Things I've found while just trying to get this to work:

• If you've made an update to either of the build.gradle.kts files in api or server, run ./gradlew rebuildPaperSingleFilePatches after adding to git (no commit)
• To create a file patch:
  • Make the changes you need and have no other staged changes
  • cd paper-api or paper-server or parchment-server/src/minecraft/java
  • git add .
  • git commit --amend
    • This ammends it to the specific 'File Patch Commit'
  • Then run one of the following
    • ./gradlew rebuildPaperApiFilePatches
    • ./gradlew rebuildPaperServerFilePatches
    • ./gradlew rebuildMinecraftFilePatches