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code_store: handle unapplied changes to files not in target

Jarod Wilsonrequested to merge
jwilsonrh/patchpal-gui:missing-files into main

This lets us cleanly handle omitting changes to files that do not exist in the target project.

Fixes: RHELMISC-15248

Signed-off-by: Jarod Wilson jarod@redhat.com

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