Merge branch 'bug/268' into 'master'

Only force files to be included when run from CLI

Previously we added support so users can do:

    $ flake8 bin/executable

But this broke the fact that git hooks shouldn't check things like
reStructuredText doc files. This commit restores that functionality but
will cause bin/executable to be ignored in the git hook. This seems fair
since folks can amend their filename patterns to include it explicitly.

Closes #268

See merge request !157