Implement shed_lint.

Lint a shed repository instead of just tools. This is a meta-issue to track 4 issues open by @peterjc.
- [ ] Check sample files #96.
- [x] Check for a README #89.
- [x] Check rst in any `.rst` files #91.
- [x] Lint `tool_dependencies.xml`.
- [x] ~Cross reference `tool_dependencies.xml` with tools #90.~
- [x] Lint `.shed.yml`
- [x] Lint `repository_dependencies.xml`.
- [x] Check that packages belong only to the category `Tool Dependency Packages`. 8c2a45a14605e9695575ad1ce80d0791ba571d3d
- [x] Check tool dependency actions that are difficult to verify with XSD. 8117e038917f9c2914e7871d519e1af448cec54b
- [x] Check for required type based on repository type. #156
- [x] ~Check for changeset and tool shed attributes in `tool_dependencies.xml` files. (https://github.com/galaxyproject/tools-iuc/pull/149#issuecomment-104311715)~

Start with the remaining checklist item, “Check sample files” (#96), and inspect the repository-linting work referenced by the completed items for README, .rst, tool_dependencies.xml, .shed.yml, and repository_dependencies.xml. Confirm which checks are already implemented and what #96 still requires; done means shed_lint covers the remaining repository check.

Written by the indexing model from the issue text.