Experiment with applying rebase patches without recreation

[premun]

Context

Instead of recreating the previous flows to form the working branch and then rebasing it, we should try applying the source patch directly on top of the target branch.

However, there's at least one case that breaks it - file removed in the target branch, which was modified in the source branch will fail the patch application with the following error:

Exit code: 1
Std err:
Falling back to direct application...
Applied patch to 'src/product-repo1/FileChangedAndPartiallyReverted.txt' cleanly.
error: src/product-repo1/FileInConflict.txt: does not exist in index
Falling back to direct application...

Goal

• Try to see which other combinations of conflicts are not supported.
• Try if we can re-generate the patch without these broken files and then manifest the conflict in the working tree manually somehow (maybe flipping the index flag by the file?).