Fix Leftover Cleanup and Directory Linking

Three major issues fixed:
1) IFS was _not_ set to a newline, it was set to 'n'.

2) By quoting the input to the loops, word splitting wasn't being
used to split lines properly.

3) Directories need to be removed in reverse order.
Localizew the OLDPWD fixing to within functions
Refine submodule skipping loginc