crossref links with --paths links to wrong directory

[jshipley]

If I have a project like this:

submodule_a/
    a.py
submodule_b/
    b.py

And I run pycco like this pycco -p */*.py

Then if I have a crossref link in submodule_b/b.py to submodule_a/a.py, the directory structure is ignored and the link comes out relative to the file where the crossref is located instead of linking to the correct file.

In other words, [[submodule_a/a.py]] in b.py will end up being a link to submodule_b/a.py