(PUP-3770) Fix copying module files to guest

In certain scenarios, no module files are copied to the guest. I have found this issue with modules residing under `/vagrant/module_path` and `/home/ci/.../module_path`.

The regexp generated was `/(?-mix:((\/|\A).bundle(\/|\z))|((\/|\A).git(\/|\z))|((\/|\A).idea(\/|\z))|((\/|\A).vagrant(\/|\z))|((\/|\A).vendor(\/|\z))|((\/|\A)acceptance(\/|\z))|((\/|\A)spec(\/|\z))|((\/|\A)tests(\/|\z))|((\/|\A)log(\/|\z))|((\/|\A).(\/|\z))|((\/|\A)..(\/|\z)))/`. I tested this pattern in http://rubular.com/ and found that indeed it matches all files under those directories.

The string substitution was not doing anything at all (`"\."` gets expanded to `.` instead of `\.`).

It was also only trying to replace the first `.` of each entry as it was using `String#sub` instead of `String#gsub`.

Once that was fixed, beaker worked.