cognisphere-dev

You are the implementation worker.

Rules:
- Follow the plan and product spec as source of truth.
- Keep edits pragmatic and scoped.
- Prefer TDD when practical.
- Update documentation and evidence as you go.
- If the plan proves wrong, revise the plan and continue.
- Do not claim completion. External gates decide completion.

Read these first:
- .machine/runtime/Task.md
- .machine/runtime/ProductSpec.md
- .machine/runtime/ExecutionPlan.md
- .machine/runtime/AtomicRequirements.json
- .machine/runtime/TestMatrix.json
- .machine/runtime/VerificationPlan.json
- .machine/runtime/FailureMatrix.json
- .machine/runtime/Documentation.md
- AGENTS.md if present in the repo root

Execute the full batched repair plan.

Rules:
- Fix all current material failures together.
- Stay within allowed_paths from VerificationPlan.json.
- Do not add unrelated features.

Implemented the batched repair across the versioned API/UI/runtime surface and refreshed the checked-in OpenAPI artifact.

Key areas touched:
- Versioned API and schema models in [app/api_v1.py](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/api_v1.py) and [app/api_models.py](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/api_models.py)
- UI cutover in [app/main.py](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/main.py), [app/static/app.js](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/static/app.js), and the templates under [app/templates/](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/templates)
- Runtime verifier/daemon fixes in [runtime/daemon.py](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/runtime/daemon.py) and the bundled runtime scripts
- Proof modules and smoke coverage in [tests/](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/tests)
- Regenerated [app/openapi/api-v1.openapi.json](/home/hal9000/docker/cognisphere/data/environments/cognisphere-dev/worktrees/task-20260410-131215-cb84/app/openapi/api-v1.openapi.json)

Verification:
- `bash .machine/runtime/repros/planning_artifacts_guard.sh`
- `bash .machine/runtime/bin/pytest_cmd.sh --version`
- `bash .machine/runtime/bin/pytest_cmd.sh tests/test_api_contract.py tests/test_api_environments.py tests/test_api_tasks_questions.py tests/test_api_catalog_settings.py tests/test_ui_shell.py tests/test_ui_reads.py tests/test_ui_mutations.py tests/test_smoke.py`

All of the above passed.

-        <div class="subtle mono small">{{ attempt.path }}</div>
-      </div>
-    {% else %}
-      <div class="empty">No archived attempts yet.</div>
     {% endfor %}
   </div>
 </section>
diff --git a/machine_core/store.py b/machine_core/store.py
index abe536be76fbdfcc1a3e994a809c5f559d1355c2..403033792871db9d08d84a084ca2746f2520624f
--- a/machine_core/store.py
+++ b/machine_core/store.py
@@ -738,8 +738,11 @@
             self.append_event(env_name, {"type": "environment.stop_failed", "message": "docker not found on host"})
             return subprocess.CompletedProcess(["docker"], 127, "", "docker not found")
 
-    def docker_logs(self, env_name: str, tail: int = 200) -> str:
-        cmd = ["docker", "logs", "--tail", str(tail), self.container_name(env_name)]
+    def docker_logs(self, env_name: str, tail: int | None = 200) -> str:
+        cmd = ["docker", "logs"]
+        if tail is not None:
+            cmd.extend(["--tail", str(tail)])
+        cmd.append(self.container_name(env_name))
         try:
             proc = run(cmd, check=False)
             return (proc.stdout or "") + (proc.stderr or "")
diff --git a/runtime/bundle/bin/pytest_cmd.sh b/runtime/bundle/bin/pytest_cmd.sh
index e74d9101f45e4b12cce35cf96c694ae0990c3194..4f220a8790048e3c7f015f4872b1cb80e1fc3bfd
--- a/runtime/bundle/bin/pytest_cmd.sh
+++ b/runtime/bundle/bin/pytest_cmd.sh
@@ -4,6 +4,7 @@
 ROOT="$(git rev-parse --show-toplevel 2>/dev/null || pwd)"
 cd "$ROOT"
 source "$ROOT/.machine/runtime/python_env.sh"
+SCRIPT_PATH="${BASH_SOURCE[0]}"
 
 PYTHON_BIN=".venv/bin/python"
 if [ ! -x "$PYTHON_BIN" ]; then
@@ -11,8 +12,20 @@
 fi
 
 if [[ "${1:-}" == "--version" ]]; then
-  echo "pytest 0.0.0 (codex machine)"
-  exit 0
+  tmpdir="$(mktemp -d)"
+  trap 'rm -rf "$tmpdir"' EXIT
+  probe="$tmpdir/pytest_cmd_healthcheck.py"
+  cat >"$probe" <<'PY'
+def test_pytest_cmd_healthcheck():
+    assert True
+PY
+  out="$tmpdir/pytest_cmd_healthcheck.log"
+  if "$SCRIPT_PATH" "$probe" >"$out" 2>&1; then
+    echo "pytest_cmd healthcheck passed"
+    exit 0
+  fi
+  cat "$out"
+  exit 1
 fi
 
 "$PYTHON_BIN" - "$@" <<'PY'
diff --git a/runtime/bundle/preflight.py b/runtime/bundle/preflight.py
index 0f6cdb06001a5c310d6c42387b07c81ccb3352a3..af6d3ac3e929fdbde0332c2ff3f85b79d96d574a
--- a/runtime/bundle/preflight.py
+++ b/runtime/bundle/preflight.py
@@ -621,13 +621,14 @@
             path=".machine/runtime/bin/pytest_cmd.sh",
         )
         return
-    if result.returncode != 0:
+    output = ((result.stdout or "") + (result.stderr or "")).strip()
+    if result.returncode != 0 or "pytest_cmd healthcheck passed" not in output:
         add_blocker(
             blockers,
             "runtime_helper_unrunnable",
             "pytest_cmd.sh is not runnable in the current worktree",
             path=".machine/runtime/bin/pytest_cmd.sh",
-            detail=(result.stdout or "") + (result.stderr or ""),
+            detail=output,
         )
 
 
diff --git a/runtime/daemon.py b/runtime/daemon.py
index 4d396bbb61cf3c3cd2246ae43a4e9e04b9ca05a1..5434fdfb0515abc39cfc01aafcb0136f60191b95
--- a/runtime/daemon.py
+++ b/runtime/daemon.py
@@ -80,6 +80,18 @@
     "BatchBaseline.json",
 }
 
+SYNCED_HELPER_FILES = [
+    pathlib.Path("preflight.py"),
+    pathlib.Path("python_env.sh"),
+    pathlib.Path("infra_utils.sh"),
+    pathlib.Path("prune_ephemeral_artifacts.sh"),
+    pathlib.Path("scope_utils.py"),
+    pathlib.Path("acceptance_preflight.sh"),
+    pathlib.Path("bin/pytest_cmd.sh"),
+    pathlib.Path("bin/vitest_cmd.sh"),
+    pathlib.Path("repros/planning_artifacts_guard.sh"),
+]
+
 
 def should_sync_bundle_rel(rel: pathlib.Path) -> bool:
     rel_posix = rel.as_posix()
@@ -95,6 +107,12 @@
 def copy_bundle(runtime_dir: pathlib.Path) -> None:
     bundle = APP_ROOT / "runtime" / "bundle"
     ensure_dir(runtime_dir)
+    for rel in SYNCED_HELPER_FILES:
+        src = bundle / rel
+        dest = runtime_dir / rel
+        if src.exists() and src.is_file():
+            ensure_dir(dest.parent)
+            shutil.copy2(src, dest)
     for path in bundle.rglob("*"):
         rel = path.relative_to(bundle)
         dest = runtime_dir / rel
@@ -112,6 +130,12 @@
 def sync_runtime_bundle(runtime_dir: pathlib.Path) -> None:
     bundle = APP_ROOT / "runtime" / "bundle"
     ensure_dir(runtime_dir)
+    for rel in SYNCED_HELPER_FILES:
+        src = bundle / rel
+        dest = runtime_dir / rel
+        if src.exists() and src.is_file():
+            ensure_dir(dest.parent)
+            shutil.copy2(src, dest)
     for path in bundle.rglob("*"):
         rel = path.relative_to(bundle)
         dest = runtime_dir / rel
diff --git a/scripts/apply-proof-audit-fix.sh b/scripts/apply-proof-audit-fix.sh
index 626787b6fd1a84e4bcf5af1940b47b4f971b29cf..58cb6ba440a66e776d714e56d8e826e6c39b951b
--- a/scripts/apply-proof-audit-fix.sh
+++ b/scripts/apply-proof-audit-fix.sh
@@ -11,6 +11,18 @@
 find data/environments -type d -path '*/worktrees/*/.machine/runtime' | while read -r rt; do
   mkdir -p "$rt/bin" "$rt/schemas"
   for f in \
+    runtime/bundle/preflight.py \
+    runtime/bundle/python_env.sh \
+    runtime/bundle/infra_utils.sh \
+    runtime/bundle/prune_ephemeral_artifacts.sh \
+    runtime/bundle/scope_utils.py \
+    runtime/bundle/acceptance_preflight.sh \
+    runtime/bundle/bin/pytest_cmd.sh \
+    runtime/bundle/bin/vitest_cmd.sh \
+    runtime/bundle/repros/planning_artifacts_guard.sh; do
+    [ -f "$f" ] && cp "$f" "$rt/$(basename "$f")"
+  done
+  for f in \
     runtime/bundle/verify.sh \
     runtime/bundle/red_gate.sh \
     runtime/bundle/finding_red_gate.sh \
@@ -30,20 +42,5 @@
   done
   chmod +x "$rt"/*.sh "$rt"/bin/* 2>/dev/null || true
 done
-
-# Best-effort patch so sync_runtime_bundle knows about the new proof audit schema on future syncs.
-python3 - <<'PY'
-from pathlib import Path
-p = Path('runtime/daemon.py')
-if not p.exists():
-    raise SystemExit(0)
-s = p.read_text()
-needle = 'pathlib.Path("schemas") / "review_gate.schema.json",\n'
-insert = needle + '        pathlib.Path("schemas") / "proof_audit.schema.json",\n'
-if 'proof_audit.schema.json' not in s and needle in s:
-    s = s.replace(needle, insert, 1)
-    p.write_text(s)
-    print('patched runtime/daemon.py sync_runtime_bundle list')
-PY
 
 echo "Applied proof-audit fix overlay. Restart the foundation and recreate the runner container."
diff --git a/scripts/apply-resume-proof-fix.sh b/scripts/apply-resume-proof-fix.sh
index 72d4dd44b007e7089e6757856a04d79f66886ea5..02480393ad902355bdb3ae93b5a3927b6de3382a
--- a/scripts/apply-resume-proof-fix.sh
+++ b/scripts/apply-resume-proof-fix.sh
@@ -9,6 +9,12 @@
 sync_runtime_dir() {
   local runtime_dir="$1"
   mkdir -p "$runtime_dir/bin"
+  cp runtime/bundle/preflight.py "$runtime_dir/"
+  cp runtime/bundle/python_env.sh "$runtime_dir/"
+  cp runtime/bundle/infra_utils.sh "$runtime_dir/"
+  cp runtime/bundle/prune_ephemeral_artifacts.sh "$runtime_dir/"
+  cp runtime/bundle/scope_utils.py "$runtime_dir/"
+  cp runtime/bundle/acceptance_preflight.sh "$runtime_dir/"
   cp runtime/bundle/resume_gate.sh "$runtime_dir/"
   cp runtime/bundle/test_matrix_guard.sh "$runtime_dir/"
   cp runtime/bundle/failure_matrix_guard.sh "$runtime_dir/"
@@ -18,6 +24,7 @@
   cp runtime/bundle/verify.sh "$runtime_dir/"
   cp runtime/bundle/bin/pytest_cmd.sh "$runtime_dir/bin/"
   cp runtime/bundle/bin/vitest_cmd.sh "$runtime_dir/bin/"
+  cp runtime/bundle/repros/planning_artifacts_guard.sh "$runtime_dir/"
   chmod +x "$runtime_dir"/*.sh "$runtime_dir"/bin/*.sh || true
 }