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

gsd-core/workflows/add-tests.md

@@ -308,7 +308,7 @@ If there are passing tests to commit:
 
 ```bash
 git add {test files}
-git commit -m "test(phase-${phase_number}): add unit and E2E tests from add-tests command"
+git commit -m "test(phase-${phase_number}): add unit and E2E tests from add-tests command" -- {test files}
 ```
 
 Present next steps:

gsd-core/workflows/spec-phase.md

@@ -456,7 +456,7 @@ Write to: `{phase_dir}/{padded_phase}-SPEC.md`
 
 ```bash
 git add "${phase_dir}/${padded_phase}-SPEC.md"
-git commit -m "spec(phase-${phase_number}): add SPEC.md for ${phase_name} — ${requirement_count} requirements (#2213)"
+git commit -m "spec(phase-${phase_number}): add SPEC.md for ${phase_name} — ${requirement_count} requirements (#2213)" -- "${phase_dir}/${padded_phase}-SPEC.md"
 ```
 
 If `commit_docs` is false: Skip commit. Note that SPEC.md was written but not committed.