Include `app` in default directories

Since Rails is so prevalent I believe it makes sense to include this.
Merge pull request #18 from andyw8/include-app-in-default-dirs

Include `app` in default directories
Revert pull request #16, as it broke functionality
Add Coveralls
Add Coveralls badge
Use minitest directly

Since Ruby 1.9, `test/unit` has just been a wrapper
around minitest for legacy support:

http://www.rubyinside.com/a-minitestspec-tutorial-elegant-spec-style-testing-that-comes-with-ruby-5354.html
Merge pull request #21 from andyw8/use-minitest

Use minitest directly
Revert coverage ratchet
Documentation improvements
Fix markdown syntax
Test suppressed tools
Small cleanups
Separate out process running
Make ProcessRunner injectable
Mock out process runner
Put ProcessRunner into a module
Add test for ProcessRunner
Add class documentation
Remove blank line
Remove popener pass-through DI