Since we now only look at changed files we need to handle
the case where a .py file changed and the .pyc didn't, and
remove the now stale .pyc files.
Previously we looked at all files, so we detected this via
the stale .pyc file.
This changes what files we look at to only those in this module,
which is generally right, but to handle the base-layer sdk
case we also have to run the python fixup in the initial layer.
