Update docs

docs/README.md

@@ -1,27 +1,13 @@
 # Documentation
 
-## General
+For more information, see [the docs](http://clowder.readthedocs.io/en/latest/)
 
+- [Command Reference](commands.md)
+- [Command behavior with forks](forks.md)
+  - Description of the behavior of `clowder` commands with forks
+- [clowder.yml Syntax Reference](clowder-yml-syntax-reference.md)
+  - Description of the `clowder.yaml` file
+- [cats example](clowder-yml-cats.md)
+- [forks example](clowder-yml-forks.md)
 - [clowder repo](clowder-repo.md)
   - Description of the clowder repo cloned into the `.clowder` directory with `clowder init`
-- [clowder.yaml](clowder-yaml.md)
-  - Description of the `clowder.yaml` file
-- [Forks](forks.md)
-  - Description of the behavior of `clowder` commands with forks
-
-## Commands
-
-- [Command Reference](commands.md)
-  - Description of all `clowder` commands
-- [clowder branch](examples/clowder-branch.md)
-- [clowder clean and clowder diff](examples/clowder-clean-diff.md)
-- [clowder forall](examples/clowder-forall.md)
-- [clowder herd](examples/clowder-herd.md)
-- [clowder prune and clowder start](examples/clowder-prune-start.md)
-
-## Swift
-
-- [Swift update_checkout json config](swift-update-checkout-config-json.md)
-  - Comparison between `clowder.yaml` and Swift's [update-checkout-config.json](https://github.com/apple/swift/blob/master/utils/update-checkout-config.json) schemes
-- [Swift update_checkout script](swift-update-checkout-py.md)
-  - Comparison between `clowder` and Swift's [update_checkout.py](https://github.com/apple/swift/blob/master/utils/update_checkout.py) script

docs/forks.md

@@ -1,6 +1,6 @@
 # Forks
 
-`clowder` simplifies some common fork workflows. Currently, it's only possible to add one fork for a project. Forks are handled specially by certain commands
+`clowder` simplifies some common fork workflows. Currently, it's only possible to add one fork for a project. Forks are handled specially by certain commands.
 
 ---
 
@@ -16,7 +16,7 @@ $ clowder herd -d 1
 - If any projects don't have a clean git status then `clowder` exits
 - Projects are cloned from the upstream remote if they don't currently exist
 - Each project fetches the latest changes from upstream
-- If the current git ref checked out doesn't match the `clowder.yaml` configuration, the correct ref will be checked out
+- If the current git ref checked out doesn't match the `clowder.yml` configuration, the correct ref will be checked out
 - The latest changes are pulled from upstream for branches. For commits and tags, the commits are checked out into a detached `HEAD` state
 
 ```bash

docs/rst/general_documentation.rst

@@ -6,7 +6,7 @@ General Documentation
    :maxdepth: 2
 
    Command Reference <../commands>
+   Command behavior with forks <../forks>
    clowder.yml Syntax Reference <../clowder-yml-syntax-reference>
+   Examples <examples>
    The clowder repo <../clowder-repo>
-   Forks <../forks>
-   Examples <../examples>