fix(#1369): refresh wave manifest and re-check base before each wave in execute-phase (#1492)

* fix(#1369): refresh wave manifest and re-check base before each wave in execute-phase

Two compounding issues caused wave N+1 worktrees to fork from the stale
pre-wave-N commit, immediately tripping the worktree_branch_check FATAL
guard in every executor:

1. worktree.base-check auto-degrade only ran once at initialize time.
   After wave N merges advanced orchestrator HEAD past origin/HEAD, new
   worktrees were still forked from origin/HEAD (Claude Code "fresh" base).

2. WAVE_WORKTREE_MANIFEST was never unset between waves, so wave N+1
   reused the consumed wave-N manifest file, which would have blocked the
   step 5.5 manifest guard (#3384) on subsequent waves.

Fix: add two safeguards in execute-phase.md —
- Step 0.5 (start of each wave): re-runs worktree.base-check; auto-degrades
  USE_WORKTREES=false for that wave when HEAD has diverged from origin/HEAD.
- Step 7c (end of each wave): unsets WAVE_WORKTREE_MANIFEST so wave N+1
  creates a fresh per-wave manifest; re-asserts worktree.set-baseref
  (idempotent) and re-evaluates base degradation after wave merges land.

17 regression tests added in tests/bug-1369-wave-stale-base.test.cjs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(#1369): rename test to fix-NNN convention; update workflow size baseline

Rename tests/bug-1369-wave-stale-base.test.cjs → tests/fix-1369-wave-stale-base.test.cjs
to satisfy the lint-regression-test-names gate (new files cannot use bug-NNN prefix).

Update tests/workflow-size-baseline.json for execute-phase.md: 93157 → 97393
(LF-normalized byte count after adding step 0.5 inter-wave base re-check and
step 7c between-wave manifest reset).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(#1369): add issue reference to allow-test-rule comment

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(#1369): extract new execute-phase steps to references; satisfy ADR-857 cap

Step 0.5 (inter-wave worktree base re-check) and steps 7b–7c (pre-wave
dependency check + between-wave manifest reset/base refresh) added by this
PR grew execute-phase.md to 97393 bytes, violating the ADR-857 phase-6
architectural mandate that host-loop bodies remain strictly below the
pre-phase-6 baseline of 93166 bytes.

Extract both new blocks into dedicated reference files:
- gsd-core/references/execute-phase-wave-guard.md (step 0.5)
- gsd-core/references/execute-phase-between-wave-reset.md (steps 7b + 7c)

Replace inline prose with @-reference pointers. File now measures 92851
bytes (LF-normalized), satisfying the ADR-857 capstone conformance gate.

Also update tests/workflow-size-baseline.json to 92851 and add both new
reference files to docs/INVENTORY-MANIFEST.json.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(#1369): update regression tests to read from extracted reference files

Steps 0.5 and 7b+7c were moved to reference files to satisfy the ADR-857
size cap on execute-phase.md. Tests now check @-reference pointers in the
workflow for ordering and read content assertions from the reference files.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

gsd-core/workflows/execute-phase.md

@@ -491,6 +491,8 @@ increases monotonically across waves. `{status}` is `complete` (success),
 
 **For each wave:**
 
+@~/.claude/gsd-core/references/execute-phase-wave-guard.md
+
 1. **Intra-wave files_modified overlap check (BEFORE spawning):**
 
    Before spawning any agents for this wave, inspect the `files_modified` list of all plans
@@ -1038,12 +1040,8 @@ increases monotonically across waves. `{status}` is `complete` (success),
    **Step 7.3 — `class == "unknown-failure"`:**
    Report failed plan and ask Continue/Stop; continuing may cascade into dependent plan failures.
 
-7b. **Pre-wave dependency check (waves 2+ only):**
-    Before wave N+1, run `gsd-tools.cjs query verify.key-links {phase_dir}/{plan}-PLAN.md` for each upcoming plan.
-    If any PRIOR-wave artifact link fails, present:
-    - `## Cross-Plan Wiring Gap` with plan/link/from/pattern rows
-    - Options: investigate+fix before continue, or continue with cascade risk
-    Skip key-links that reference files in the CURRENT (upcoming) wave.
+@~/.claude/gsd-core/references/execute-phase-between-wave-reset.md
+
 8. **Execute checkpoint plans between waves** — see `<checkpoint_handling>`.
 9. **Proceed to next wave.**
 </step>