Improve jsdox documentation of app object

Remove docs/api-app.md and docs/api.md, as they are no longer referenced
from docs.json.

Add few missing bits from docs/api-app.md to lib/application.js
comments.
Remove docs/rest.md

The documentation of the REST interface is maintained on
docs.strongloop.com
Fix heading levels in docs/ markdown files.
Merge pull request #132 from strongloop/feature/move-app-doc-to-jsdox

Move the documentation of app object to jsdox