "entry-id", rev: "2-b" }));
+    const filenameToUnifiedKey = vi.fn(
+        (_path: string, term?: string) =>
+            `ix:${term ?? currentTerm}/${options.category ?? "CONFIG"}/app.json.md` as FilePathWithPrefix
+    );
+    const filenameWithUnifiedKey = vi.fn(
+        (_path: string, term?: string) =>
+            `ix:${term ?? currentTerm}/${options.category ?? "CONFIG"}/app.json%app.json` as FilePathWithPrefix
+    );
+    const dependencies: SnapshotPersistenceDependencies = {
+        getLocalDatabase: () => ({ getDBEntryMeta, getDBEntryFromMeta, putDBEntry, putRaw }),
+        storageAccess: { statHidden, readHiddenFileBinary },
+        path: {
+            getFileCategory: () => options.category ?? "CONFIG",
+            filenameToUnifiedKey,
+            filenameWithUnifiedKey,
+            path2id: vi.fn(async (path) => path),
+            isMarkedAsSameChanges: vi.fn(),
+            markChangesAreSame: vi.fn(),
+        },
+        log: vi.fn(),
+        getConfigDir: () => ".obsidian",
+    };
+    return {
+        database: { getDBEntryMeta, getDBEntryFromMeta, putDBEntry, putRaw },
+        dependencies,
+        filenameToUnifiedKey,
+        filenameWithUnifiedKey,
+        persistence: new SnapshotPersistence(dependencies),
+        readHiddenFileBinary,
+        statHidden,
+    };
+}
+
+describe("Customisation Sync snapshot persistence", () => {
+    it("persists a V2 file and returns a fire-and-forget catalogue refresh", async () => {
+        const fixture = createPersistence();
+
+        const mutation = await fixture.persistence.storeCustomisationFileV2(CONFIG_PATH, "device-a");
+
+        expect(mutation).toMatchObject({
+            value: { ok: true, id: "entry-id", rev: "2-b" },
+            status: "saved",
+            refreshes: [{ mode: "v2", timing: "fire-and-forget", path: V2_PATH }],
+        });
+        expect(fixture.database.putDBEntry).toHaveBeenCalledOnce();
+        expect(fixture.filenameWithUnifiedKey).toHaveBeenNthCalledWith(1, CONFIG_PATH, "device-a");
+        expect(fixture.filenameWithUnifiedKey).toHaveBeenNthCalledWith(2, CONFIG_PATH);
+    });
+
+    it("aggregates the V1 plug-in file set and returns an awaited refresh", async () => {
+        const fixture = createPersistence({ category: "PLUGIN_MAIN" });
+
+        const mutation = await fixture.persistence.storeCustomizationFiles(
+            ".obsidian/plugins/example/main.js" as FilePath,
+            "device-a"
+        );
+
+        expect(mutation).toMatchObject({
+            value: { ok: true },
+            status: "saved",
+            refreshes: [{ mode: "v1", timing: "await", path: "ix:device-a/PLUGIN_MAIN/app.json.md" }],
+        });
+        expect(fixture.readHiddenFileBinary).toHaveBeenCalledTimes(3);
+        expect(fixture.database.putDBEntry).toHaveBeenCalledOnce();
+    });
+
+    it("keeps the inherited duplicate V1 refresh on the empty-file deletion path", async () => {
+        const old = {
+            ...loadedV2Entry("old"),
+            path: V1_PATH,
+            datatype: "newnote",
+            type: "newnote",
+            deleted: false,
+        } as LoadedEntry;
+        const fixture = createPersistence({ old, stat: null });
+
+        const mutation = await fixture.persistence.storeCustomizationFiles(CONFIG_PATH, "device-a");
+
+        expect(mutation.value).toBeUndefined();
+        expect(mutation.status).toBe("deleted");
+        expect(mutation.refreshes).toEqual([
+            { mode: "v1", timing: "await", path: V1_PATH },
+            { mode: "v1", timing: "await", path: V1_PATH },
+        ]);
+        expect(fixture.database.putRaw).toHaveBeenCalledOnce();
+    });
+
+    it.each([
+        ["missing", false, "missing"],
+        ["already deleted", { ...loadedV2Entry("old"), deleted: true } as LoadedEntry, "already-deleted"],
+    ] as const)("treats an absent or %s document as a successful no-op", async (_label, old, status) => {
+        const fixture = createPersistence({ old, stat: null });
+
+        const mutation = await fixture.persistence.deleteConfigOnDatabase(V1_PATH);
+
+        expect(mutation).toMatchObject({ value: true, status, refreshes: [] });
+        expect(fixture.database.putRaw).not.toHaveBeenCalled();
+    });
+
+    it("returns an awaited refresh only when deletion writes a live document", async () => {
+        const old = {
+            ...loadedV2Entry("old"),
+            path: V1_PATH,
+            deleted: false,
+        } as LoadedEntry;
+        const fixture = createPersistence({ old });
+
+        const mutation = await fixture.persistence.deleteConfigOnDatabase(V1_PATH);
+
+        expect(mutation).toMatchObject({
+            value: true,
+            status: "deleted",
+            refreshes: [{ mode: "v1", timing: "await", path: V1_PATH }],
+        });
+        expect(fixture.database.putRaw).toHaveBeenCalledOnce();
+    });
+
+    it("preserves the V2 marker and same-content skips", async () => {
+        const markerFixture = createPersistence({ old: loadedV2Entry("old") });
+        const marker = markerFixture.dependencies.path.isMarkedAsSameChanges as ReturnType<typeof vi.fn>;
+        marker.mockReturnValue(EVEN);
+        await expect(
+            markerFixture.persistence.storeCustomisationFileV2(CONFIG_PATH, "device-a")
+        ).resolves.toMatchObject({
+            value: undefined,
+            status: "skipped",
+            refreshes: [],
+        });
+        expect(markerFixture.database.putDBEntry).not.toHaveBeenCalled();
+
+        const sameContentFixture = createPersistence({ old: loadedV2Entry("hello") });
+        await expect(
+            sameContentFixture.persistence.storeCustomisationFileV2(CONFIG_PATH, "device-a")
+        ).resolves.toMatchObject({
+            value: true,
+            status: "skipped",
+            refreshes: [],
+        });
+        expect(sameContentFixture.database.putDBEntry).not.toHaveBeenCalled();
+    });
+});

src/features/HiddenFileSync/hiddenFileSyncContext.ownership.unit.spec.ts

@@ -53,6 +53,9 @@ describe("HiddenFileSyncContext ownership and start-up lifecycle", () => {
         expect(getPrivate<unknown>(first.context, "changeProcessor")).not.toBe(
             getPrivate<unknown>(second.context, "changeProcessor")
         );
+        expect(getPrivate<unknown>(first.context, "reconciliation")).not.toBe(
+            getPrivate<unknown>(second.context, "reconciliation")
+        );
         expect(getPrivate<unknown>(first.context, "periodicInternalFileScanProcessor")).toBe(first.periodicProcessor);
         expect(getPrivate<unknown>(second.context, "periodicInternalFileScanProcessor")).toBe(second.periodicProcessor);
 
@@ -67,8 +70,10 @@ describe("HiddenFileSyncContext ownership and start-up lifecycle", () => {
         "preserves start-up scan notice selection for the processed-file cache",
         async (processedFiles, forcedNotice) => {
             const { context } = createContext(processedFiles);
-            const applyOfflineChanges = vi.fn(async () => undefined);
+            const reconciliation = getPrivate<{
-            context.applyOfflineChanges = applyOfflineChanges;
+                applyOfflineChanges(showNotice: boolean): Promise<unknown>;
+            }>(context, "reconciliation");
+            const applyOfflineChanges = vi.spyOn(reconciliation, "applyOfflineChanges").mockResolvedValue(undefined);
 
             await context.serviceHandlers.onDatabaseInitialised(false);
 

src/features/HiddenFileSync/hiddenFileSyncContext.ts

@@ -6,28 +6,15 @@ import {
     LOG_LEVEL_INFO,
     LOG_LEVEL_NOTICE,
     LOG_LEVEL_VERBOSE,
-    type DocumentID,
     type MetaEntry,
     type ObsidianLiveSyncSettings,
     type LOG_LEVEL,
 } from "@vrtmrz/livesync-commonlib/compat/common/types";
-import { type InternalFileInfo, ICHeader, ICHeaderEnd } from "@/common/types.ts";
+import { ICHeader, ICHeaderEnd } from "@/common/types.ts";
 import { type CustomRegExp } from "@vrtmrz/livesync-commonlib/compat/common/utils";
-import {
+import { isInternalMetadata, cancelTask, scheduleTask } from "@/common/utils.ts";
-    compareMTime,
+import { serialized } from "octagonal-wheels/concurrency/lock";
-    isInternalMetadata,
-    TARGET_IS_NEW,
-    cancelTask,
-    scheduleTask,
-    getLogLevel,
-    onlyInNTimes,
-    BASE_IS_NEW,
-    EVEN,
-} from "@/common/utils.ts";
-import { serialized, skipIfDuplicated } from "octagonal-wheels/concurrency/lock";
 import { addPrefix, stripAllPrefixes } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/path";
-import { Semaphore } from "octagonal-wheels/concurrency/semaphore";
-import { tryGetFilePath } from "@vrtmrz/livesync-commonlib/compat/common/utils.doc";
 import { configureHiddenFileSyncMode, type ConfigureHiddenFileSyncResult } from "./configureHiddenFileSyncMode.ts";
 import type { OptionalSyncFeatureMode } from "@/features/optionalSyncFeatures.ts";
 import { $msg } from "@/common/translation";
@@ -42,14 +29,9 @@ import {
     type HiddenFileSyncCommandView,
     type HiddenFileSyncRepairView,
     type HiddenFileSyncServiceHandlerView,
-    type HiddenFileSyncTestingRebuild,
     type HiddenFileSyncTestingView,
 } from "./hiddenFileSyncViews.ts";
-import { describeHiddenFileSyncDocument, getHiddenFileSyncComparisonMTime } from "./hiddenFileSyncState.ts";
+import type { OptionalFileSyncFileTreeDependencies } from "@/features/optionalFileSyncFileTree.ts";
-import {
-    collectOptionalFileSyncFiles,
-    type OptionalFileSyncFileTreeDependencies,
-} from "@/features/optionalFileSyncFileTree.ts";
 import {
     deleteHiddenFileFromStorage,
     ensureHiddenFileDirectory,
@@ -81,21 +63,20 @@ import {
     createHiddenFileSyncChangeProcessor,
     type HiddenFileSyncChangeProcessor,
 } from "./hiddenFileSyncChangeProcessor.ts";
-import {
+import { createHiddenFileSyncPathAdmission, type HiddenFileSyncPathAdmission } from "./hiddenFileSyncPathAdmission.ts";
-    createHiddenFileSyncPathAdmission,
-    type HiddenFileSyncPathAdmission,
-} from "./hiddenFileSyncPathAdmission.ts";
 import {
     createHiddenFileSyncChangeNotifier,
     type HiddenFileSyncChangeNotifier,
 } from "./hiddenFileSyncChangeNotifier.ts";
-type SyncDirection = "push" | "pull" | "safe" | "pullForce" | "pushForce";
+import {
+    createReconciliation,
+    type InitialisationDirection,
+    type ReconciliationProgress,
+    type Reconciliation,
+} from "./reconciliation.ts";
 
-export type HiddenFileSyncProgress = {
+export type { ReconciliationProgress as HiddenFileSyncProgress } from "./reconciliation.ts";
-    log(message: string): void;
+type SyncDirection = InitialisationDirection;
-    once(message: string): void;
-    done(message?: string): void;
-};
 
 type HiddenFileSyncSettings = Pick<
     ObsidianLiveSyncSettings,
@@ -145,7 +126,7 @@ export type HiddenFileSyncContextDependencies = OptionalFileSyncFileTreeDependen
         getKeyValueDatabase(): KeyValueDatabase;
         databaseFileAccess: HiddenFileSyncDatabaseFileAccess;
         path: Pick<IPathService, "getPath" | "markChangesAreSame" | "path2id" | "unmarkChanges">;
-        createProgress(prefix?: string, level?: LOG_LEVEL): HiddenFileSyncProgress;
+        createProgress(prefix?: string, level?: LOG_LEVEL): ReconciliationProgress;
         createPeriodicProcessor(process: () => Promise<unknown>): HiddenFileSyncPeriodicProcessor;
         isReady(): boolean;
         isSuspended(): boolean;
@@ -180,13 +161,13 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
     private readonly databaseExtractionOperations: HiddenFileSyncDatabaseExtractionOperations;
     private readonly conflictResolution: HiddenFileSyncConflictResolution;
     private readonly changeProcessor: HiddenFileSyncChangeProcessor;
+    private readonly reconciliation: Reconciliation;
     private readonly pathAdmission: HiddenFileSyncPathAdmission;
     private readonly changeNotifier: HiddenFileSyncChangeNotifier;
     readonly serviceHandlers: HiddenFileSyncServiceHandlerView;
     readonly testing: HiddenFileSyncTestingView;
     readonly repair: HiddenFileSyncRepairView;
     private readonly periodicInternalFileScanProcessor: HiddenFileSyncPeriodicProcessor;
-    private rebuildMergingHook: HiddenFileSyncTestingRebuild | undefined;
     private disposed = false;
 
     constructor(dependencies: HiddenFileSyncContextDependencies) {
@@ -303,8 +284,21 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
             log: (message, level, key) => dependencies.log(message, level, key),
             publishActivity: (eventCount, processingCount) => dependencies.publishActivity(eventCount, processingCount),
         });
+        this.reconciliation = createReconciliation({
+            listFiles: async (path) => await dependencies.listFiles(path),
+            getLocalDatabase: () => dependencies.getLocalDatabase(),
+            storageAccess: dependencies.storageAccess,
+            getRootPath: () => dependencies.getRootPath(),
+            getPath: (entry) => dependencies.path.getPath(entry),
+            isTargetFile: async (path) => await this.pathAdmission.isTargetFile(path),
+            isIgnoredByIgnoreFile: async (path) => await dependencies.isIgnoredByIgnoreFile(path),
+            createProgress: (prefix, level) => dependencies.createProgress(prefix, level),
+            processedState: this.processedState,
+            changeProcessor: this.changeProcessor,
+            log: (message, level, key) => dependencies.log(message, level, key),
+        });
         this.repair = createHiddenFileSyncRepairView({
-            scanInternalFiles: async () => await this.scanInternalFiles(),
+            scanInternalFiles: async () => await this.reconciliation.scanInternalFiles(),
             storeInternalFileToDatabase: async (file, forceWrite) =>
                 await this.databaseWriteOperations.store(file, forceWrite),
             storeInternalFileToDatabaseWithBaseRevision: async (file, baseRevision, createIfDifferent) =>
@@ -337,19 +331,7 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
             readFileWithInfo: async (path) => await readHiddenFileWithInfo(dependencies, path),
             showConfigurationChangeNotice: (updatedFolders) =>
                 this.changeNotifier.showConfigurationChangeNotice(updatedFolders),
-            interceptRebuildMerging: (interceptor) => {
+            interceptRebuildMerging: (interceptor) => this.reconciliation.interceptRebuildMerging(interceptor),
-                const previousHook = this.rebuildMergingHook;
-                const runRebuild = async (showNotice: boolean, targetFiles?: FilePath[] | false) =>
-                    await this.rebuildMerging(showNotice, targetFiles);
-                const hook: HiddenFileSyncTestingRebuild = async (showNotice, targetFiles) =>
-                    await interceptor(runRebuild, showNotice, targetFiles);
-                this.rebuildMergingHook = hook;
-                return () => {
-                    if (this.rebuildMergingHook === hook) {
-                        this.rebuildMergingHook = previousHook;
-                    }
-                };
-            },
         });
         this.periodicInternalFileScanProcessor = dependencies.createPeriodicProcessor(
             async () =>
@@ -361,18 +343,6 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
         return this.dependencies.getSettings();
     }
 
-    private get localDatabase() {
-        return this.dependencies.getLocalDatabase();
-    }
-
-    private get storageAccess() {
-        return this.dependencies.storageAccess;
-    }
-
-    private get databaseFileAccess() {
-        return this.dependencies.databaseFileAccess;
-    }
-
     private getPath(entry: AnyEntry): FilePathWithPrefix {
         return this.dependencies.path.getPath(entry);
     }
@@ -393,10 +363,6 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
         this.dependencies.log(message, level, key);
     }
 
-    private _verbose(message: unknown, key?: string) {
-        this._log(message, LOG_LEVEL_VERBOSE, key);
-    }
-
     private _progress(prefix: string = "", level: LOG_LEVEL = LOG_LEVEL_NOTICE) {
         return this.dependencies.createProgress(prefix, level);
     }
@@ -410,10 +376,10 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
         this.disposed = true;
         this.periodicInternalFileScanProcessor?.disable();
         this.changeProcessor.dispose();
+        this.reconciliation.dispose();
         this.conflictResolution.dispose();
         this.pathAdmission.dispose();
         this.changeNotifier.dispose();
-        this.rebuildMergingHook = undefined;
         this.dependencies.closeJsonConflictDialogs();
     }
 
@@ -492,7 +458,7 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
 
     private async processOptionalFileEvent(path: FilePath): Promise<boolean> {
         if (this.isReady()) {
-            return (await this.trackStorageFileModification(path)) || false;
+            return (await this.reconciliation.processStorageChange(path)) || false;
         }
         return false;
     }
@@ -511,7 +477,7 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
                     // We should return true, we made sure that document is a internalMetadata.
                     return true;
                 }
-                if (!(await this.processReplicationResult(doc))) {
+                if (!(await this.reconciliation.processDatabaseDocument(doc))) {
                     this._log(`Failed to process sync file:${unprefixedPath}`, LOG_LEVEL_NOTICE);
                     // Do not yield false, this file had been processed.
                 }
@@ -521,290 +487,8 @@ export class HiddenFileSyncContext implements HiddenFileSyncCommandView {
         return false;
     }
 
-    private async adoptCurrentStorageFilesAsProcessed(targetFiles: FilePath[] | false) {
-        const allFiles = await this.scanInternalFileNames();
-        const files = targetFiles ? allFiles.filter((e) => targetFiles.some((t) => e.indexOf(t) !== -1)) : allFiles;
-        for (const file of files) {
-            await this.processedState.updateLastProcessedAsActualFile(file);
-        }
-    }
-    private async adoptCurrentDatabaseFilesAsProcessed(targetFiles: FilePath[] | false) {
-        const allFiles = await this.getAllDatabaseFiles();
-        const files = targetFiles
-            ? allFiles.filter((e) => targetFiles.some((t) => e.path.indexOf(t) !== -1))
-            : allFiles;
-        for (const file of files) {
-            const path = stripAllPrefixes(this.getPath(file));
-            await this.processedState.updateLastProcessedAsActualDatabase(path, file);
-        }
-    }
-
-    private async trackScannedStorageChanges(
-        processFiles: FilePath[],
-        showNotice: boolean = false,
-        onlyNew = false,
-        forceWriteAll = false,
-        includeDeleted = true
-    ) {
-        const logLevel = getLogLevel(showNotice);
-        const p = this._progress(`[⚙ Storage -> DB ]\n`, logLevel);
-        const notifyProgress = onlyInNTimes(100, (progress) => p.log(`${progress}/${processFiles.length}`));
-        const processes = processFiles.map(async (file, i) => {
-            try {
-                await this.trackStorageFileModification(file, onlyNew, forceWriteAll, includeDeleted);
-                notifyProgress();
-            } catch (ex) {
-                p.once(`Failed to process storage change file:${file}`);
-                this._log(ex, LOG_LEVEL_VERBOSE);
-            }
-        });
-        await Promise.all(processes);
-        p.done();
-    }
-    async scanAllStorageChanges(
-        showNotice: boolean = false,
-        onlyNew = false,
-        forceWriteAll = false,
-        includeDeleted = true
-    ) {
-        return await skipIfDuplicated("scanAllStorageChanges", async () => {
-            const logLevel = getLogLevel(showNotice);
-            const p = this._progress(`[⚙ Scanning Storage -> DB ]\n`, logLevel);
-            p.log(`Scanning storage files...`);
-            const knownNames = [...this.processedState.getLastProcessedFileKeys()] as FilePath[];
-            const existNames = await this.scanInternalFileNames();
-            const files = new Set([...knownNames, ...existNames]);
-
-            this._log(
-                `Known/Exist ${knownNames.length}/${existNames.length}, Totally ${files.size} files.`,
-                LOG_LEVEL_VERBOSE
-            );
-            const taskNameAndMeta = [...files].map(async (e) => [e, await this.storageAccess.statHidden(e)] as const);
-            const nameAndMeta = await Promise.all(taskNameAndMeta);
-            const processFiles = nameAndMeta
-                .filter(([path, stat]) => {
-                    if (forceWriteAll) return true;
-                    const key = this.processedState.getLastProcessedFileKey(path);
-                    const newKey = this.processedState.storageStateKey(stat);
-                    return key != newKey;
-                })
-                .map(([path, stat]) => path);
-
-            const staticsMessage = `[Storage hidden file statics]
-Known files: ${knownNames.length}
-Actual files: ${existNames.length}
-All files: ${files.size}
-Offline Changed files: ${processFiles.length}`;
-            // this._log(staticsMessage, logLevel, "scan-changes");
-            p.once(staticsMessage);
-            await this.trackScannedStorageChanges(processFiles, showNotice, onlyNew, forceWriteAll, includeDeleted);
-            p.done();
-        });
-    }
-
-    /**
-     * check the file is changed or not, and if changed, process it.
-     */
-    private async trackStorageFileModification(
-        path: FilePath,
-        onlyNew = false,
-        forceWrite = false,
-        includeDeleted = true
-    ): Promise<boolean | undefined> {
-        if (!(await this.pathAdmission.isTargetFile(path))) {
-            this._log(
-                `Storage file tracking: Hidden file skipped: ${path} is filtered out by the defined patterns.`,
-                LOG_LEVEL_VERBOSE
-            );
-            return false;
-        }
-        return await this.changeProcessor.processStorageChange(path, onlyNew, forceWrite, includeDeleted);
-    }
-
-    // --> Event Source Handler (Database)
-    private async processReplicationResult(doc: LoadedEntry): Promise<boolean> {
-        const info = describeHiddenFileSyncDocument(doc, this.getPath(doc));
-        const path = info.path;
-        const headerLine = `Tracking DB ${info.path} (${info.revDisplay}) :`;
-        const ret = await this.trackDatabaseFileModification(path, headerLine);
-        this._log(`${headerLine} Done: ${info.shortenedId})`, LOG_LEVEL_VERBOSE);
-        return ret;
-    }
-
-    // <-- Event Source Handler (Database)
-
     // --> Database Event Functions
 
-    private async trackScannedDatabaseChange(
-        processFiles: MetaEntry[],
-        showNotice: boolean = false,
-        onlyNew = false,
-        forceWriteAll = false,
-        includeDeletion = true
-    ) {
-        const logLevel = getLogLevel(showNotice);
-        const p = this._progress(`[⚙ DB -> Storage ]\n`, logLevel);
-        const notifyProgress = onlyInNTimes(100, (progress) => p.log(`${progress}/${processFiles.length}`));
-        const processes = processFiles.map(async (file) => {
-            try {
-                const path = stripAllPrefixes(this.getPath(file));
-                if (!(await this.pathAdmission.isTargetFile(path))) {
-                    this._log(
-                        `Database file tracking: Hidden file skipped: ${path} is filtered out by the defined patterns.`,
-                        LOG_LEVEL_VERBOSE
-                    );
-                } else {
-                    await this.trackDatabaseFileModification(
-                        path,
-                        "[Hidden file scan]",
-                        !forceWriteAll,
-                        onlyNew,
-                        file,
-                        includeDeletion
-                    );
-                }
-                notifyProgress();
-            } catch (ex) {
-                this._log(`Failed to process storage change file:${tryGetFilePath(file)}`, logLevel);
-                this._log(ex, LOG_LEVEL_VERBOSE);
-            }
-        });
-        await Promise.all(processes);
-        p.done();
-    }
-
-    async applyOfflineChanges(showNotice: boolean) {
-        const logLevel = getLogLevel(showNotice);
-        return await serialized("applyOfflineChanges", async () => {
-            const p = this._progress("[⚙ Apply untracked changes ]\n", logLevel);
-            this._log(`Track changes.`, logLevel);
-            p.log("Enumerating local files...");
-            const currentStorageFiles = await this.scanInternalFileNames();
-            p.log("Enumerating database files...");
-            const currentDatabaseFiles = await this.getAllDatabaseFiles();
-            const allDatabaseMap = Object.fromEntries(
-                currentDatabaseFiles.map((e) => [stripAllPrefixes(this.getPath(e)), e])
-            );
-            const currentDatabaseFileNames = [...Object.keys(allDatabaseMap)] as FilePath[];
-            const untrackedLocal = currentStorageFiles.filter((e) => !this.processedState.hasLastProcessedFile(e));
-            const untrackedDatabase = currentDatabaseFileNames.filter(
-                (e) => !this.processedState.hasLastProcessedDatabase(e)
-            );
-            const bothUntracked = untrackedLocal.filter((e) => untrackedDatabase.indexOf(e) !== -1);
-            p.log("Applying untracked changes...");
-            const stat = `Tracking statics:
-Local files: ${currentStorageFiles.length}
-Database files: ${currentDatabaseFileNames.length}
-Untracked local files: ${untrackedLocal.length}
-Untracked database files: ${untrackedDatabase.length}
-Common untracked files: ${bothUntracked.length}`;
-            p.once(stat);
-            const semaphores = Semaphore(10);
-            const notifyProgress = onlyInNTimes(25, (progress) => p.log(`${progress}/${bothUntracked.length}`));
-            const allProcesses = bothUntracked.map(async (file) => {
-                notifyProgress();
-                const rel = await semaphores.acquire();
-                try {
-                    const fileStat = await this.storageAccess.statHidden(file);
-                    if (fileStat == null) {
-                        // This should not be happened. But, if it happens, we should skip this.
-                        this._log(`Unexpected error: Failed to stat file during applyOfflineChange :${file}`);
-                        return;
-                    }
-                    const dbInfo = allDatabaseMap[file];
-                    if (dbInfo.deleted || dbInfo._deleted) {
-                        // Applying deletion can be harmful if the local file is not tracked.
-                        // So, we should skip this.
-                        return;
-                    }
-                    const fileMTime = getHiddenFileSyncComparisonMTime(fileStat);
-                    const dbMTime = getHiddenFileSyncComparisonMTime(dbInfo);
-                    const diff = compareMTime(fileMTime, dbMTime);
-                    if (diff == BASE_IS_NEW) {
-                        // Local file is newer than the database file.
-                        // So, we should apply the local file to the database.
-                        await this.trackStorageFileModification(file, true);
-                    } else if (diff == TARGET_IS_NEW) {
-                        // Database file is newer than the local file.
-                        // So, we should apply the database file to the local file.
-                        await this.trackDatabaseFileModification(file, "[Apply]", true, true, dbInfo);
-                    } else if (diff == EVEN) {
-                        // Both are same, we may skip this but should update the last processed key.
-                        this.processedState.updateLastProcessed(file, dbInfo, fileStat);
-                    }
-                } finally {
-                    rel();
-                }
-            });
-            await Promise.all(allProcesses);
-            await this.scanAllStorageChanges(showNotice);
-            await this.scanAllDatabaseChanges(showNotice);
-
-            p.done();
-        });
-    }
-
-    async scanAllDatabaseChanges(
-        showNotice: boolean = false,
-        onlyNew = false,
-        forceWriteAll = false,
-        includeDeletion = true
-    ) {
-        return await skipIfDuplicated("scanAllDatabaseChanges", async () => {
-            const databaseFiles = await this.getAllDatabaseFiles();
-            const files = databaseFiles.filter((e) => {
-                const doc = e;
-                const key = this.processedState.databaseStateKey(doc);
-                const path = stripAllPrefixes(this.getPath(doc));
-                const lastKey = this.processedState.getLastProcessedDatabaseKey(path);
-                return lastKey != key;
-            });
-            const logLevel = getLogLevel(showNotice);
-            const staticsMessage = `[Database hidden file statics]
-All files: ${databaseFiles.length}
-Offline Changed files: ${files.length}`;
-            this._log(staticsMessage, logLevel, "scan-changes");
-            return await this.trackScannedDatabaseChange(files, showNotice, onlyNew, forceWriteAll, includeDeletion);
-        });
-    }
-
-    private async useDatabaseFiles(files: MetaEntry[], showNotice = false, onlyNew = false) {
-        const logLevel = getLogLevel(showNotice);
-        const p = this._progress(`[⚙ Scanning DB -> Storage ]\n`, logLevel);
-        p.log("Scanning database files...");
-        const notifyProgress = onlyInNTimes(25, (progress) => p.log(`${progress}/${files.length}`));
-        const processFiles = files.map(async (file) => {
-            try {
-                const path = stripAllPrefixes(this.getPath(file));
-                await this.trackDatabaseFileModification(path, "[Scanning]", true, onlyNew, file);
-                notifyProgress();
-            } catch (ex) {
-                this._log(`Failed to process database changes:${tryGetFilePath(file)}`);
-                this._log(ex, LOG_LEVEL_VERBOSE);
-            }
-            return;
-        });
-        await Promise.all(processFiles);
-        p.done();
-        return true;
-    }
-
-    private async trackDatabaseFileModification(
-        path: FilePath,
-        headerLine: string,
-        preventDoubleProcess = false,
-        onlyNew = false,
-        meta: MetaEntry | false = false,
-        includeDeletion = true
-    ): Promise<boolean> {
-        return await this.changeProcessor.processDatabaseChange(path, headerLine, {
-            preventDoubleProcess,
-            onlyNew,
-            metaEntry: meta,
-            includeDeletion,
-        });
-    }
-
     private queueConflict(path: FilePathWithPrefix): Promise<boolean> {
         this.conflictResolution.queue(path);
         return Promise.resolve(true);
@@ -812,188 +496,42 @@ Offline Changed files: ${files.length}`;
 
     // <-- Database Event Functions
 
-    // --> Initialization functions
+    async scanAllStorageChanges(
-
+        showNotice: boolean = false,
-    private async rebuildMerging(showNotice: boolean, targetFiles: FilePath[] | false = false) {
+        onlyNew = false,
-        const logLevel = getLogLevel(showNotice);
+        forceWriteAll = false,
-        const p = this._progress("[⚙ Rebuild by Merge ]\n", logLevel);
+        includeDeleted = true
-        this._log(`Rebuilding hidden files from the storage and the local database.`, logLevel);
+    ): Promise<unknown> {
-        p.log("Enumerating local files...");
+        return await this.reconciliation.scanAllStorageChanges(showNotice, onlyNew, forceWriteAll, includeDeleted);
-        const currentStorageFilesAll = await this.scanInternalFileNames();
-        const currentStorageFiles = targetFiles
-            ? currentStorageFilesAll.filter((e) => targetFiles.some((f) => f == e))
-            : currentStorageFilesAll;
-        p.log("Enumerating database files...");
-        const allDatabaseFiles = await this.getAllDatabaseFiles();
-        const allDatabaseMap = new Map(allDatabaseFiles.map((e) => [stripAllPrefixes(this.getPath(e)), e]));
-        const currentDatabaseFiles = targetFiles
-            ? allDatabaseFiles.filter((e) => targetFiles.some((f) => f == stripAllPrefixes(this.getPath(e))))
-            : allDatabaseFiles;
-
-        const allFileNames = new Set([
-            ...currentStorageFiles,
-            ...currentDatabaseFiles.map((e) => stripAllPrefixes(this.getPath(e))),
-        ]);
-        const storageToDatabase = [] as FilePath[];
-        const databaseToStorage = [] as MetaEntry[];
-
-        const eachProgress = onlyInNTimes(100, (progress) => p.log(`Checking ${progress}/${allFileNames.size}`));
-        for (const file of allFileNames) {
-            eachProgress();
-            const storageMTime = await this.storageAccess.statHidden(file);
-            const mtimeStorage = getHiddenFileSyncComparisonMTime(storageMTime);
-            const dbEntry = allDatabaseMap.get(file)!;
-            const mtimeDB = getHiddenFileSyncComparisonMTime(dbEntry);
-            const diff = compareMTime(mtimeStorage, mtimeDB);
-            if (diff == BASE_IS_NEW) {
-                storageToDatabase.push(file);
-            } else if (diff == TARGET_IS_NEW) {
-                databaseToStorage.push(dbEntry);
-            } else if (diff == EVEN) {
-                // For safety, storage to database.
-                storageToDatabase.push(file);
-            }
-        }
-        p.once(
-            `Storage to Database: ${storageToDatabase.length} files\n Database to Storage: ${databaseToStorage.length} files`
-        );
-        this.processedState.resetLastProcessedDatabase(targetFiles);
-        this.processedState.resetLastProcessedFile(targetFiles);
-        const processes = [
-            this.trackScannedStorageChanges(storageToDatabase, showNotice, false, true),
-            this.useDatabaseFiles(databaseToStorage, showNotice, false),
-        ];
-        p.log("Start processing...");
-        await Promise.all(processes);
-        p.done();
-        return [...allFileNames];
     }
 
-    private async runRebuildMerging(showNotice: boolean, targetFiles: FilePath[] | false = false) {
+    async scanAllDatabaseChanges(
-        return this.rebuildMergingHook
+        showNotice: boolean = false,
-            ? await this.rebuildMergingHook(showNotice, targetFiles)
+        onlyNew = false,
-            : await this.rebuildMerging(showNotice, targetFiles);
+        forceWriteAll = false,
+        includeDeletion = true
+    ): Promise<unknown> {
+        return await this.reconciliation.scanAllDatabaseChanges(showNotice, onlyNew, forceWriteAll, includeDeletion);
     }
 
-    private async rebuildFromStorage(showNotice: boolean, targetFiles: FilePath[] | false = false, onlyNew = false) {
+    async applyOfflineChanges(showNotice: boolean): Promise<unknown> {
-        // reset processed file markers
+        return await this.reconciliation.applyOfflineChanges(showNotice);
-        const logLevel = getLogLevel(showNotice);
-        this._verbose(`Rebuilding hidden files from the storage.`);
-        this._log(`Rebuilding hidden files from the storage.`, logLevel);
-        const p = this._progress("[⚙ Rebuild by Storage ]\n", logLevel);
-        p.log("Enumerating local files...");
-        const currentFilesAll = await this.scanInternalFileNames();
-        const currentFiles = targetFiles
-            ? currentFilesAll.filter((e) => targetFiles.some((f) => f == e))
-            : currentFilesAll;
-        p.once(`Storage to Database: ${currentFiles.length} files.`);
-        p.log("Start processing...");
-        this.processedState.resetLastProcessedFile(targetFiles);
-        await this.trackScannedStorageChanges(currentFiles, showNotice, onlyNew, true);
-        p.done();
-        return currentFiles;
-    }
-
-    private async getAllDatabaseFiles() {
-        const allFiles = (
-            await this.localDatabase.allDocsRaw({ startkey: ICHeader, endkey: ICHeaderEnd, include_docs: true })
-        ).rows
-            .filter((e) => isInternalMetadata(e.id as DocumentID))
-            .map((e) => e.doc) as MetaEntry[];
-        const files = [] as MetaEntry[];
-        for (const file of allFiles) {
-            if (await this.pathAdmission.isTargetFile(stripAllPrefixes(this.getPath(file)))) {
-                files.push(file);
-            }
-        }
-        return files;
-    }
-
-    private async rebuildFromDatabase(showNotice: boolean, targetFiles: FilePath[] | false = false, onlyNew = false) {
-        const logLevel = getLogLevel(showNotice);
-        this._verbose(`Rebuilding hidden files from the local database.`);
-        const p = this._progress("[⚙ Rebuild by Database ]\n", logLevel);
-        p.log("Enumerating database files...");
-        const allFiles = await this.getAllDatabaseFiles();
-
-        // THINKING: Should we exclude conflicted or deleted files?
-        // Current implementation is to include all files, and following processes will handle for them.
-        // However, in perspective of performance and future-proofing, I feel somewhat justified in doing it here.
-
-        const currentFiles = targetFiles
-            ? allFiles.filter((e) => targetFiles.some((f) => f == stripAllPrefixes(this.getPath(e))))
-            : allFiles;
-
-        p.once(`Database to Storage: ${currentFiles.length} files.`);
-        this.processedState.resetLastProcessedDatabase(targetFiles);
-        p.log("Start processing...");
-        await this.useDatabaseFiles(currentFiles, showNotice, onlyNew);
-        p.done();
-        return currentFiles;
     }
 
     async initialiseInternalFileSync(
         direction: SyncDirection,
         showMessage: boolean,
-        // filesAll: InternalFileInfo[] | false = false,
         targetFilesSrc: string[] | false = false,
-        initialisationProgress?: HiddenFileSyncProgress
+        initialisationProgress?: ReconciliationProgress
-    ) {
+    ): Promise<void> {
-        const logLevel = showMessage ? LOG_LEVEL_NOTICE : LOG_LEVEL_INFO;
+        return await this.reconciliation.initialiseInternalFileSync(
-        const p = initialisationProgress ?? this._progress("[⚙ Initialise]\n", logLevel);
+            direction,
-        // Compatibility question: the legacy preflight was already disabled.
+            showMessage,
-        // Enabling it would change initialisation timing and could open a
+            targetFilesSrc,
-        // conflict dialogue while the feature is being configured.
+            initialisationProgress
-        // p.log("Resolving conflicts before starting...");
+        );
-        // await this.conflictResolution.resolveAll();
-        p.log("Initialising hidden files sync...");
-        // The initialisation progress owns the user-visible Notice. Its child
-        // rebuild and scan operations still write ordinary log entries, but
-        // must not each create another keep-alive Notice.
-        const showChildNotices = false;
-        // TODO: Handling ignore files cannot be performed to the hidden files.
-
-        const targetFiles = targetFilesSrc
-            ? targetFilesSrc.map((e) => stripAllPrefixes(e as FilePathWithPrefix))
-            : false;
-        if (direction == "pushForce" || direction == "push") {
-            const onlyNew = direction == "push";
-            p.log(`Started: Storage --> Database ${onlyNew ? "(Only New)" : ""}`);
-            const updatedFiles = await this.rebuildFromStorage(showChildNotices, targetFiles, onlyNew);
-            // making doubly sure, No more losing files.
-            // I did so many times during the development.
-            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
-            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
-            // And, scan other changes on the database (i.e. files which are on only other devices)
-            p.log("Checking for remaining storage and database changes...");
-            await this.scanAllStorageChanges(showChildNotices, true, false);
-            await this.scanAllDatabaseChanges(showChildNotices, true, false);
-        }
-        if (direction == "pullForce" || direction == "pull") {
-            const onlyNew = direction == "pull";
-            p.log(`Started: Database --> Storage ${onlyNew ? "(Only New)" : ""}`);
-            const updatedEntries = await this.rebuildFromDatabase(showChildNotices, targetFiles, onlyNew);
-            const updatedFiles = updatedEntries.map((e) => stripAllPrefixes(this.getPath(e)));
-            // making doubly sure, No more losing files.
-            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
-            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
-            // And, scan other changes on the database (i.e. files which are on only other devices)
-            p.log("Checking for remaining database and storage changes...");
-            await this.scanAllDatabaseChanges(showChildNotices, true, false);
-            await this.scanAllStorageChanges(showChildNotices, true, false);
-        }
-        if (direction == "safe") {
-            p.log(`Started: Database <--> Storage (by modified date)`);
-            const updatedFiles = await this.runRebuildMerging(showChildNotices, targetFiles);
-            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
-            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
-            // And, scan other changes on the database (i.e. files which are on only other devices)
-            p.log("Checking for remaining storage and database changes...");
-            await this.scanAllStorageChanges(showChildNotices, true, false);
-            await this.scanAllDatabaseChanges(showChildNotices, true, false);
-        }
-        p.done();
     }
+
     // <-- Initialization functions
 
     private suspendExtraSync(): Promise<boolean> {
@@ -1016,7 +554,7 @@ Offline Changed files: ${files.length}`;
     }
 
     private async configureHiddenFileSync(mode: OptionalSyncFeatureMode) {
-        let initialisationProgress: HiddenFileSyncProgress | undefined;
+        let initialisationProgress: ReconciliationProgress | undefined;
         let result: ConfigureHiddenFileSyncResult;
         try {
             result = await configureHiddenFileSyncMode(mode, {
@@ -1058,47 +596,5 @@ Offline Changed files: ${files.length}`;
     }
     // <-- Configuration handling
 
-    // --> Local Storage SubFunctions
-    private async scanInternalFileNames() {
-        const findRoot = this.dependencies.getRootPath();
-
-        const filenames = await collectOptionalFileSyncFiles(this.dependencies, findRoot, {
-            shouldInclude: (path) => this.pathAdmission.isTargetFile(path as FilePath),
-            onError: (path, error) => {
-                this._log(`Could not traverse(HiddenSync):${path}`, LOG_LEVEL_INFO);
-                this._log(error, LOG_LEVEL_VERBOSE);
-            },
-        });
-
-        return filenames as FilePath[];
-    }
-
-    private async scanInternalFiles(): Promise<InternalFileInfo[]> {
-        const fileNames = await this.scanInternalFileNames();
-        const files = fileNames.map(async (e) => {
-            return {
-                path: e,
-                stat: await this.storageAccess.statHidden(e),
-            };
-        });
-        const result: InternalFileInfo[] = [];
-        for (const f of files) {
-            const w = await f;
-            if (await this.dependencies.isIgnoredByIgnoreFile(w.path)) {
-                continue;
-            }
-            const mtime = w.stat?.mtime ?? 0;
-            const ctime = w.stat?.ctime ?? mtime;
-            const size = w.stat?.size ?? 0;
-            result.push({
-                ...w,
-                mtime,
-                ctime,
-                size,
-            });
-        }
-        return result;
-    }
-
     // <-- Local Storage SubFunctions
 }

src/features/HiddenFileSync/hiddenFileSyncContext.unit.spec.ts

@@ -19,6 +19,7 @@ describe("HiddenFileSyncContext lifecycle", () => {
         const periodicInternalFileScanProcessor = { disable: vi.fn() };
         const conflictResolution = { dispose: vi.fn() };
         const changeProcessor = { dispose: vi.fn() };
+        const reconciliation = { dispose: vi.fn() };
         const pathAdmission = { dispose: vi.fn() };
         const changeNotifier = { dispose: vi.fn() };
         const closeJsonConflictDialogs = vi.fn();
@@ -28,6 +29,7 @@ describe("HiddenFileSyncContext lifecycle", () => {
             periodicInternalFileScanProcessor,
             conflictResolution,
             changeProcessor,
+            reconciliation,
             pathAdmission,
             changeNotifier,
             eventCount: 4,
@@ -40,6 +42,7 @@ describe("HiddenFileSyncContext lifecycle", () => {
         expect(periodicInternalFileScanProcessor.disable).toHaveBeenCalledOnce();
         expect(conflictResolution.dispose).toHaveBeenCalledOnce();
         expect(changeProcessor.dispose).toHaveBeenCalledOnce();
+        expect(reconciliation.dispose).toHaveBeenCalledOnce();
         expect(pathAdmission.dispose).toHaveBeenCalledOnce();
         expect(changeNotifier.dispose).toHaveBeenCalledOnce();
         expect(closeJsonConflictDialogs).toHaveBeenCalledOnce();
@@ -60,35 +63,6 @@ describe("HiddenFileSyncContext lifecycle", () => {
         expect(callPrivate<() => boolean>(hiddenFileSync, "isReady")()).toBe(false);
     });
 
-    it("keeps subordinate initialisation phases below Notice level so one progress Notice owns the scan", async () => {
-        const progress = {
-            log: vi.fn(),
-            once: vi.fn(),
-            done: vi.fn(),
-        };
-        const rebuildMerging = vi.fn(async () => []);
-        const adoptCurrentStorageFilesAsProcessed = vi.fn(async () => undefined);
-        const adoptCurrentDatabaseFilesAsProcessed = vi.fn(async () => undefined);
-        const scanAllStorageChanges = vi.fn(async () => undefined);
-        const scanAllDatabaseChanges = vi.fn(async () => undefined);
-        const hiddenFileSync = Object.create(HiddenFileSyncContext.prototype) as HiddenFileSyncContext;
-        Object.assign(hiddenFileSync, {
-            _progress: vi.fn(() => progress),
-            rebuildMerging,
-            adoptCurrentStorageFilesAsProcessed,
-            adoptCurrentDatabaseFilesAsProcessed,
-            scanAllStorageChanges,
-            scanAllDatabaseChanges,
-        });
-
-        await hiddenFileSync.initialiseInternalFileSync("safe", true);
-
-        expect(rebuildMerging).toHaveBeenCalledWith(false, false);
-        expect(scanAllStorageChanges).toHaveBeenCalledWith(false, true, false);
-        expect(scanAllDatabaseChanges).toHaveBeenCalledWith(false, true, false);
-        expect(progress.done).toHaveBeenCalledOnce();
-    });
-
     it("retirement guard: does not restore separate gathering and restart Notices", async () => {
         vi.mocked(configureHiddenFileSyncMode).mockImplementation(async (_mode, handlers) => {
             await handlers.enable();

src/features/HiddenFileSync/reconciliation.ts

@@ -0,0 +1,683 @@
+import {
+    type AnyEntry,
+    type DocumentID,
+    type FilePath,
+    type FilePathWithPrefix,
+    type LoadedEntry,
+    LOG_LEVEL_INFO,
+    LOG_LEVEL_NOTICE,
+    LOG_LEVEL_VERBOSE,
+    type LOG_LEVEL,
+    type MetaEntry,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+import type { StorageAccess } from "@vrtmrz/livesync-commonlib/compat/interfaces/StorageAccess";
+import type { LiveSyncLocalDB } from "@vrtmrz/livesync-commonlib/compat/pouchdb/LiveSyncLocalDB";
+import type { LogFunction } from "@vrtmrz/livesync-commonlib/compat/services/lib/logUtils";
+import { tryGetFilePath } from "@vrtmrz/livesync-commonlib/compat/common/utils.doc";
+import { stripAllPrefixes } from "@vrtmrz/livesync-commonlib/compat/string_and_binary/path";
+import { Semaphore } from "octagonal-wheels/concurrency/semaphore";
+import { serialized, skipIfDuplicated } from "octagonal-wheels/concurrency/lock";
+
+import { type InternalFileInfo, ICHeader, ICHeaderEnd } from "@/common/types.ts";
+import {
+    BASE_IS_NEW,
+    compareMTime,
+    EVEN,
+    getLogLevel,
+    isInternalMetadata,
+    onlyInNTimes,
+    TARGET_IS_NEW,
+} from "@/common/utils.ts";
+import {
+    collectOptionalFileSyncFiles,
+    type OptionalFileSyncFileTreeDependencies,
+} from "@/features/optionalFileSyncFileTree.ts";
+import type { HiddenFileSyncChangeProcessor } from "./hiddenFileSyncChangeProcessor.ts";
+import type { HiddenFileSyncProcessedState } from "./hiddenFileSyncProcessedState.ts";
+import { describeHiddenFileSyncDocument, getHiddenFileSyncComparisonMTime } from "./hiddenFileSyncState.ts";
+import type {
+    HiddenFileSyncInitialisationDirection as InitialisationDirection,
+    HiddenFileSyncTestingRebuild,
+    HiddenFileSyncTestingRebuildInterceptor,
+} from "./hiddenFileSyncViews.ts";
+
+export type { HiddenFileSyncInitialisationDirection as InitialisationDirection } from "./hiddenFileSyncViews.ts";
+
+export type ReconciliationProgress = {
+    log(message: string): void;
+    once(message: string): void;
+    done(message?: string): void;
+};
+
+type ReconciliationDatabase = Pick<LiveSyncLocalDB, "allDocsRaw">;
+type ReconciliationStorage = Pick<StorageAccess, "statHidden">;
+
+type ReconciliationProcessedState = Pick<
+    HiddenFileSyncProcessedState,
+    | "databaseStateKey"
+    | "getLastProcessedDatabaseKey"
+    | "getLastProcessedFileKey"
+    | "getLastProcessedFileMTime"
+    | "hasLastProcessedDatabase"
+    | "hasLastProcessedFile"
+    | "getLastProcessedFileKeys"
+    | "resetLastProcessedDatabase"
+    | "resetLastProcessedFile"
+    | "storageStateKey"
+    | "updateLastProcessed"
+    | "updateLastProcessedAsActualDatabase"
+    | "updateLastProcessedAsActualFile"
+>;
+
+type ReconciliationChangeProcessor = Pick<
+    HiddenFileSyncChangeProcessor,
+    "processStorageChange" | "processDatabaseChange"
+>;
+
+export type ReconciliationDependencies = OptionalFileSyncFileTreeDependencies & {
+    getLocalDatabase(): ReconciliationDatabase;
+    storageAccess: ReconciliationStorage;
+    getRootPath(): string;
+    getPath(entry: AnyEntry): FilePathWithPrefix;
+    isTargetFile(path: FilePath): Promise<boolean>;
+    isIgnoredByIgnoreFile(path: string): Promise<boolean>;
+    createProgress(prefix?: string, level?: LOG_LEVEL): ReconciliationProgress;
+    processedState: ReconciliationProcessedState;
+    changeProcessor: ReconciliationChangeProcessor;
+    log: LogFunction;
+};
+
+export type Reconciliation = {
+    processStorageChange(
+        path: FilePath,
+        onlyNew?: boolean,
+        forceWrite?: boolean,
+        includeDeleted?: boolean
+    ): Promise<boolean | undefined>;
+    processDatabaseDocument(doc: LoadedEntry): Promise<boolean>;
+    scanInternalFiles(): Promise<InternalFileInfo[]>;
+    scanAllStorageChanges(
+        showNotice?: boolean,
+        onlyNew?: boolean,
+        forceWriteAll?: boolean,
+        includeDeleted?: boolean
+    ): Promise<unknown>;
+    scanAllDatabaseChanges(
+        showNotice?: boolean,
+        onlyNew?: boolean,
+        forceWriteAll?: boolean,
+        includeDeletion?: boolean
+    ): Promise<unknown>;
+    applyOfflineChanges(showNotice: boolean): Promise<unknown>;
+    initialiseInternalFileSync(
+        direction: InitialisationDirection,
+        showMessage: boolean,
+        targetFilesSrc?: string[] | false,
+        initialisationProgress?: ReconciliationProgress
+    ): Promise<void>;
+    interceptRebuildMerging(interceptor: HiddenFileSyncTestingRebuildInterceptor): () => void;
+    dispose(): void;
+};
+
+class ReconciliationOwner implements Reconciliation {
+    private rebuildMergingHook: HiddenFileSyncTestingRebuild | undefined;
+
+    constructor(private readonly dependencies: ReconciliationDependencies) {}
+
+    private get localDatabase() {
+        return this.dependencies.getLocalDatabase();
+    }
+
+    private get storageAccess() {
+        return this.dependencies.storageAccess;
+    }
+
+    private getPath(entry: AnyEntry): FilePathWithPrefix {
+        return this.dependencies.getPath(entry);
+    }
+
+    private _log(message: unknown, level?: LOG_LEVEL, key?: string): void {
+        this.dependencies.log(message, level, key);
+    }
+
+    private _verbose(message: unknown, key?: string): void {
+        this._log(message, LOG_LEVEL_VERBOSE, key);
+    }
+
+    private _progress(prefix: string = "", level: LOG_LEVEL = LOG_LEVEL_NOTICE): ReconciliationProgress {
+        return this.dependencies.createProgress(prefix, level);
+    }
+
+    async processStorageChange(
+        path: FilePath,
+        onlyNew = false,
+        forceWrite = false,
+        includeDeleted = true
+    ): Promise<boolean | undefined> {
+        if (!(await this.dependencies.isTargetFile(path))) {
+            this._log(
+                `Storage file tracking: Hidden file skipped: ${path} is filtered out by the defined patterns.`,
+                LOG_LEVEL_VERBOSE
+            );
+            return false;
+        }
+        return await this.dependencies.changeProcessor.processStorageChange(path, onlyNew, forceWrite, includeDeleted);
+    }
+
+    async processDatabaseDocument(doc: LoadedEntry): Promise<boolean> {
+        const info = describeHiddenFileSyncDocument(doc, this.getPath(doc));
+        const path = info.path;
+        const headerLine = `Tracking DB ${info.path} (${info.revDisplay}) :`;
+        const ret = await this.trackDatabaseFileModification(path, headerLine);
+        this._log(`${headerLine} Done: ${info.shortenedId})`, LOG_LEVEL_VERBOSE);
+        return ret;
+    }
+
+    private async scanInternalFileNames(): Promise<FilePath[]> {
+        const findRoot = this.dependencies.getRootPath();
+
+        const filenames = await collectOptionalFileSyncFiles(this.dependencies, findRoot, {
+            shouldInclude: (path) => this.dependencies.isTargetFile(path as FilePath),
+            onError: (path, error) => {
+                this._log(`Could not traverse(HiddenSync):${path}`, LOG_LEVEL_INFO);
+                this._log(error, LOG_LEVEL_VERBOSE);
+            },
+        });
+
+        return filenames as FilePath[];
+    }
+
+    async scanInternalFiles(): Promise<InternalFileInfo[]> {
+        const fileNames = await this.scanInternalFileNames();
+        const files = fileNames.map(async (e) => {
+            return {
+                path: e,
+                stat: await this.storageAccess.statHidden(e),
+            };
+        });
+        const result: InternalFileInfo[] = [];
+        for (const f of files) {
+            const w = await f;
+            if (await this.dependencies.isIgnoredByIgnoreFile(w.path)) {
+                continue;
+            }
+            const mtime = w.stat?.mtime ?? 0;
+            const ctime = w.stat?.ctime ?? mtime;
+            const size = w.stat?.size ?? 0;
+            result.push({
+                ...w,
+                mtime,
+                ctime,
+                size,
+            });
+        }
+        return result;
+    }
+
+    private async adoptCurrentStorageFilesAsProcessed(targetFiles: FilePath[] | false): Promise<void> {
+        const allFiles = await this.scanInternalFileNames();
+        const files = targetFiles ? allFiles.filter((e) => targetFiles.some((t) => e.indexOf(t) !== -1)) : allFiles;
+        for (const file of files) {
+            await this.dependencies.processedState.updateLastProcessedAsActualFile(file);
+        }
+    }
+
+    private async adoptCurrentDatabaseFilesAsProcessed(targetFiles: FilePath[] | false): Promise<void> {
+        const allFiles = await this.getAllDatabaseFiles();
+        const files = targetFiles
+            ? allFiles.filter((e) => targetFiles.some((t) => e.path.indexOf(t) !== -1))
+            : allFiles;
+        for (const file of files) {
+            const path = stripAllPrefixes(this.getPath(file));
+            await this.dependencies.processedState.updateLastProcessedAsActualDatabase(path, file);
+        }
+    }
+
+    private async trackScannedStorageChanges(
+        processFiles: FilePath[],
+        showNotice: boolean = false,
+        onlyNew = false,
+        forceWriteAll = false,
+        includeDeleted = true
+    ): Promise<void> {
+        const logLevel = getLogLevel(showNotice);
+        const p = this._progress(`[⚙ Storage -> DB ]\n`, logLevel);
+        const notifyProgress = onlyInNTimes(100, (progress) => p.log(`${progress}/${processFiles.length}`));
+        const processes = processFiles.map(async (file, i) => {
+            try {
+                await this.processStorageChange(file, onlyNew, forceWriteAll, includeDeleted);
+                notifyProgress();
+            } catch (ex) {
+                p.once(`Failed to process storage change file:${file}`);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+            }
+        });
+        await Promise.all(processes);
+        p.done();
+    }
+
+    async scanAllStorageChanges(
+        showNotice: boolean = false,
+        onlyNew = false,
+        forceWriteAll = false,
+        includeDeleted = true
+    ): Promise<unknown> {
+        return await skipIfDuplicated("scanAllStorageChanges", async () => {
+            const logLevel = getLogLevel(showNotice);
+            const p = this._progress(`[⚙ Scanning Storage -> DB ]\n`, logLevel);
+            p.log(`Scanning storage files...`);
+            const knownNames = [...this.dependencies.processedState.getLastProcessedFileKeys()] as FilePath[];
+            const existNames = await this.scanInternalFileNames();
+            const files = new Set([...knownNames, ...existNames]);
+
+            this._log(
+                `Known/Exist ${knownNames.length}/${existNames.length}, Totally ${files.size} files.`,
+                LOG_LEVEL_VERBOSE
+            );
+            const taskNameAndMeta = [...files].map(async (e) => [e, await this.storageAccess.statHidden(e)] as const);
+            const nameAndMeta = await Promise.all(taskNameAndMeta);
+            const processFiles = nameAndMeta
+                .filter(([path, stat]) => {
+                    if (forceWriteAll) return true;
+                    const key = this.dependencies.processedState.getLastProcessedFileKey(path);
+                    const newKey = this.dependencies.processedState.storageStateKey(stat);
+                    return key != newKey;
+                })
+                .map(([path, stat]) => path);
+
+            const staticsMessage = `[Storage hidden file statics]
+Known files: ${knownNames.length}
+Actual files: ${existNames.length}
+All files: ${files.size}
+Offline Changed files: ${processFiles.length}`;
+            // this._log(staticsMessage, logLevel, "scan-changes");
+            p.once(staticsMessage);
+            await this.trackScannedStorageChanges(processFiles, showNotice, onlyNew, forceWriteAll, includeDeleted);
+            p.done();
+        });
+    }
+
+    private async trackScannedDatabaseChange(
+        processFiles: MetaEntry[],
+        showNotice: boolean = false,
+        onlyNew = false,
+        forceWriteAll = false,
+        includeDeletion = true
+    ): Promise<void> {
+        const logLevel = getLogLevel(showNotice);
+        const p = this._progress(`[⚙ DB -> Storage ]\n`, logLevel);
+        const notifyProgress = onlyInNTimes(100, (progress) => p.log(`${progress}/${processFiles.length}`));
+        const processes = processFiles.map(async (file) => {
+            try {
+                const path = stripAllPrefixes(this.getPath(file));
+                if (!(await this.dependencies.isTargetFile(path))) {
+                    this._log(
+                        `Database file tracking: Hidden file skipped: ${path} is filtered out by the defined patterns.`,
+                        LOG_LEVEL_VERBOSE
+                    );
+                } else {
+                    await this.trackDatabaseFileModification(
+                        path,
+                        "[Hidden file scan]",
+                        !forceWriteAll,
+                        onlyNew,
+                        file,
+                        includeDeletion
+                    );
+                }
+                notifyProgress();
+            } catch (ex) {
+                this._log(`Failed to process storage change file:${tryGetFilePath(file)}`, logLevel);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+            }
+        });
+        await Promise.all(processes);
+        p.done();
+    }
+
+    async applyOfflineChanges(showNotice: boolean): Promise<unknown> {
+        const logLevel = getLogLevel(showNotice);
+        return await serialized("applyOfflineChanges", async () => {
+            const p = this._progress("[⚙ Apply untracked changes ]\n", logLevel);
+            this._log(`Track changes.`, logLevel);
+            p.log("Enumerating local files...");
+            const currentStorageFiles = await this.scanInternalFileNames();
+            p.log("Enumerating database files...");
+            const currentDatabaseFiles = await this.getAllDatabaseFiles();
+            const allDatabaseMap = Object.fromEntries(
+                currentDatabaseFiles.map((e) => [stripAllPrefixes(this.getPath(e)), e])
+            );
+            const currentDatabaseFileNames = [...Object.keys(allDatabaseMap)] as FilePath[];
+            const untrackedLocal = currentStorageFiles.filter(
+                (e) => !this.dependencies.processedState.hasLastProcessedFile(e)
+            );
+            const untrackedDatabase = currentDatabaseFileNames.filter(
+                (e) => !this.dependencies.processedState.hasLastProcessedDatabase(e)
+            );
+            const bothUntracked = untrackedLocal.filter((e) => untrackedDatabase.indexOf(e) !== -1);
+            p.log("Applying untracked changes...");
+            const stat = `Tracking statics:
+Local files: ${currentStorageFiles.length}
+Database files: ${currentDatabaseFileNames.length}
+Untracked local files: ${untrackedLocal.length}
+Untracked database files: ${untrackedDatabase.length}
+Common untracked files: ${bothUntracked.length}`;
+            p.once(stat);
+            const semaphores = Semaphore(10);
+            const notifyProgress = onlyInNTimes(25, (progress) => p.log(`${progress}/${bothUntracked.length}`));
+            const allProcesses = bothUntracked.map(async (file) => {
+                notifyProgress();
+                const rel = await semaphores.acquire();
+                try {
+                    const fileStat = await this.storageAccess.statHidden(file);
+                    if (fileStat == null) {
+                        // This should not be happened. But, if it happens, we should skip this.
+                        this._log(`Unexpected error: Failed to stat file during applyOfflineChange :${file}`);
+                        return;
+                    }
+                    const dbInfo = allDatabaseMap[file];
+                    if (dbInfo.deleted || dbInfo._deleted) {
+                        // Applying deletion can be harmful if the local file is not tracked.
+                        // So, we should skip this.
+                        return;
+                    }
+                    const fileMTime = getHiddenFileSyncComparisonMTime(fileStat);
+                    const dbMTime = getHiddenFileSyncComparisonMTime(dbInfo);
+                    const diff = compareMTime(fileMTime, dbMTime);
+                    if (diff == BASE_IS_NEW) {
+                        // Local file is newer than the database file.
+                        // So, we should apply the local file to the database.
+                        await this.processStorageChange(file, true);
+                    } else if (diff == TARGET_IS_NEW) {
+                        // Database file is newer than the local file.
+                        // So, we should apply the database file to the local file.
+                        await this.trackDatabaseFileModification(file, "[Apply]", true, true, dbInfo);
+                    } else if (diff == EVEN) {
+                        // Both are same, we may skip this but should update the last processed key.
+                        this.dependencies.processedState.updateLastProcessed(file, dbInfo, fileStat);
+                    }
+                } finally {
+                    rel();
+                }
+            });
+            await Promise.all(allProcesses);
+            await this.scanAllStorageChanges(showNotice);
+            await this.scanAllDatabaseChanges(showNotice);
+
+            p.done();
+        });
+    }
+
+    async scanAllDatabaseChanges(
+        showNotice: boolean = false,
+        onlyNew = false,
+        forceWriteAll = false,
+        includeDeletion = true
+    ): Promise<unknown> {
+        return await skipIfDuplicated("scanAllDatabaseChanges", async () => {
+            const databaseFiles = await this.getAllDatabaseFiles();
+            const files = databaseFiles.filter((e) => {
+                const doc = e;
+                const key = this.dependencies.processedState.databaseStateKey(doc);
+                const path = stripAllPrefixes(this.getPath(doc));
+                const lastKey = this.dependencies.processedState.getLastProcessedDatabaseKey(path);
+                return lastKey != key;
+            });
+            const logLevel = getLogLevel(showNotice);
+            const staticsMessage = `[Database hidden file statics]
+All files: ${databaseFiles.length}
+Offline Changed files: ${files.length}`;
+            this._log(staticsMessage, logLevel, "scan-changes");
+            return await this.trackScannedDatabaseChange(files, showNotice, onlyNew, forceWriteAll, includeDeletion);
+        });
+    }
+
+    private async useDatabaseFiles(files: MetaEntry[], showNotice = false, onlyNew = false): Promise<boolean> {
+        const logLevel = getLogLevel(showNotice);
+        const p = this._progress(`[⚙ Scanning DB -> Storage ]\n`, logLevel);
+        p.log("Scanning database files...");
+        const notifyProgress = onlyInNTimes(25, (progress) => p.log(`${progress}/${files.length}`));
+        const processFiles = files.map(async (file) => {
+            try {
+                const path = stripAllPrefixes(this.getPath(file));
+                await this.trackDatabaseFileModification(path, "[Scanning]", true, onlyNew, file);
+                notifyProgress();
+            } catch (ex) {
+                this._log(`Failed to process database changes:${tryGetFilePath(file)}`);
+                this._log(ex, LOG_LEVEL_VERBOSE);
+            }
+            return;
+        });
+        await Promise.all(processFiles);
+        p.done();
+        return true;
+    }
+
+    private async trackDatabaseFileModification(
+        path: FilePath,
+        headerLine: string,
+        preventDoubleProcess = false,
+        onlyNew = false,
+        meta: MetaEntry | false = false,
+        includeDeletion = true
+    ): Promise<boolean> {
+        return await this.dependencies.changeProcessor.processDatabaseChange(path, headerLine, {
+            preventDoubleProcess,
+            onlyNew,
+            metaEntry: meta,
+            includeDeletion,
+        });
+    }
+
+    private async rebuildMerging(showNotice: boolean, targetFiles: FilePath[] | false = false): Promise<FilePath[]> {
+        const logLevel = getLogLevel(showNotice);
+        const p = this._progress("[⚙ Rebuild by Merge ]\n", logLevel);
+        this._log(`Rebuilding hidden files from the storage and the local database.`, logLevel);
+        p.log("Enumerating local files...");
+        const currentStorageFilesAll = await this.scanInternalFileNames();
+        const currentStorageFiles = targetFiles
+            ? currentStorageFilesAll.filter((e) => targetFiles.some((f) => f == e))
+            : currentStorageFilesAll;
+        p.log("Enumerating database files...");
+        const allDatabaseFiles = await this.getAllDatabaseFiles();
+        const allDatabaseMap = new Map(allDatabaseFiles.map((e) => [stripAllPrefixes(this.getPath(e)), e]));
+        const currentDatabaseFiles = targetFiles
+            ? allDatabaseFiles.filter((e) => targetFiles.some((f) => f == stripAllPrefixes(this.getPath(e))))
+            : allDatabaseFiles;
+
+        const allFileNames = new Set([
+            ...currentStorageFiles,
+            ...currentDatabaseFiles.map((e) => stripAllPrefixes(this.getPath(e))),
+        ]);
+        const storageToDatabase = [] as FilePath[];
+        const databaseToStorage = [] as MetaEntry[];
+
+        const eachProgress = onlyInNTimes(100, (progress) => p.log(`Checking ${progress}/${allFileNames.size}`));
+        for (const file of allFileNames) {
+            eachProgress();
+            const storageMTime = await this.storageAccess.statHidden(file);
+            const mtimeStorage = getHiddenFileSyncComparisonMTime(storageMTime);
+            const dbEntry = allDatabaseMap.get(file)!;
+            const mtimeDB = getHiddenFileSyncComparisonMTime(dbEntry);
+            const diff = compareMTime(mtimeStorage, mtimeDB);
+            if (diff == BASE_IS_NEW) {
+                storageToDatabase.push(file);
+            } else if (diff == TARGET_IS_NEW) {
+                databaseToStorage.push(dbEntry);
+            } else if (diff == EVEN) {
+                // For safety, storage to database.
+                storageToDatabase.push(file);
+            }
+        }
+        p.once(
+            `Storage to Database: ${storageToDatabase.length} files\n Database to Storage: ${databaseToStorage.length} files`
+        );
+        this.dependencies.processedState.resetLastProcessedDatabase(targetFiles);
+        this.dependencies.processedState.resetLastProcessedFile(targetFiles);
+        const processes = [
+            this.trackScannedStorageChanges(storageToDatabase, showNotice, false, true),
+            this.useDatabaseFiles(databaseToStorage, showNotice, false),
+        ];
+        p.log("Start processing...");
+        await Promise.all(processes);
+        p.done();
+        return [...allFileNames];
+    }
+
+    private async runRebuildMerging(showNotice: boolean, targetFiles: FilePath[] | false = false): Promise<FilePath[]> {
+        return this.rebuildMergingHook
+            ? await this.rebuildMergingHook(showNotice, targetFiles)
+            : await this.rebuildMerging(showNotice, targetFiles);
+    }
+
+    private async rebuildFromStorage(
+        showNotice: boolean,
+        targetFiles: FilePath[] | false = false,
+        onlyNew = false
+    ): Promise<FilePath[]> {
+        // reset processed file markers
+        const logLevel = getLogLevel(showNotice);
+        this._verbose(`Rebuilding hidden files from the storage.`);
+        this._log(`Rebuilding hidden files from the storage.`, logLevel);
+        const p = this._progress("[⚙ Rebuild by Storage ]\n", logLevel);
+        p.log("Enumerating local files...");
+        const currentFilesAll = await this.scanInternalFileNames();
+        const currentFiles = targetFiles
+            ? currentFilesAll.filter((e) => targetFiles.some((f) => f == e))
+            : currentFilesAll;
+        p.once(`Storage to Database: ${currentFiles.length} files.`);
+        p.log("Start processing...");
+        this.dependencies.processedState.resetLastProcessedFile(targetFiles);
+        await this.trackScannedStorageChanges(currentFiles, showNotice, onlyNew, true);
+        p.done();
+        return currentFiles;
+    }
+
+    private async getAllDatabaseFiles(): Promise<MetaEntry[]> {
+        const allFiles = (
+            await this.localDatabase.allDocsRaw({ startkey: ICHeader, endkey: ICHeaderEnd, include_docs: true })
+        ).rows
+            .filter((e) => isInternalMetadata(e.id as DocumentID))
+            .map((e) => e.doc) as MetaEntry[];
+        const files = [] as MetaEntry[];
+        for (const file of allFiles) {
+            if (await this.dependencies.isTargetFile(stripAllPrefixes(this.getPath(file)))) {
+                files.push(file);
+            }
+        }
+        return files;
+    }
+
+    private async rebuildFromDatabase(
+        showNotice: boolean,
+        targetFiles: FilePath[] | false = false,
+        onlyNew = false
+    ): Promise<MetaEntry[]> {
+        const logLevel = getLogLevel(showNotice);
+        this._verbose(`Rebuilding hidden files from the local database.`);
+        this._log(`Rebuilding hidden files from the local database.`, logLevel);
+        const p = this._progress("[⚙ Rebuild by Database ]\n", logLevel);
+        p.log("Enumerating database files...");
+        const allFiles = await this.getAllDatabaseFiles();
+
+        // THINKING: Should we exclude conflicted or deleted files?
+        // Current implementation is to include all files, and following processes will handle for them.
+        // However, in perspective of performance and future-proofing, I feel somewhat justified in doing it here.
+
+        const currentFiles = targetFiles
+            ? allFiles.filter((e) => targetFiles.some((f) => f == stripAllPrefixes(this.getPath(e))))
+            : allFiles;
+
+        p.once(`Database to Storage: ${currentFiles.length} files.`);
+        this.dependencies.processedState.resetLastProcessedDatabase(targetFiles);
+        p.log("Start processing...");
+        await this.useDatabaseFiles(currentFiles, showNotice, onlyNew);
+        p.done();
+        return currentFiles;
+    }
+
+    async initialiseInternalFileSync(
+        direction: InitialisationDirection,
+        showMessage: boolean,
+        // filesAll: InternalFileInfo[] | false = false,
+        targetFilesSrc: string[] | false = false,
+        initialisationProgress?: ReconciliationProgress
+    ): Promise<void> {
+        const logLevel = showMessage ? LOG_LEVEL_NOTICE : LOG_LEVEL_INFO;
+        const p = initialisationProgress ?? this._progress("[⚙ Initialise]\n", logLevel);
+        // Compatibility question: the legacy preflight was already disabled.
+        // Enabling it would change initialisation timing and could open a
+        // conflict dialogue while the feature is being configured.
+        // p.log("Resolving conflicts before starting...");
+        // await this.conflictResolution.resolveAll();
+        p.log("Initialising hidden files sync...");
+        // The initialisation progress owns the user-visible Notice. Its child
+        // rebuild and scan operations still write ordinary log entries, but
+        // must not each create another keep-alive Notice.
+        const showChildNotices = false;
+        // TODO: Handling ignore files cannot be performed to the hidden files.
+
+        const targetFiles = targetFilesSrc
+            ? targetFilesSrc.map((e) => stripAllPrefixes(e as FilePathWithPrefix))
+            : false;
+        if (direction == "pushForce" || direction == "push") {
+            const onlyNew = direction == "push";
+            p.log(`Started: Storage --> Database ${onlyNew ? "(Only New)" : ""}`);
+            const updatedFiles = await this.rebuildFromStorage(showChildNotices, targetFiles, onlyNew);
+            // making doubly sure, No more losing files.
+            // I did so many times during the development.
+            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
+            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
+            // And, scan other changes on the database (i.e. files which are on only other devices)
+            p.log("Checking for remaining storage and database changes...");
+            await this.scanAllStorageChanges(showChildNotices, true, false);
+            await this.scanAllDatabaseChanges(showChildNotices, true, false);
+        }
+        if (direction == "pullForce" || direction == "pull") {
+            const onlyNew = direction == "pull";
+            p.log(`Started: Database --> Storage ${onlyNew ? "(Only New)" : ""}`);
+            const updatedEntries = await this.rebuildFromDatabase(showChildNotices, targetFiles, onlyNew);
+            const updatedFiles = updatedEntries.map((e) => stripAllPrefixes(this.getPath(e)));
+            // making doubly sure, No more losing files.
+            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
+            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
+            // And, scan other changes on the database (i.e. files which are on only other devices)
+            p.log("Checking for remaining database and storage changes...");
+            await this.scanAllDatabaseChanges(showChildNotices, true, false);
+            await this.scanAllStorageChanges(showChildNotices, true, false);
+        }
+        if (direction == "safe") {
+            p.log(`Started: Database <--> Storage (by modified date)`);
+            const updatedFiles = await this.runRebuildMerging(showChildNotices, targetFiles);
+            await this.adoptCurrentStorageFilesAsProcessed(updatedFiles);
+            await this.adoptCurrentDatabaseFilesAsProcessed(updatedFiles);
+            // And, scan other changes on the database (i.e. files which are on only other devices)
+            p.log("Checking for remaining storage and database changes...");
+            await this.scanAllStorageChanges(showChildNotices, true, false);
+            await this.scanAllDatabaseChanges(showChildNotices, true, false);
+        }
+        p.done();
+    }
+
+    interceptRebuildMerging(interceptor: HiddenFileSyncTestingRebuildInterceptor): () => void {
+        const previousHook = this.rebuildMergingHook;
+        const runRebuild = async (showNotice: boolean, targetFiles?: FilePath[] | false) =>
+            await this.rebuildMerging(showNotice, targetFiles);
+        const hook: HiddenFileSyncTestingRebuild = async (showNotice, targetFiles) =>
+            await interceptor(runRebuild, showNotice, targetFiles);
+        this.rebuildMergingHook = hook;
+        return () => {
+            if (this.rebuildMergingHook === hook) {
+                this.rebuildMergingHook = previousHook;
+            }
+        };
+    }
+
+    dispose(): void {
+        this.rebuildMergingHook = undefined;
+    }
+}
+
+export function createReconciliation(dependencies: ReconciliationDependencies): Reconciliation {
+    return new ReconciliationOwner(dependencies);
+}

src/features/HiddenFileSync/reconciliation.unit.spec.ts

@@ -0,0 +1,168 @@
+import { describe, expect, it, vi } from "vitest";
+import {
+    LOG_LEVEL_INFO,
+    LOG_LEVEL_NOTICE,
+    type FilePath,
+    type MetaEntry,
+    type UXStat,
+} from "@vrtmrz/livesync-commonlib/compat/common/types";
+
+vi.mock("@/deps.ts", () => ({}));
+
+import {
+    createReconciliation,
+    type ReconciliationProgress,
+    type ReconciliationDependencies,
+} from "./reconciliation.ts";
+
+const targetPath = ".obsidian/app.json" as FilePath;
+const filteredPath = ".obsidian/plugins/other/data.json" as FilePath;
+
+function createFixture(options: { files?: FilePath[]; databaseFiles?: MetaEntry[] } = {}) {
+    const files = options.files ?? [targetPath];
+    const databaseFiles = options.databaseFiles ?? [];
+    const processedFiles = new Map<string, string>();
+    const progress = {
+        log: vi.fn(),
+        once: vi.fn(),
+        done: vi.fn(),
+    } satisfies ReconciliationProgress;
+    const createProgress = vi.fn((_prefix = "", _level = LOG_LEVEL_NOTICE) => progress);
+    const statHidden = vi.fn(
+        async (path: FilePath): Promise<UXStat | null> => ({
+            ctime: 10,
+            mtime: path == targetPath ? 20 : 30,
+            size: 10,
+            type: "file",
+        })
+    );
+    const isTargetFile = vi.fn(async (path: FilePath) => path == targetPath);
+    const allDocsRaw = vi.fn(async () => ({
+        rows: databaseFiles.map((doc) => ({ id: doc._id, doc })),
+    }));
+    const processedState = {
+        databaseStateKey: vi.fn((entry: MetaEntry) => `${entry._rev}`),
+        getLastProcessedDatabaseKey: vi.fn(() => undefined as string | undefined),
+        getLastProcessedFileKey: vi.fn(() => undefined as string | undefined),
+        getLastProcessedFileMTime: vi.fn(() => 0),
+        hasLastProcessedDatabase: vi.fn(() => false),
+        hasLastProcessedFile: vi.fn(() => false),
+        getLastProcessedFileKeys: vi.fn(() => processedFiles.keys()),
+        resetLastProcessedDatabase: vi.fn(),
+        resetLastProcessedFile: vi.fn(),
+        storageStateKey: vi.fn((stat: UXStat | null) => `${stat?.mtime ?? 0}`),
+        updateLastProcessed: vi.fn(),
+        updateLastProcessedAsActualDatabase: vi.fn(async () => undefined),
+        updateLastProcessedAsActualFile: vi.fn(async () => undefined),
+    };
+    const changeProcessor = {
+        processStorageChange: vi.fn(async () => true),
+        processDatabaseChange: vi.fn(async () => true),
+    };
+    const dependencies = {
+        listFiles: vi.fn(async () => ({ files, folders: [] })),
+        getLocalDatabase: () => ({ allDocsRaw }),
+        storageAccess: { statHidden },
+        getRootPath: () => "root",
+        getPath: (entry: MetaEntry) => entry.path,
+        isTargetFile,
+        isIgnoredByIgnoreFile: vi.fn(async () => false),
+        createProgress,
+        processedState,
+        changeProcessor,
+        log: vi.fn(),
+    } as unknown as ReconciliationDependencies;
+    return {
+        dependencies,
+        progress,
+        createProgress,
+        isTargetFile,
+        statHidden,
+        processedState,
+        changeProcessor,
+    };
+}
+
+function metadata(path: FilePath = targetPath): MetaEntry {
+    return {
+        _id: `i:${path}`,
+        _rev: "2-current",
+        path: `i:${path}`,
+        type: "plain",
+        datatype: "plain",
+        ctime: 10,
+        mtime: 20,
+        size: 10,
+        children: [],
+        eden: {},
+        deleted: false,
+    } as unknown as MetaEntry;
+}
+
+describe("Reconciliation", () => {
+    it("keeps push initialisation direction and follow-up scan order", async () => {
+        const fixture = createFixture();
+        const reconciliation = createReconciliation(fixture.dependencies);
+        const order: string[] = [];
+        const scanStorageChanges = vi.spyOn(reconciliation, "scanAllStorageChanges").mockImplementation(async () => {
+            order.push("storage-scan");
+        });
+        const scanDatabaseChanges = vi.spyOn(reconciliation, "scanAllDatabaseChanges").mockImplementation(async () => {
+            order.push("database-scan");
+        });
+
+        await reconciliation.initialiseInternalFileSync("push", true);
+
+        expect(fixture.changeProcessor.processStorageChange).toHaveBeenCalledWith(targetPath, true, true, true);
+        expect(order).toEqual(["storage-scan", "database-scan"]);
+        expect(scanStorageChanges).toHaveBeenCalledWith(false, true, false);
+        expect(scanDatabaseChanges).toHaveBeenCalledWith(false, true, false);
+        expect(fixture.createProgress).toHaveBeenCalledWith("[⚙ Initialise]\n", LOG_LEVEL_NOTICE);
+        expect(fixture.createProgress).toHaveBeenCalledWith("[⚙ Rebuild by Storage ]\n", LOG_LEVEL_INFO);
+        expect(fixture.progress.done).toHaveBeenCalledTimes(3);
+    });
+
+    it("restores rebuild interception in stack order without clobbering a newer hook", async () => {
+        const fixture = createFixture({ files: [] });
+        const reconciliation = createReconciliation(fixture.dependencies);
+        const events: string[] = [];
+        const first = vi.fn(async (run, showNotice, targetFiles) => {
+            events.push("first:start");
+            const result = await run(showNotice, targetFiles);
+            events.push("first:end");
+            return result;
+        });
+        const second = vi.fn(async (run, showNotice, targetFiles) => {
+            events.push("second:start");
+            const result = await run(showNotice, targetFiles);
+            events.push("second:end");
+            return result;
+        });
+        const restoreFirst = reconciliation.interceptRebuildMerging(first);
+        const restoreSecond = reconciliation.interceptRebuildMerging(second);
+
+        restoreFirst();
+        await reconciliation.initialiseInternalFileSync("safe", false);
+        expect(second).toHaveBeenCalledOnce();
+
+        restoreSecond();
+        await reconciliation.initialiseInternalFileSync("safe", false);
+        expect(first).toHaveBeenCalledOnce();
+        expect(events[0]).toBe("second:start");
+        expect(events[events.length - 1]).toBe("first:end");
+    });
+
+    it("uses admission and processed-state keys when selecting storage scan work", async () => {
+        const fixture = createFixture({ files: [targetPath, filteredPath] });
+        const reconciliation = createReconciliation(fixture.dependencies);
+
+        await reconciliation.scanAllStorageChanges(false);
+
+        expect(fixture.isTargetFile).toHaveBeenCalledWith(targetPath);
+        expect(fixture.isTargetFile).toHaveBeenCalledWith(filteredPath);
+        expect(fixture.processedState.getLastProcessedFileKey).toHaveBeenCalledWith(targetPath);
+        expect(fixture.changeProcessor.processStorageChange).toHaveBeenCalledWith(targetPath, false, false, true);
+        expect(fixture.changeProcessor.processStorageChange).not.toHaveBeenCalledWith(filteredPath, false, false, true);
+        expect(fixture.progress.once).toHaveBeenCalledWith(expect.stringContaining("Offline Changed files: 1"));
+    });
+});

test/e2e-obsidian/scripts/hidden-file-snippet-sync.ts

@@ -202,7 +202,8 @@ async function autoMergeHiddenJsonConflict(cliBinary: string, env: NodeJS.Proces
             "return JSON.stringify({ok:true,path});",
             "})()",
         ].join(""),
-        env
+        env,
+        hiddenFileCliTimeoutMs
     );
 }
 
@@ -567,7 +568,9 @@ async function runMixedOwnership(context: RunnerContext, vault: TemporaryVault):
                 "const hidden=plugin.optionalFileSync.testing.hiddenFileSync;",
                 "core.services.setting.setDeviceAndVaultName('mixed-ownership');",
                 "await customisation.scanAllConfigFiles(false);",
-                "await hidden.scanAllStorageChanges(false,false,true,true);",
+                // The testing view exposes the command-level one-argument scan.
+                // Extra internal scan flags passed here were previously ignored by the view wrapper.
+                "await hidden.scanAllStorageChanges(false);",
                 "const customisationPaths=[];",
                 "for await(const entry of core.localDatabase.findEntries('ix:','ix;')){customisationPaths.push(entry.path);}",
                 "const hiddenPaths=[];",