So if I understand you correctly, the following files should be deleted from the Manifest (but not from the repository):
.rspec
.rvmrc
.travis.yml
CHANGELOG
Gemfile
Gemfile.lock
config/cucumber.yml

Also, I would need to add the spec and lib files for the UnusedParameter in the Manifest.

If I've gotten this correctly, I'll update the pull request to fix this.