* fix(#2998): populate gsd-pristine/ from install transform pipeline so verifier has a real baseline
saveLocalPatches declared a pristineDir variable and JSDoc'd 'saves
pristine copies to gsd-pristine/' but no code ever wrote there. Effect:
/gsd-reapply-patches Step 5 verifier (#2972) silently fell back to its
over-broad heuristic ('every significant backup line') -- exactly the
silent-success-on-lost-content failure mode #2969 was designed to
prevent.
Fix: new populatePristineDir({...}) helper runs copyWithPathReplacement
(the install transform pipeline) into a tmp staging dir, then copies out
only the modified-file paths into gsd-pristine/. saveLocalPatches now
accepts a pristineCtx and calls the helper when local patches are
detected. Soft-fails on transform errors (logs warning, continues with
empty pristine -- no worse than pre-fix).
Pristine reflects the about-to-install version's content, which is the
right baseline for 'what would survive without the user's modifications'.
Tests: bug-2998-pristine-dir-populated.test.cjs asserts the helper is
exported, no-ops on empty input, writes one pristine file per source-
existing path, skips ghost paths, and produces deterministic output
(byte-identical across runs -- the property pristine_hashes depends on).
Closes#2998
* chore(#2998): add changeset fragment for PR #3004
* fix(#2998): expand pristine to all manifest install roots; clear stale pristine on populate (CR)
CodeRabbit on PR #3004 caught two issues:
1. populatePristineDir only staged packageSrc/get-shit-done/ but
manifest.files records edits under several install roots (commands/,
agents/, hooks/, skills/, root files like .clinerules). Modified
paths outside get-shit-done/ were silently skipped, leaving the
verifier with no baseline for those edits. Fixed by computing the
set of top-level dirs from the modified set and staging each one
that exists in source. Root-level files (no slash) bypass the
transform pipeline and are copied directly.
2. populatePristineDir did not wipe pre-existing gsd-pristine/ before
populating. A previous run's stale pristine could survive into the
current run's diff baseline. Now wipe before populate AND in the
catch path so soft-failures don't leave half-populated data on disk.
Tests: bug-2998-pristine-dir-populated.test.cjs grows by 2 cases:
- agents/ paths are staged and copied (was silently skipped pre-fix)
- mixed get-shit-done/ + agents/ in same modified list both stage
9f09246f3b