7b. **Pre-wave dependency check (waves 2+ only):**
    Before wave N+1, run `gsd_run 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.

7c. **Between-wave manifest reset and worktree base refresh (waves 2+ only — #1369):**

   **REQUIRED before each wave transition when `USE_WORKTREES != "false"` and
   `ISOLATION = "harness-worktree"`** (#2652 — keyed on the negotiated isolation model, not the
   runtime name).

   Wave N's `WAVE_WORKTREE_MANIFEST` was consumed by `worktree.cleanup-wave` in step 5.5. It must be
   unset so wave N+1's step 3 creates a fresh manifest for the new wave's worktrees. Without this,
   the wave N+1 manifest guard (step 5.5, #3384) blocks on the stale/empty consumed file.

   After wave N merges and tracking commits, the orchestrator HEAD has advanced past the commit the
   Claude Code harness may have cached as the worktree fork base at session start. New worktrees
   spawned for wave N+1 could fork from the stale pre-wave-N HEAD, causing every executor to trip the
   `worktree_branch_check` FATAL guard immediately (symptom: `HEAD is <old-sha>, expected <new-sha>`).

   ```bash
   # Unset per-wave manifest so wave N+1 creates a fresh one (#3384, #1369).
   unset WAVE_WORKTREE_MANIFEST

   # Between-wave base re-check (#1369, #3659): after wave N merges and tracking commits,
   # HEAD has advanced. Re-asserting worktree.baseRef:"head" is deliberately NOT done here —
   # the runtime harness does not read project-settings baseRef (#48), so in
   # harness-worktree mode the setting cannot influence the fork base. The safety re-check
   # below compares HEAD against the REAL fork base and degrades the remaining waves
   # whenever they diverge, avoiding the base-mismatch FATAL in executor agents.
   if [ "$ISOLATION" = "harness-worktree" ] && [ "$USE_WORKTREES" != "false" ]; then
     _BETWEEN_DEGRADE=$(gsd_run query worktree.base-check --mode "$ISOLATION" --pick shouldDegrade 2>/dev/null || echo "false")
     if [ "$_BETWEEN_DEGRADE" = "true" ]; then
       _DEGRADE_MSG=$(gsd_run query worktree.base-check --mode "$ISOLATION" --pick message 2>/dev/null || true)
       [ -n "$_DEGRADE_MSG" ] && printf '%s\n' "$_DEGRADE_MSG" >&2
       printf 'Degrading to sequential mode for remaining waves: HEAD advanced past worktree fork base after wave %s merge (#1369).\n' "${N}" >&2
       # Both must move together (#2652): dispatch keys on ISOLATION.
       USE_WORKTREES=false
       ISOLATION=none
     fi
   fi
   ```