Avoid unnecessary os.path.realpath() calls in _ensure_real_directory()

Staging performance has been quite slow for me and the biggest offender when profiling has been os.path.realpath() being called from _ensure_real_directory().

When tracing calls to this function, I found that we called os.path.realpath() on the same directory many times. This is unnecessary as we process the filelist in directory-first order. The code is now changed to only ensure directories exist when we hit a directory; the rest of the time this isn't needed.

In my profile of bst shell on base.bst from the gnome-modulesets repo, time spent in _ensure_real_directory() goes from 11 seconds to 0.12 seconds.

Depends on !198 (closed)

Fixes #174 (closed)