Make filegroup paths relative to module dir in mixed builds

filegroup.srcs must have a .rel() version of their paths
that is relative to the module directory. Previously in
mixed builds, the relative path wasn't filled in.

Bug: 229251008
Bug: 204244290
Test: go tests, and USE_BAZEL_ANALYSIS=1 m apexer with the following cl
Change-Id: I11a2a8b96139e0e7b956fa4c256a9a99c02f88f3