Fix assorted file/path handling bugs

Hey Clay,

I ran into a few problems using `motion_require` with files in `app/`, which are relative paths. This patch fixes the problems I ran into. I haven't tested these changes on a gem, like Formotion.

1. Add to app.files by union, to avoid duplicates in file list.
2. Prefix relative files with ./ to match RubyMotion build system.
3. Preserve relative/absolute-ness when generating path of required file.