I am not sure I understand the exact problem or the purpose of
splitting the files in that manner, but I think you will need to
divide your workflow into logical chunks that can be sent to the
correct place.

It is possible that what you have is two different projects that
belong in separate project directories that would be sent track by
completely separate repositories. For example, if you have Mac and
Windows versions of a program, I would keep them in separate
projects.  If some material is common to both, I would put that in a
third project.

Another alternative might to always maintain separate branches that
help to divide the files or changes into the correct divisions (one
branch for each version).  The risk of the multi-branch approach is
that you will inevitably get confused about which branch you are on
and you will mangle everything.  The general idea is to checkout V2,
work on version two, add files, commit, check the status to be sure it
is clean (perhaps use 'git add -u .' to account for deleted files),
then checkout V1 and work on that, add files, commit, double check the
status, then checkout the V2 branch.  It would help to become a
compulsive checker of git status while you are learning this process.
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