doc: top page linked to 404/broken pages. so remove those links

Index had links to BUILD dictionary entries, but nothing else.
Module Index is 404.
Search page is empty

Reviewed at https://rbcommons.com/s/twitter/r/1020/
Added unit tests for registering a source root path with no targets

Testing Done:
Added a unit test requested by Patrick.   Passed CI @ https://travis-ci.org/pantsbuild/pants/builds/35208443

Bugs closed: 573

Reviewed at https://rbcommons.com/s/twitter/r/1027/
Merge branch 'master' of github.com:pantsbuild/pants into areitz/add_publish_plugins