Revert "Merge pull request #5400 from kit-ty-kate/no-gpatch"

[kit-ty-kate]

Reverts #5400

After a couple of weeks of tests, git apply turned out to be bad choice for 2 main reason:

• the format accepted by it is too strict and will make applications of a number of patches from opam-repository fail. See for example Package slack.0.1 opam-repository#25430 (comment)
• The --unsafe-paths option is not just used When git apply is used as a "better GNU patch" (as the git documentation puts it), but is actually highly unsafe (who could have guessed!) and allows the application of patches outside of the selected path using ../. However opam requires one part of the behaviour of this option to work: accepting to apply changes inside of a .git directory. This is required for opam update to function properly.

I've also observed some non-deterministic failures but it's harder to understand the reason why.

We have a couple of alternative solutions in mind, but given the critical aspect of those two issues we chose to revert it separately first to give us some more time to implement and choose a better solution.