Adds missing TOC entries for docs that fail the new Travis check in PR #2007.

Skips the checks for certain inaccessible or deprecated files and removes unused README.md files.

_data/reference.yml

@@ -15,6 +15,7 @@ toc:
     - docs/admin/service-accounts-admin.md
   - docs/api-reference/v1/operations.html
   - docs/api-reference/v1/definitions.html
+  - docs/api-reference/labels-annotations-taints.md
   - kubernetes/third_party/swagger-ui/index.md
 
 - title: Autoscaling API
@@ -183,20 +184,3 @@ toc:
   - title: Security in Kubernetes
     path: https://github.com/kubernetes/kubernetes/blob/release-1.3/docs/design/security.md
 
-- title: Federation
-  section:
-  - docs/user-guide/federation/index.md
-  - docs/user-guide/federation/configmap.md
-  - docs/user-guide/federation/daemonsets.md
-  - docs/user-guide/federation/deployment.md
-  - docs/user-guide/federation/events.md
-  - docs/user-guide/federation/federated-ingress.md
-  - docs/user-guide/federation/namespaces.md
-  - docs/user-guide/federation/replicasets.md
-  - docs/user-guide/federation/secrets.md
-  - docs/federation/api-reference/README.md
-  - title: Federation Components
-    section:
-    - docs/admin/federation-apiserver.md
-    - title : federation-controller-mananger
-      path: /docs/admin/federation-controller-manager