Reported against pacquet's configDependencies preview engine for `msw@2.12.14`: install fails with `ERR_PNPM_PATCH_FAILED ... error applying hunk #1` even though the patch is perfectly valid. Original report (patch file + error log): [Stanzilla/21648ae644068c3aef3d18693c7c32c9](https://gist.github.com/Stanzilla/21648ae644068c3aef3d18693c7c32c9). **Root cause.** When two snapshots of the same patched package hardlink (or reflink, where the filesystem doesn't break-on-write) from the same store file, pacquet's `apply_patch_to_dir` did a plain `fs::write` — which truncates and writes through the shared inode, **corrupting the on-disk store copy** and leaking patched content into every other snapshot that linked the same file. The next worker then read already-patched content and `diffy::apply` failed on the missing `-` lines. The patched output already lives in the side-effects cache after apply returns, so nothing requires the store copy to carry it. The fix is three layered changes to `apply_patch_to_dir`: - **Atomic temp + rename for Modify** ([apply.rs](pacquet/crates/patching/src/apply.rs)). Stage the patched bytes in a sibling `.{name}.{pid}.{counter}.pacquet-tmp` opened with `create_new(true)` (no symlink-follow, no truncation of an attacker-pre-seeded path), chmod the temp to match the original *before* the rename so the final mode lands atomically, then `fs::rename` over the target. `rename` is atomic on Unix and replaces in-place on Windows, so an IO failure mid-write leaves either the original or the rewritten file — never an empty dirent. As a side effect of creating a new dirent → inode mapping, it also breaks any hardlink the path previously shared with the store. Matches the [`pacquet_lockfile::save_lockfile::write_atomic`](pacquet/crates/lockfile/src/save_lockfile.rs) pattern. - **Idempotency via reverse-dry-run** (Modify/Create/Delete). When forward apply fails, try reverse-apply against the on-disk content; if it succeeds the file is already in the post-patch state and we no-op. Mirrors upstream [`@pnpm/patch-package`'s `applyPatch`](https://github.com/ds300/patch-package/blob/master/src/applyPatches.ts) which retries `executeEffects(reversePatch, { dryRun: true })` on failure. Defense in depth for re-runs that find the directory pre-patched (side-effects-cache hit that fell through, manual edits, partial install recovery) — the hardlink-break above prevents fresh installs from ever producing that state. - **Idempotency for Create and Delete**. Create skips when the existing file already contains the post-patch content; Delete treats `NotFound` on the target as already-deleted. Equivalent fix for the TS pnpm CLI side is in [`pnpm/patch-package@c97a62e`](https://github.com/pnpm/patch-package/commit/c97a62e) (`@pnpm/patch-package` is the apply implementation pnpm imports); pnpm will pick it up once that package is released and the dep gets bumped.
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Background
pnpm uses a content-addressable filesystem to store all files from all module directories on a disk. When using npm, if you have 100 projects using lodash, you will have 100 copies of lodash on disk. With pnpm, lodash will be stored in a content-addressable storage, so:
- If you depend on different versions of lodash, only the files that differ are added to the store.
If lodash has 100 files, and a new version has a change only in one of those files,
pnpm updatewill only add 1 new file to the storage. - All the files are saved in a single place on the disk. When packages are installed, their files are linked from that single place consuming no additional disk space. Linking is performed using either hard-links or reflinks (copy-on-write).
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Benchmark
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Benchmarks on an app with lots of dependencies: