fix(#2112): scope commit to --files pathspec, not entire index (#2148)

* fix(2112): scope commit to --files pathspec, not entire index

cmdCommit/cmdCommitToSubrepo/cmdPrSubrepo staged exactly the files
named in --files but then ran a bare 'git commit' with no pathspec,
absorbing anything else in the index into a commit whose message
described only the named files (#2112).

Fix: append '-- ...stagedPaths' to the commit args when the caller
declared a scope. Three guards are load-bearing:
- stagedPaths (not filesToStage) excludes skipped missing files (#2014)
- explicitFiles gate keeps the default .planning/ path byte-identical
- MERGE_HEAD check via 'git rev-parse' falls back to bare commit during merge
- --amend is left without pathspec (different operation)

cmdPrSubrepo pathspec uses changedFiles (old+new for renames) so the
full rename is captured atomically.

Also fixes workflow markdown in spec-phase.md and add-tests.md.

All-files-missing now short-circuits to nothing_to_commit instead of
absorbing the entire index under a message describing files that
were not committed.

* docs(changeset): backfill PR number (#2148)

* test: update golden-install-parity fixtures for workflow markdown changes (#2112)

* test: update golden fixtures + workflow baselines for #2112 changes

- claude-local.json golden fixture (now generated via gen script)
- workflow-size-baseline.json (add-tests.md +16, spec-phase.md +42 bytes)
- Extended gen-golden-install-parity-zcode.cjs to also regenerate the
  claude local-layout fixture

tests/workflow-size-baseline.json

@@ -1,7 +1,7 @@
 {
   "add-backlog.md": 7176,
   "add-phase.md": 7247,
-  "add-tests.md": 16945,
+  "add-tests.md": 16961,
   "add-todo.md": 8996,
   "ai-integration-phase.md": 14805,
   "analyze-dependencies.md": 3887,
@@ -75,7 +75,7 @@
   "sketch-wrap-up.md": 14267,
   "sketch.md": 20004,
   "smart-entry.md": 11124,
-  "spec-phase.md": 31945,
+  "spec-phase.md": 31987,
   "spike-wrap-up.md": 15136,
   "spike.md": 24561,
   "stats.md": 6762,