Start fleshing out the docs more - rearrange, separate out modules section, move files over to md (from rst)

docs/source/user_guidelines.md

@@ -0,0 +1,12 @@
+
+# User Guidelines
+
+
+This section of the documentation provides guidelines for users who want to use the tool,
+without needing to modify the code.
+To see the developer guidelines, see the [](development/developer_guidelines)
+
+```{note}
+This is a work in progress.
+```
+