I'm saying this because, git store whole files for each commit, not hunks or patches. Scripting it out without doing any interactions would be to have discrete steps which can be rollback. So it's better to have the changes (the patch) separate from what needs to be changed (the file). So the agents need only to edit the patch in three separate version (c1, c2, c3), then loop with the apply->update-index->commit action, each easily verifiable and revertable.