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Git file patches don't work properly when rebuilding/applying #324

Description

@Toffikk

I discovered this bug when playing around with file/git patch conversion
Turns out that when you try to rebuild patches after changing the gitFilePatches to true property in the fork-server/build.gradle.kts when you try rebuilding to convert your patches it fails on the apply* tasks

Example output of the error:

Image

I assume this is a bug since when using -x pufferfish:server:applyMinecraft(type patch)Patches it rebuilds and converts them to regular git patches properly, however it doesn't occur when going from git patches -> file patches in my testing
this was first brought up in the #build-tooling-help channel on the paper discord

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