Repo organizing

- Add doc/ directory, so publishing to gh-pages is a bit easier.
- Update .gitignore to not ignore the doc/ directory.

- Move manual documentation directory into new var directory (var/docs)
- Move example dialogue tree into new var directory (var/trees)
- Update YARD to find manual documentation in new var directory

var/docs/config_file.md

@@ -0,0 +1,66 @@
+<!--
+# @markup markdown
+# @title Configuration File
+-->
+
+# Configuration File Documentation
+
+The configuration file for `sapling` is a standard YAML file. The general
+outline looks something like this:
+
+        ---
+        -
+          trunk: "This is a description of the dialogue tree."
+        -
+          branch:
+            number: 1
+            text: "This is the overall text for the branch."
+            leaf:
+              -
+                text: "This is option 1."
+                branch: 2
+              -
+                text: "This is option 2."
+                branch: 3
+        -
+          branch:
+            number: 2
+            text: "This is the overall text for the branch."
+            leaf:
+              -
+                text: "This is option 1."
+                branch: 1
+              -
+                text: "This is option 2."
+                branch: 3
+        -
+          branch:
+            number: 3
+            text: "This is the overall text for the branch."
+
+## Outline
+
+#### Trunk
+
+The `trunk` is a metadata list. Currently, the only information we really care
+about is a general description for the tree. Because of this, `trunk` is the
+key, and the description is the value.
+
+#### Branch
+
+Branches are the content of a dialogue tree. Each `branch` has the following
+options:
+
+- `number`: The branch number. This is how leaves get around. It must be unique.
+- `text`: The text provided by getting to this branch. The first branch is shown
+  by default when the tree is opened.
+- `leaf`: [Optional] The list of options for the branch. Details for leaves are
+  below. If no leaves are provided, the branch is considered a "terminal
+  branch", and the program will end after reaching it.
+
+#### Leaf
+
+Leaves are the options of a branch. Each `leaf` has the following options:
+
+- `text`: The text shown as the option.
+- `branch`: The branch this option takes the user to.