fix(patch): keep the update marker on a no-op commit so a retry finalizes

[manzoorwanijk]

A conflicted npm patch update leaves an edit dir and a .npm-patch-update.json marker that the finalizing npm patch commit reads to finish the update — a metadata-only finalize that drops the renamed-from selector and tolerates the new version not being installed yet.

commit() deleted that marker before checking whether the edit dir produced a diff. So a first commit that did no net work — the conflict resolved to the new version verbatim, giving "nothing to commit" — consumed the marker. A corrected retry then found none, ran a full reify, and failed EPATCHUNUSED (the rebased-to version isn't installed), leaving both the old and new selector in the manifest. The same loss happened on any non-finalizing path (e.g. the EPATCHUNSAFE throw).

Fix

The marker was deleted eagerly only to keep it out of the generated patch. Instead, keep it and teach diffDirs to skip it:

• diffDirs(originalDir, editedDir, ignore = new Set()) skips a set of root-relative filenames, like it already skips the root package.json.
• commit() no longer deletes the marker — it reads/parses it (still throwing EPATCHBADMARKER on bad JSON before any diff), and passes new Set([UPDATE_MARKER]) to diffDirs.

The marker now survives any non-finalizing path, so a corrected retry still finalizes. A successful commit removes the whole edit dir (unless --keep-edit-dir), so nothing lingers.

References

Fixes #9566
Follow-up to #9439 (native dependency patching).