fix(module-25): close command-injection + lab-integrity issues

- agent-job.yml: pass untrusted issue body via env (BODY), never interpolated
  into a run: shell line (fixes GHA expression-injection). Adds security note.
- lab/.gitignore: keep propose_pr's `git add -A` from sweeping __pycache__ and
  copied scaffolding into the review diff.
- agent_runner.py: simulated reject() now removes the agent's untracked files
  (git restore can't), and the Module 2 restore line only prints for the real
  tracked-edit path.
- README: clarify --simulate uses a deterministic stand-in, not the delete issue.

Closes #24
Closes #25
Closes #26
Closes #27

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfzV5QvtPDz8LJS3Pu5VLT

modules/25-autonomous-agents/lab/agent_runner.py

@@ -146,6 +146,13 @@ def simulate_fix(variant: str, attempt: int) -> None:
         DEMO_SRC.write_text("def discount(price, pct):\n    return price - price * pct / 100\n")
 
 
+def simulate_cleanup() -> None:
+    """Discard the simulator's demo artifacts. These are UNTRACKED new files, so `git restore`
+    (which only touches tracked files) can't remove them — the simulator cleans up after itself."""
+    for path in (DEMO_SRC, DEMO_TEST):
+        path.unlink(missing_ok=True)
+
+
 # --------------------------------------------------------------------------------------------------
 # The endpoint every path shares: a PR PROPOSAL. Never a merge.
 # --------------------------------------------------------------------------------------------------
@@ -173,12 +180,20 @@ def propose_pr(message: str) -> None:
     print("\nThe agent stops here. It cannot merge. That is the whole safety model.")
 
 
-def reject(reason: str, gate_output: str) -> None:
+def reject(reason: str, gate_output: str, *, simulated: bool = False) -> None:
     print(gate_output)
     print("\n" + "=" * 80)
     print(f"GATE FAILED: {reason}")
-    print("No PR proposed. The branch is left as-is for you to inspect or discard:")
-    print("    git restore .            # throw the agent's change away (Module 2)")
+    print("No PR proposed.")
+    if simulated:
+        # The simulated agent's change is the UNTRACKED demo files, which `git restore` can't touch.
+        # Discard them directly so the failed attempt leaves a clean tree.
+        simulate_cleanup()
+        print("Discarded the simulated agent's demo files (agent_demo.py, test_agent_demo.py).")
+        print("(With a real agent editing tracked files, you'd discard with: git restore .  # Module 2)")
+    else:
+        print("The branch is left as-is for you to inspect or discard:")
+        print("    git restore .            # throw the agent's change away (Module 2)")
     print("=" * 80)
 
 
@@ -198,7 +213,7 @@ def cmd_issue_to_pr(issue_path: Path, simulate: str | None) -> int:
         print(gate_output)
         propose_pr(f"Agent: implement {issue_path.stem}")
         return 0
-    reject("the agent's change does not pass the gate", gate_output)
+    reject("the agent's change does not pass the gate", gate_output, simulated=bool(simulate))
     return 1