fix(container): kill orphaned in-container process on execute() timeout (#31)

When subprocess.run([docker exec ...], timeout=N) hits TimeoutExpired,
Python SIGKILLs the local docker exec CLI. The docker daemon does not
propagate that into the container (only SIGINT/SIGTERM propagate
gracefully), so the test process spawned inside the container keeps
running. With sleep-as-PID-1 cleanrooms it never gets reaped: it just
orphans onto PID 1 and keeps burning CPU while the next docker exec
call competes for the same resources.

On a multi-arm evaluation run over the full task set, this surfaces as:
a TUI-style task hits the 3600s outer timeout, returns rc=-1,
programbench retries the branch, the retry SIGKILLs another docker
exec, the second orphan accumulates alongside the first, and so on.
Observed cost on one run: ~2 hr wasted per arm per hang-prone task,
plus measurable CPU contention slowing surrounding evals in the same
stripe.

Fix: on TimeoutExpired, send a follow-up
  docker exec <c> bash -c "kill -KILL -1; sleep 0.2; kill -KILL -1; true"
which signals every non-PID-1 process in the container's PID namespace.
Safe here because ContainerEnvironment starts cleanrooms with a long-
lived sleep as PID 1; the only non-PID-1 processes are the test
subprocess tree we just spawned. Bounded with a 30s timeout on the
kill exec itself, and warns if it fails so the failure is debuggable
instead of silent.

Behavior on successful runs is unchanged.

Author: kunchenguid

src/programbench/container.py

@@ -89,6 +89,37 @@ def execute(self, command: str, *, timeout: int | None = None) -> dict[str, Any]
                 "exception_info": "",
             }
         except subprocess.TimeoutExpired:
+            # When subprocess.run hits its host-side timeout, Python SIGKILLs
+            # the local `docker exec` CLI. The docker daemon does not
+            # propagate that into the container (only SIGINT/SIGTERM
+            # propagate gracefully), so the process spawned inside the
+            # container keeps running. With sleep-as-PID-1 cleanrooms it
+            # never gets reaped and competes with the next docker exec call.
+            #
+            # Sweep the in-container processes by SIGKILL-ing every non-
+            # PID-1 process. Safe here because the cleanroom's only PID-1
+            # process is the long-lived `sleep` that keeps the container
+            # alive; everything else is the test subprocess tree we just
+            # spawned. Bounded with a short timeout so a stuck daemon
+            # cannot wedge us a second time.
+            try:
+                subprocess.run(
+                    [
+                        self.executable,
+                        "exec",
+                        self.container_id,
+                        "bash",
+                        "-c",
+                        "kill -KILL -1 2>/dev/null; sleep 0.2; kill -KILL -1 2>/dev/null; true",
+                    ],
+                    capture_output=True,
+                    text=True,
+                    timeout=30,
+                )
+            except Exception as e:
+                log.warning(
+                    "in-container teardown after execute() timeout failed: %s", e
+                )
             return {
                 "output": "",
                 "returncode": -1,