Let us hope this effort can be salvaged!

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Git does not strictly require you to put all of your commits into a single hierarchy. You can also have multiple root commits in the same repository i.e. multiple parallel hierarchies of commits. Then you can combine these together with merge commits if/when you want to have them in the same tree (afaik.)

See 'git commit --orphan' for introducing a new root commit into the repo.

So thinking aloud...

Perhaps for each package could you create a dedicated branch (A, B, ...) with its own root commit? This way each package would have a distinct history on its private branch and not be prone to collisions. If you want to combine multiple packages into one tree then you could create a new branch (A+B) that merges the required per-package branches (which remain isolated and pristine.)

Just an idea -- sorry if I have misunderstood your use case, and let me know if this idea requires more explanation.

Cheers,

-Luke