New repo layout (#217)

* Updated instructions to match new repo layout

* Updating file paths to match the new repo organization

* Updated one reference from /flux-system to /bootstrap

* Changed one more reference to /flux-system to /bootstrap

* Typo

* Added requested formatting and missing backslash in bootstrap command.

Co-authored-by: David Young <davidy@funkypenguin.co.nz>

manuscript/kubernetes/ingress/index.md

@@ -16,4 +16,4 @@ Choose at least one of the above (*there may be valid reasons to use both!* [^1]
   
 --8<-- "recipe-footer.md"
 
-[^1]: One cluster I manage uses traefik Traefik for public services, but Nginx for internal managemnet services such as Prometheus, etc. The idea is that you'd need one type of Ingress to help debug problems with the _other_ type!
+[^1]: One cluster I manage uses traefik Traefik for public services, but Nginx for internal management services such as Prometheus, etc. The idea is that you'd need one type of Ingress to help debug problems with the _other_ type!

manuscript/kubernetes/ingress/nginx.md

@@ -24,7 +24,7 @@ Nginx Ingress Controller does make for a nice, simple "default" Ingress controll
 
 ### Namespace
 
-We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `flux-system/namespaces/namespace-nginx-ingress-controller.yaml`:
+We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `bootstrap/namespaces/namespace-nginx-ingress-controller.yaml`:
 
 ??? example "Example NameSpace (click to expand)"
     ```yaml
@@ -36,7 +36,7 @@ We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Pe
 
 ### HelmRepository
 
-Next, we need to define a HelmRepository (*a repository of helm charts*), to which we'll refer when we create the HelmRelease. We only need to do this once per-repository. In this case, we're using the (*prolific*) [bitnami chart repository](https://github.com/bitnami/charts/tree/master/bitnami), so per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `flux-system/helmrepositories/helmrepository-bitnami.yaml`:
+Next, we need to define a HelmRepository (*a repository of helm charts*), to which we'll refer when we create the HelmRelease. We only need to do this once per-repository. In this case, we're using the (*prolific*) [bitnami chart repository](https://github.com/bitnami/charts/tree/master/bitnami), so per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `bootstrap/helmrepositories/helmrepository-bitnami.yaml`:
 
 ??? example "Example HelmRepository (click to expand)"
     ```yaml
@@ -52,7 +52,7 @@ Next, we need to define a HelmRepository (*a repository of helm charts*), to whi
 
 ### Kustomization
 
-Now that the "global" elements of this deployment (*Namespace and HelmRepository*) have been defined, we do some "flux-ception", and go one layer deeper, adding another Kustomization, telling flux to deploy any YAMLs found in the repo at `/nginx-ingress-controller`. I create this Kustomization in my flux repo at `flux-system/kustomizations/kustomization-nginx-ingress-controller.yaml`:
+Now that the "global" elements of this deployment (*Namespace and HelmRepository*) have been defined, we do some "flux-ception", and go one layer deeper, adding another Kustomization, telling flux to deploy any YAMLs found in the repo at `/nginx-ingress-controller`. I create this Kustomization in my flux repo at `bootstrap/kustomizations/kustomization-nginx-ingress-controller.yaml`:
 
 ??? example "Example Kustomization (click to expand)"
     ```yaml

manuscript/kubernetes/ingress/traefik/index.md

@@ -25,7 +25,7 @@ Traefik natively includes some features which Nginx lacks:
 
 ### Namespace
 
-We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `flux-system/namespaces/namespace-traefik.yaml`:
+We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `bootstrap/namespaces/namespace-traefik.yaml`:
 
 ??? example "Example NameSpace (click to expand)"
     ```yaml
@@ -37,7 +37,7 @@ We need a namespace to deploy our HelmRelease and associated ConfigMaps into. Pe
 
 ### HelmRepository
 
-Next, we need to define a HelmRepository (*a repository of helm charts*), to which we'll refer when we create the HelmRelease. We only need to do this once per-repository. In this case, we're using the official [Traefik helm chart](https://github.com/traefik/traefik-helm-chart), so per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `flux-system/helmrepositories/helmrepository-traefik.yaml`:
+Next, we need to define a HelmRepository (*a repository of helm charts*), to which we'll refer when we create the HelmRelease. We only need to do this once per-repository. In this case, we're using the official [Traefik helm chart](https://github.com/traefik/traefik-helm-chart), so per the [flux design](/kubernetes/deployment/flux/), I create this in my flux repo at `bootstrap/helmrepositories/helmrepository-traefik.yaml`:
 
 ??? example "Example HelmRepository (click to expand)"
     ```yaml
@@ -53,7 +53,7 @@ Next, we need to define a HelmRepository (*a repository of helm charts*), to whi
 
 ### Kustomization
 
-Now that the "global" elements of this deployment (*Namespace and HelmRepository*) have been defined, we do some "flux-ception", and go one layer deeper, adding another Kustomization, telling flux to deploy any YAMLs found in the repo at `/traefik`. I create this Kustomization in my flux repo at `flux-system/kustomizations/kustomization-traefik.yaml`:
+Now that the "global" elements of this deployment (*Namespace and HelmRepository*) have been defined, we do some "flux-ception", and go one layer deeper, adding another Kustomization, telling flux to deploy any YAMLs found in the repo at `/traefik`. I create this Kustomization in my flux repo at `bootstrap/kustomizations/kustomization-traefik.yaml`:
 
 ??? example "Example Kustomization (click to expand)"
     ```yaml