feat(pipeline): add stop and prune commands to pipeline engine and CLI

- Add stop_pipeline and prune_pipelines to bin/pipeline_engine.py
- Support prefix matching and custom cancellation reason
- Wire 'super pipeline stop <run_id>' and 'super pipeline prune [--max-age H]' into bin/super-cli.py

bin/pipeline_engine.py

@@ -158,9 +158,61 @@ def fail_pipeline(run_id, reason="failed"):
         save_pipelines(data)
 
 
+def stop_pipeline(run_id, reason="cancelled_by_operator"):
+    """Manually cancel or stop an active pipeline run."""
+    data = load_pipelines()
+    # Support prefix matching
+    target_key = None
+    for k in data.keys():
+        if k == run_id or k.startswith(run_id):
+            target_key = k
+            break
+
+    if not target_key:
+        return None
+
+    entry = data[target_key]
+    entry["status"] = "canceled"
+    entry["canceled_at"] = utcnow()
+    entry["updated_at"] = utcnow()
+    entry["cancel_reason"] = reason
+    save_pipelines(data)
+    return entry
+
+
+def prune_pipelines(max_age_hours=24):
+    """Mark stale running pipeline runs older than max_age_hours as timed_out."""
+    data = load_pipelines()
+    now = datetime.now(timezone.utc)
+    pruned = []
+    for k, v in data.items():
+        if v.get("status") == "running":
+            created_str = v.get("created_at")
+            if created_str:
+                try:
+                    dt = datetime.fromisoformat(created_str.replace("Z", "+00:00"))
+                    diff_h = (now - dt).total_seconds() / 3600.0
+                    if diff_h >= max_age_hours:
+                        v["status"] = "timed_out"
+                        v["completed_at"] = utcnow()
+                        v["updated_at"] = utcnow()
+                        v["timeout_reason"] = f"stale_exceeded_{max_age_hours}h"
+                        pruned.append(k)
+                except Exception:
+                    pass
+    if pruned:
+        save_pipelines(data)
+    return pruned
+
+
 def get_pipeline(run_id):
     data = load_pipelines()
-    return data.get(run_id)
+    if run_id in data:
+        return data[run_id]
+    for k, v in data.items():
+        if k.startswith(run_id):
+            return v
+    return None
 
 
 def list_active_pipelines():
@@ -176,3 +228,4 @@ def list_pipeline_history(limit=20):
         reverse=True,
     )
     return sorted_runs[:limit]
+

bin/super-cli.py

@@ -2271,6 +2271,32 @@ def cmd_pipeline_history(args):
     print_table(headers, rows)
     print(c_dim("\n  Commands: super pipeline status | super pipeline run <name>\n"))
 
+
+def cmd_pipeline_stop(args):
+    import pipeline_engine
+    run_id = args.run_id.strip()
+    reason = getattr(args, "reason", "cancelled_by_operator") or "cancelled_by_operator"
+    entry = pipeline_engine.stop_pipeline(run_id, reason=reason)
+    if not entry:
+        print(c_red(f"Error: Pipeline run '{run_id}' not found."), file=sys.stderr)
+        sys.exit(1)
+    print(c_green(f"✔ Pipeline run '{entry.get('run_id')}' stopped/canceled."))
+    if getattr(args, "json", False):
+        print(json.dumps(entry, indent=2))
+
+
+def cmd_pipeline_prune(args):
+    import pipeline_engine
+    max_age = getattr(args, "max_age", 1) or 1
+    pruned = pipeline_engine.prune_pipelines(max_age_hours=max_age)
+    if pruned:
+        print(c_green(f"✔ Pruned {len(pruned)} stale pipeline runs (> {max_age}h): {', '.join(pruned)}"))
+    else:
+        print(c_dim(f"✔ No stale running pipelines found (> {max_age}h)."))
+    if getattr(args, "json", False):
+        print(json.dumps({"pruned": pruned, "count": len(pruned)}, indent=2))
+
+
 # ---------------------------------------------------------------------------
 # Domain: LOOP (Intrinsic Loop Strategy, Health, Break Taxonomy, and Control)
 # ---------------------------------------------------------------------------
@@ -3019,6 +3045,13 @@ def build_parser():
     p_pipe_hist = pipe_sub.add_parser("history", parents=[common], help="Show historical pipeline runs and outcomes")
     p_pipe_hist.add_argument("-n", "--limit", type=int, default=20, help="Number of records to display")
 
+    p_pipe_stop = pipe_sub.add_parser("stop", parents=[common], help="Cancel/stop an active pipeline run")
+    p_pipe_stop.add_argument("run_id", help="Pipeline run ID (prefix match supported)")
+    p_pipe_stop.add_argument("--reason", default="cancelled_by_operator", help="Cancellation reason")
+
+    p_pipe_prune = pipe_sub.add_parser("prune", parents=[common], help="Prune/timeout stale running pipelines")
+    p_pipe_prune.add_argument("--max-age", type=float, default=1.0, help="Max age in hours (default 1.0)")
+
     # Top-level domain aliases: strat and vars
     p_strat_alias = subparsers.add_parser("strat", parents=[common], help="Shortcut for 'loop strat'")
     strat_alias_sub = p_strat_alias.add_subparsers(dest="strat_action")
@@ -3186,6 +3219,10 @@ def main():
             cmd_pipeline_run(args)
         elif act == "history":
             cmd_pipeline_history(args)
+        elif act == "stop":
+            cmd_pipeline_stop(args)
+        elif act == "prune":
+            cmd_pipeline_prune(args)
         else:
             parser.print_help()
     elif args.domain == "loop":