Add .shed.yml file to each repository.

**PRO**: keeps track of which directories map to which repositories.
**PRO**: simple uploads with planemo
  - Upload a directory to either shed with `planemo shed_upload --shed_target [testtoolshed|toolshed]` (after configuring shed credentials).

**CON**: Kind of makes it harder to upload these repositories to the tool shed without planemo (got to make sure to exclude .shed.yml from tar if tarring outside `planemo`).

This is how I would do it - but I do not want to shove Planemo down anyone's throat.