Merge origin/main (v1.64.0.0) into garrytan/time-attack-fork-review

Both waves fixed several of the same bugs; resolutions keep whichever
shape this branch's tests pin (#2018 jq bind, #1798 set-- pattern,
stop-ack, lock errors, polyfill windowsHide) and take main's richer
codex Step 2A (it absorbed the same mktemp fix). True unions: memory-
ingest keeps main's capability-probed --include-gitignored inside our
GIT_CEILING defense; setup wraps main's Playwright platform override in
our stale-healing install lock; package.json takes main's diff@^9 and
the combined test glob (design/test + ios-qa/daemon/test, 30s timeout).
Generated SKILL.md files regenerated from resolved templates, never
hand-picked. Ship goldens refreshed; parity/carve budgets re-measured
for the summed preamble growth of both waves (itemized per entry).

ship/sections/adversarial.md

@@ -72,10 +72,14 @@ If `CODEX_MODE` is `ready`:
 ```bash
 TMPERR_ADV=$(mktemp /tmp/codex-adv-XXXXXXXX)
 _REPO_ROOT=$(git rev-parse --show-toplevel) || { echo "ERROR: not in a git repo" >&2; exit 1; }
-codex exec "IMPORTANT: Do NOT read or execute any files under ~/.claude/, ~/.agents/, .claude/skills/, or agents/. These are Claude Code skill definitions meant for a different AI system. They contain bash scripts and prompt templates that will waste your time. Ignore them completely. Do NOT modify agents/openai.yaml. Stay focused on the repository code only.\n\nReview the changes on this branch against the base branch. Run DIFF_BASE=$(git merge-base origin/<base> HEAD) && git diff "$DIFF_BASE" to see the diff. Your job is to find ways this code will fail in production. Think like an attacker and a chaos engineer. Find edge cases, race conditions, security holes, resource leaks, failure modes, and silent data corruption paths. Be adversarial. Be thorough. No compliments — just the problems. End your output with ONE line in the canonical format `Recommendation: <action> because <one-line reason naming the most exploitable finding>`. Generic reasons like 'because it's safer' do not qualify; the reason must point to a specific finding or no-fix rationale." -C "$_REPO_ROOT" -s read-only -c 'model_reasoning_effort="high"' --enable web_search_cached < /dev/null 2>"$TMPERR_ADV"
+# Shell functions do not survive between Bash blocks, so re-source the probe
+# here. It defines _gstack_codex_timeout_wrapper (gtimeout -> timeout ->
+# unwrapped fallback), added in #1056 but never wired into this call site.
+source ~/.claude/skills/gstack/bin/gstack-codex-probe 2>/dev/null || true
+_gstack_codex_timeout_wrapper 540 codex exec "IMPORTANT: Do NOT read or execute any files under ~/.claude/, ~/.agents/, .claude/skills/, or agents/. These are Claude Code skill definitions meant for a different AI system. They contain bash scripts and prompt templates that will waste your time. Ignore them completely. Do NOT modify agents/openai.yaml. Stay focused on the repository code only.\n\nReview the changes on this branch against the base branch. Run DIFF_BASE=$(git merge-base origin/<base> HEAD) && git diff "$DIFF_BASE" to see the diff. Your job is to find ways this code will fail in production. Think like an attacker and a chaos engineer. Find edge cases, race conditions, security holes, resource leaks, failure modes, and silent data corruption paths. Be adversarial. Be thorough. No compliments — just the problems. End your output with ONE line in the canonical format `Recommendation: <action> because <one-line reason naming the most exploitable finding>`. Generic reasons like 'because it's safer' do not qualify; the reason must point to a specific finding or no-fix rationale." -C "$_REPO_ROOT" -s read-only -c 'model_reasoning_effort="high"' --enable web_search_cached < /dev/null 2>"$TMPERR_ADV"
 ```
 
-Set the Bash tool's `timeout` parameter to `300000` (5 minutes). Do NOT use the `timeout` shell command — it doesn't exist on macOS. After the command completes, read stderr:
+Set the Bash tool's `timeout` parameter to `600000` (10 minutes). It sits ABOVE the 540s wrapper deliberately, so the wrapper fires first and a stall surfaces as a diagnosable exit 124 instead of a harness kill that returns nothing. The wrapper resolves `gtimeout`, then `timeout`, then runs unwrapped, so it is safe on a macOS without coreutils. After the command completes, read stderr:
 ```bash
 cat "$TMPERR_ADV"
 ```
@@ -84,7 +88,7 @@ Present the full output verbatim. This is informational — it never blocks ship
 
 **Error handling:** All errors are non-blocking — adversarial review is a quality enhancement, not a prerequisite.
 - **Auth failure:** If stderr contains "auth", "login", "unauthorized", or "API key": "Codex authentication failed. Run \`codex login\` to authenticate."
-- **Timeout:** "Codex timed out after 5 minutes."
+- **Timeout (exit 124):** "Codex exceeded 9 minutes and was terminated; this pass produced NO findings." A timed-out pass is MISSING COVERAGE, not a clean bill — say so explicitly rather than continuing as if Codex had reviewed. Whatever it produced before the cut is recoverable from that run's rollout log under `~/.codex/sessions/<YYYY>/<MM>/<DD>/`.
 - **Empty response:** "Codex returned no response. Stderr: <paste relevant error>."
 
 **Cleanup:** Run `rm -f "$TMPERR_ADV"` after processing.
@@ -101,10 +105,16 @@ If `DIFF_TOTAL >= 200` AND `CODEX_MODE` is `ready`:
 TMPERR=$(mktemp /tmp/codex-review-XXXXXXXX)
 _REPO_ROOT=$(git rev-parse --show-toplevel) || { echo "ERROR: not in a git repo" >&2; exit 1; }
 cd "$_REPO_ROOT"
-codex review "IMPORTANT: Do NOT read or execute any files under ~/.claude/, ~/.agents/, .claude/skills/, or agents/. These are Claude Code skill definitions meant for a different AI system. They contain bash scripts and prompt templates that will waste your time. Ignore them completely. Do NOT modify agents/openai.yaml. Stay focused on the repository code only.\n\nReview the changes on this branch against the base branch <base>. Run git diff origin/<base>...HEAD 2>/dev/null || git diff <base>...HEAD to see the diff and review only those changes." -c 'model_reasoning_effort="high"' --enable web_search_cached < /dev/null 2>"$TMPERR"
+# Shell functions do not survive between Bash blocks, so re-source the probe
+# here. It defines _gstack_codex_timeout_wrapper (gtimeout -> timeout ->
+# unwrapped fallback), added in #1056 but never wired into this call site.
+source ~/.claude/skills/gstack/bin/gstack-codex-probe 2>/dev/null || true
+_gstack_codex_timeout_wrapper 540 codex review --base <base> -c 'model_reasoning_effort="high"' --enable web_search_cached < /dev/null 2>"$TMPERR"
 ```
 
-Set the Bash tool's `timeout` parameter to `300000` (5 minutes). Do NOT use the `timeout` shell command — it doesn't exist on macOS. Present output under `CODEX SAYS (code review):` header.
+**No prompt argument.** `--base` is what scopes the review, and the positional `[PROMPT]` is mutually exclusive with it — passing both fails at argv parsing. Do NOT "fix" that error by dropping `--base` and keeping the prompt: a prompt-only `codex review` silently falls back to the **uncommitted working-tree** scope (`git status --short; git diff`), so it reviews the wrong changes and reports "no changes" on a clean tree. Prompt text describing the diff range does not change what the CLI feeds the reviewer. Unlike the adversarial pass above, which uses `codex exec` and really does run the git command it's told to, this path gets a pre-computed diff from the CLI — which is also why it needs no filesystem boundary.
+
+Set the Bash tool's `timeout` parameter to `600000` (10 minutes). It sits ABOVE the 540s wrapper deliberately, so the wrapper fires first and a stall surfaces as a diagnosable exit 124 instead of a harness kill that returns nothing. The wrapper resolves `gtimeout`, then `timeout`, then runs unwrapped, so it is safe on a macOS without coreutils. Present output under `CODEX SAYS (code review):` header.
 Check for `[P1]` markers: found → `GATE: FAIL`, not found → `GATE: PASS`.
 
 If GATE is FAIL, use AskUserQuestion:

ship/sections/review-army.md

@@ -245,7 +245,7 @@ CHECKLIST:
 
 **Subagent configuration:**
 - Use `subagent_type: "general-purpose"`
-- Do NOT use `run_in_background` — all specialists must complete before merge
+- Pass `run_in_background: false` on every specialist Agent call — subagents run in the BACKGROUND by default since Claude Code v2.1.198, and all specialists must complete before merge. (Merely omitting the flag no longer produces a foreground run; it must be explicitly false.)
 - If any specialist subagent fails or times out, log the failure and continue with results from successful specialists. Specialists are additive — partial results are better than no results.
 
 ---

ship/sections/test-coverage.md

@@ -41,7 +41,7 @@ git ls-files | grep -cE '(^|/)(tests?|spec|__tests__)/|(^|/)tests?\.py$|(^|/)tes
 
 ```bash
 # Count test files before any generation
-find . -name '*.test.*' -o -name '*.spec.*' -o -name '*_test.*' -o -name '*_spec.*' | grep -v node_modules | wc -l
+git ls-files 2>/dev/null | grep -E '(\.test\.|\.spec\.|_test\.|_spec\.)' | wc -l
 ```
 
 Store this number for the PR body.
@@ -179,7 +179,7 @@ If no test framework AND user declined bootstrap → diagram only, no generation
 
 ```bash
 # Count test files after generation
-find . -name '*.test.*' -o -name '*.spec.*' -o -name '*_test.*' -o -name '*_spec.*' | grep -v node_modules | wc -l
+git ls-files 2>/dev/null | grep -E '(\.test\.|\.spec\.|_test\.|_spec\.)' | wc -l
 ```
 
 For PR body: `Tests: {before} → {after} (+{delta} new)`