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
  • git add .
  • git commit --ammend
    • This ammends it to the specific 'File Patch Commit'
  • ./gradlew rebuildPaper<Api/Server>FilePatches