save: include only necessary dependencies

Currently, 'godep save' imports the Godeps.json (if any) of imported
path, which is a full list of dependencies. And in some cases, this
is more than what the importing package needs.
For example, the importing package might only need few sub-packages
from a rather big libraries.

This patch skips importing the full list from Godeps.json, but
recursively traverse them as normal imported dependencies.
This requires escaping them from the containsPathPrefix() function.

fixes #93
Note that walking the file tree skips all directories that start with _, just a few lines above here.