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The updater wrote the manifest and copied two files, but never removed anything, so `flathub/org.triliumnotes.Trilium` still tracks flip-fuses.mts, stamp-build-info.mts and trim-locales.mts — staged copies from before the manifest ran the checkout's own scripts. The vendored manifest references none of them. Without a prune the next packaging pull request would add trilium.sh and flathub.json while leaving all three behind, and the repo would keep drifting from the recipe that claims to generate it. Everything tracked outside KEPT_FILES now goes; create-pull-request stages the working tree wholesale, so the deletions travel in the same pull request. The list is an allowlist, so a file the recipe keeps but does not write — anything Flathub adds to that repo later — has to be added to it or the next run removes it. `git ls-files` keeps listing a deletion that is staged but uncommitted, so a second run against the same checkout found the files already gone and died on ENOENT. Verified against a clone of the real repo: the three deletions show up in `git status`, and a re-run is clean. Co-Authored-By: Claude Opus 5 <[email protected]>