chore(memory,seedgo): memory modernization + seedgo audit fix (#72)

Memory: 30 files — symbolic orchestrator, handlers, modules cleanup
Seedgo: branch_audit.py fix

Co-authored-by: @devpulse <devpulse@aipass>

src/aipass/memory/apps/handlers/archive/indexer.py

@@ -25,6 +25,7 @@ from datetime import datetime
 from typing import Dict, Any, List
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -271,6 +272,8 @@ def check_for_new_files() -> Dict[str, Any]:
 
     save_index(index)
 
+    log_operation("index_sync", {"new_files": len(new_files), "deleted_files": len(deleted_files), "success": True})
+
     return {
         'success': True,
         'new_files': len(new_files),

src/aipass/memory/apps/handlers/central_writer.py

@@ -24,6 +24,7 @@ from datetime import datetime
 from typing import Dict, Any
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -259,6 +260,8 @@ def update_central(verbose: bool = False) -> Dict[str, Any]:
         if verbose:
             result["stats"] = stats
 
+        log_operation("update_central", {"vectors": stats.get("total_vectors", 0), "success": True})
+
         return result
 
     except Exception as e:

src/aipass/memory/apps/handlers/dashboard_push.py

@@ -26,6 +26,7 @@ from datetime import datetime
 from typing import Dict, Any, List
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -430,6 +431,8 @@ def push_memory_bank_dashboard() -> bool:
             "memory_bank", section_data, branch_paths
         )
 
+        log_operation("dashboard_push", {"branches_updated": success_count, "success": success_count > 0})
+
         return success_count > 0
 
     except Exception:

src/aipass/memory/apps/handlers/intake/plans_processor.py

@@ -27,6 +27,7 @@ from datetime import datetime
 from typing import Dict, Any, List
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # Subprocess scripts
 _HANDLERS_DIR = Path(__file__).resolve().parent.parent
@@ -321,4 +322,6 @@ def process_plans() -> Dict[str, Any]:
     if errors:
         result['errors'] = errors
 
+    log_operation("process_plans", {"files_processed": files_processed, "total_chunks": total_chunks, "success": result['success']})
+
     return result

src/aipass/memory/apps/handlers/intake/pool_processor.py

@@ -34,6 +34,8 @@ from pathlib import Path
 from datetime import datetime
 from typing import List, Dict, Any
 
+from aipass.memory.apps.handlers.json.json_handler import log_operation
+
 # Paths
 _MEMORY_ROOT = Path(__file__).resolve().parent.parent.parent.parent  # handlers/intake/ → handlers/ → apps/ → memory/
 CONFIG_PATH = _MEMORY_ROOT / "config" / "memory_bank.config.json"
@@ -446,6 +448,8 @@ def process_memory_pool() -> dict:
     if results['files_processed'] > 0:
         _update_central_and_dashboard()
 
+    log_operation("process_memory_pool", {"files_processed": results['files_processed'], "total_chunks": results['total_chunks'], "success": results['success']})
+
     return results
 
 

src/aipass/memory/apps/handlers/json/memory_files.py

@@ -33,6 +33,7 @@ from typing import Dict, Any, Optional
 from datetime import datetime
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -151,6 +152,8 @@ def write_memory_file(file_path: Path, data: Dict[str, Any]) -> Dict[str, Any]:
             # Atomic rename (overwrites original)
             Path(temp_path).rename(file_path)
 
+            log_operation("write_memory_file", {"file": file_path.name, "success": True})
+
             return {
                 'success': True,
                 'file': str(file_path)

src/aipass/memory/apps/handlers/learnings/manager.py

@@ -34,11 +34,12 @@ from typing import Dict, Any, List, Tuple
 from datetime import datetime
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
 # Handler imports (relative within package)
-from aipass.memory.apps.handlers.json.json_handler import (
+from aipass.memory.apps.handlers.json.memory_files import (
     read_memory_file_data,
     write_memory_file_simple
 )
@@ -493,6 +494,8 @@ def ensure_timestamps(file_path: Path) -> Dict[str, Any]:
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 
@@ -543,6 +546,8 @@ def enforce_limit(file_path: Path) -> Dict[str, Any]:
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 
@@ -592,6 +597,8 @@ def enforce_limit(file_path: Path) -> Dict[str, Any]:
     except Exception as e:
         return {'success': False, 'error': f'Failed to write file: {e}'}
 
+    log_operation("enforce_limit", {"removed": to_remove_count, "remaining": len(to_keep), "success": True})
+
     return {
         'success': True,
         'removed': to_remove_count,
@@ -623,6 +630,8 @@ def ensure_timestamps_completed(file_path: Path) -> Dict[str, Any]:
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 
@@ -676,6 +685,8 @@ def enforce_limit_completed(file_path: Path) -> Dict[str, Any]:
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 
@@ -756,6 +767,8 @@ def add_learning(
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 
@@ -778,6 +791,8 @@ def add_learning(
     # Enforce limit after adding
     enforce_result = enforce_limit(file_path)
 
+    log_operation("add_learning", {"key": key, "action": "updated" if is_update else "added", "success": True})
+
     return {
         'success': True,
         'action': 'updated' if is_update else 'added',
@@ -808,6 +823,8 @@ def update_status_counts(file_path: Path) -> Dict[str, Any]:
 
     try:
         data = read_memory_file_data(file_path)
+        if data is None:
+            return {'success': False, 'error': f'Failed to parse file: {file_path.name}'}
     except Exception as e:
         return {'success': False, 'error': f'Failed to read file: {e}'}
 

src/aipass/memory/apps/handlers/monitor/detector.py

@@ -27,6 +27,7 @@ from typing import List, Dict, Any
 from dataclasses import dataclass
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 

src/aipass/memory/apps/handlers/monitor/memory_watcher.py

@@ -24,7 +24,11 @@ Independence:
 
 import logging
 from pathlib import Path
-from typing import Optional, Dict, Any
+from typing import TYPE_CHECKING, Optional, Dict, Any
+
+if TYPE_CHECKING:
+    from watchdog.observers import Observer as _ObserverType
+    from watchdog.events import FileSystemEventHandler as _HandlerType
 
 try:
     from watchdog.observers import Observer
@@ -33,12 +37,13 @@ try:
 except ImportError:
     WATCHDOG_AVAILABLE = False
     Observer = None
-    FileSystemEventHandler = object
+    FileSystemEventHandler = object  # type: ignore[assignment,misc]
 
 # Handler imports (relative within package)
 from aipass.memory.apps.handlers.tracking.line_counter import update_line_count
 from aipass.memory.apps.handlers.monitor.detector import check_single_file
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -46,7 +51,7 @@ logger = get_system_logger()
 _MEMORY_ROOT = Path(__file__).resolve().parents[3]
 
 # Global observer instance
-_observer: Optional[Observer] = None
+_observer: Any = None
 
 
 # =============================================================================
@@ -222,6 +227,8 @@ def check_and_rollover() -> Dict[str, Any]:
     # Check code_archive for new files to index
     results['code_archive'] = _check_code_archive()
 
+    log_operation("check_and_rollover", {"files_checked": results.get('files_checked', 0), "rollover_triggered": results.get('rollover_triggered', False)})
+
     return results
 
 
@@ -425,7 +432,7 @@ def _is_memory_file(file_path: Path) -> bool:
 # FILE SYSTEM EVENT HANDLER
 # =============================================================================
 
-class MemoryFileWatcher(FileSystemEventHandler):
+class MemoryFileWatcher(FileSystemEventHandler):  # type: ignore[misc]
     """Watch for memory file modifications"""
 
     def __init__(self):
@@ -525,7 +532,7 @@ def start_memory_watcher() -> Dict[str, Any]:
     watcher = MemoryFileWatcher()
 
     # Create observer
-    new_observer = Observer()
+    new_observer = Observer()  # type: ignore[misc]
 
     # Schedule watcher for each branch path (silent - no logging during startup)
     watched_paths = []

src/aipass/memory/apps/handlers/rollover/extractor.py

@@ -33,7 +33,8 @@ from typing import Dict, List, Any, Tuple
 from datetime import datetime
 
 # Handler imports (relative within package)
-from aipass.memory.apps.handlers.json.json_handler import read_memory_file_data, write_memory_file_simple
+from aipass.memory.apps.handlers.json.json_handler import log_operation
+from aipass.memory.apps.handlers.json.memory_files import read_memory_file_data, write_memory_file_simple
 from aipass.prax.apps.modules.logger import get_system_logger
 
 logger = get_system_logger()
@@ -125,8 +126,8 @@ def restore_from_backup(file_path: Path) -> Dict[str, Any]:
 # FILE OPERATIONS
 # =============================================================================
 
-def _read_memory_file(file_path: Path) -> Dict[str, Any]:
-    """Read memory JSON file using json_handler"""
+def _read_memory_file(file_path: Path) -> Dict[str, Any] | None:
+    """Read memory JSON file using memory_files handler."""
     return read_memory_file_data(file_path)
 
 
@@ -380,6 +381,11 @@ def extract_items(
     # Read file
     try:
         data = _read_memory_file(file_path)
+        if data is None:
+            return {
+                'success': False,
+                'error': f"Failed to parse memory file: {file_path.name}"
+            }
         current_lines = _count_file_lines(file_path)
     except Exception as e:
         return {

src/aipass/memory/apps/handlers/rollover/orchestrator.py

@@ -26,6 +26,7 @@ from pathlib import Path
 from typing import List, Dict, Any
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # logger imported from aipass.prax
 
@@ -502,6 +503,13 @@ def execute_rollover() -> Dict[str, Any]:
         except Exception as e:
             logger.info(f"[rollover] Memory pool check: {e}")
 
+    log_operation("rollover_execute", {
+        "triggers": len(triggers),
+        "success_count": success_count,
+        "failed_count": len(failed),
+        "success": success_count > 0 or len(triggers) == 0,
+    })
+
     return {
         'success': success_count > 0 or len(triggers) == 0,
         'triggers_count': len(triggers),

src/aipass/memory/apps/handlers/schema/normalize.py

@@ -28,6 +28,7 @@ from typing import Dict, Any
 from datetime import datetime
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -124,6 +125,8 @@ def normalize_memory_file(file_path: Path, dry_run: bool = False) -> Dict[str, A
         except Exception as e:
             return {'success': False, 'error': f"Failed to write: {e}"}
 
+    log_operation("normalize_memory_file", {"file": file_path.name, "changes": len(changes), "success": True})
+
     return {
         'success': True,
         'file': str(file_path),

src/aipass/memory/apps/handlers/search/query_executor.py

@@ -26,6 +26,7 @@ from pathlib import Path
 from typing import Dict, Any
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # Subprocess scripts for ML operations (run in memory venv)
 _HANDLERS_DIR = Path(__file__).resolve().parent.parent
@@ -274,6 +275,7 @@ def execute_search(
 
     logger.info(f"[search] Filtered to {len(filtered_results)} relevant results")
 
+    log_operation("search_execute", {"query_len": len(query), "results": len(filtered_results), "success": True})
     return {
         'success': True,
         'query': query,

src/aipass/memory/apps/handlers/search/vector_search.py

@@ -33,6 +33,7 @@ from typing import List, Dict, Any
 from pathlib import Path
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -317,6 +318,7 @@ def search_collection(
                 'collection': collection_name
             }
 
+        log_operation("vector_search_collection", {"collection": collection_name, "count": result.get('count', 0), "success": True})
         return {
             'success': True,
             **result
@@ -485,11 +487,13 @@ def search_all_collections(
                     'count': coll_result['count']
                 }
 
+        total = sum(r['count'] for r in results.values())
+        log_operation("vector_search_all", {"collections": len(results), "total_results": total, "success": True})
         return {
             'success': True,
             'results': results,
             'collections_searched': len(results),
-            'total_results': sum(r['count'] for r in results.values())
+            'total_results': total
         }
 
     except Exception as e:

src/aipass/memory/apps/handlers/storage/chroma.py

@@ -33,6 +33,7 @@ from pathlib import Path
 from datetime import datetime
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -315,6 +316,7 @@ def store_vectors(
         service = _get_service(db_path)
         result = service.store_vectors(branch, memory_type, embeddings, documents, metadatas)
 
+        log_operation("chroma_store_vectors", {"collection": result.get('collection'), "count": result.get('count', 0), "success": True})
         return {
             'success': True,
             **result
@@ -492,6 +494,7 @@ def search_vectors(
         # Sort by distance (lower is better)
         all_results.sort(key=lambda x: x['distance'] if x['distance'] is not None else float('inf'))
 
+        log_operation("chroma_search_vectors", {"collections": len(collection_names), "results": len(all_results), "success": True})
         return {
             'success': True,
             'results': all_results[:n_results * len(collection_names)] if all_results else [],

src/aipass/memory/apps/handlers/symbolic/chroma_client.py

@@ -34,6 +34,8 @@ Key Functions:
 from typing import Dict, Any
 from pathlib import Path
 
+from aipass.memory.apps.handlers.json.json_handler import log_operation
+
 
 # =============================================================================
 # CONSTANTS
@@ -128,6 +130,7 @@ def get_collection(
                 embedding_function=None
             )
 
+        log_operation("chroma_get_collection", {"collection": collection_name, "create": create, "success": True})
         return {
             'success': True,
             'collection': collection

src/aipass/memory/apps/handlers/symbolic/deduplicator.py

@@ -32,6 +32,8 @@ import re
 from typing import Dict, List, Any, Optional
 from pathlib import Path
 
+from aipass.memory.apps.handlers.json.json_handler import log_operation
+
 # memory/ root resolved from symbolic/deduplicator.py
 _MEMORY_ROOT = Path(__file__).resolve().parent.parent.parent.parent
 
@@ -189,6 +191,8 @@ def deduplicate_fragment(
     action = parsed['action']
     reason = parsed.get('reason', 'No reason provided')
 
+    log_operation("symbolic_dedup", {"action": action, "existing_count": len(existing_fragments), "success": True})
+
     # Apply action to fragment
     if action == 'UPDATE':
         # Merge content from LLM response into fragment

src/aipass/memory/apps/handlers/symbolic/extractor.py

@@ -31,6 +31,8 @@ from datetime import datetime
 from pathlib import Path
 from typing import Dict, List, Any, Optional
 
+from aipass.memory.apps.handlers.json.json_handler import log_operation
+
 # memory/ root resolved from symbolic/extractor.py
 _MEMORY_ROOT = Path(__file__).resolve().parent.parent.parent.parent
 
@@ -450,7 +452,7 @@ def analyze_conversation_llm(chat_history: List[Dict[str, Any]]) -> Dict[str, An
                 'message_count': 0, 'error': None}
     llm = extract_fragments_llm(chat_history)
     reg = analyze_conversation(chat_history)
-    return {
+    result = {
         'success': llm.get('success', False),
         'fragments': llm.get('fragments', []),
         'metadata': {
@@ -462,3 +464,5 @@ def analyze_conversation_llm(chat_history: List[Dict[str, Any]]) -> Dict[str, An
             'chunk_count': llm.get('chunk_count', 0)},
         'message_count': reg.get('message_count', len(chat_history)),
         'error': llm.get('error')}
+    log_operation("symbolic_extract", {"fragments": len(result['fragments']), "messages": result['message_count'], "success": True})
+    return result

src/aipass/memory/apps/handlers/symbolic/hook.py

@@ -36,7 +36,8 @@ from typing import Dict, List, Any, Tuple
 
 # Handler imports (domain-organized, no modules)
 from aipass.memory.apps.handlers.symbolic import retriever
-from aipass.memory.apps.handlers.json import json_handler
+from aipass.memory.apps.handlers.json import memory_files
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # memory/ root resolved from symbolic/hook.py
 _MEMORY_ROOT = Path(__file__).resolve().parent.parent.parent.parent
@@ -82,7 +83,7 @@ def load_config(config_path: Path | None = None) -> Dict[str, Any]:
     path = config_path or DEFAULT_CONFIG_PATH
 
     if path.exists():
-        result = json_handler.read_memory_file(path)
+        result = memory_files.read_memory_file(path)
         if result.get('success'):
             config = result.get('data', {})
             # Merge with defaults for any missing keys
@@ -107,7 +108,7 @@ def save_config(config: Dict[str, Any], config_path: Path | None = None) -> Dict
     # Ensure parent directory exists
     path.parent.mkdir(parents=True, exist_ok=True)
 
-    return json_handler.write_memory_file(path, config)
+    return memory_files.write_memory_file(path, config)
 
 
 # =============================================================================
@@ -634,6 +635,7 @@ def process_hook(
     # Record the surface
     record_surface(fragment)
 
+    log_operation("symbolic_hook", {"fragment_id": fragment.get('id'), "surfaced": True, "success": True})
     return {
         'success': True,
         'surfaced': True,

src/aipass/memory/apps/handlers/symbolic/retriever.py

@@ -38,6 +38,7 @@ from pathlib import Path
 # Handler imports (domain-organized, no modules)
 from aipass.memory.apps.handlers.vector import embedder
 from aipass.memory.apps.handlers.symbolic.chroma_client import get_chroma_client
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 
 # =============================================================================
@@ -402,6 +403,7 @@ def retrieve_fragments(
     # Return top n_results
     final_results = ranked[:n_results]
 
+    log_operation("symbolic_retrieve", {"results": len(final_results), "methods": search_methods_used, "success": True})
     return {
         'success': True,
         'results': final_results,

src/aipass/memory/apps/handlers/symbolic/storage.py

@@ -40,6 +40,7 @@ from pathlib import Path
 
 # Handler imports (domain-organized, no modules)
 from aipass.memory.apps.handlers.vector import embedder
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 
 # =============================================================================
@@ -306,11 +307,13 @@ def store_fragment(
             metadatas=[flat_meta]
         )
 
+        total = collection.count()
+        log_operation("symbolic_store_fragment", {"fragment_id": frag_id, "total": total, "success": True})
         return {
             'success': True,
             'fragment_id': frag_id,
             'collection': COLLECTION_NAME,
-            'total_fragments': collection.count()
+            'total_fragments': total
         }
 
     except Exception as e:
@@ -416,11 +419,13 @@ def store_fragments_batch(
             metadatas=batch_metadatas
         )
 
+        total = collection.count()
+        log_operation("symbolic_store_batch", {"stored": len(batch_ids), "total": total, "success": True})
         return {
             'success': True,
             'stored': len(batch_ids),
             'collection': COLLECTION_NAME,
-            'total_fragments': collection.count()
+            'total_fragments': total
         }
 
     except Exception as e:
@@ -534,11 +539,13 @@ def store_llm_fragment(
             metadatas=[flat_meta]
         )
 
+        total = collection.count()
+        log_operation("symbolic_store_llm_fragment", {"fragment_id": frag_id, "total": total, "success": True})
         return {
             'success': True,
             'fragment_id': frag_id,
             'collection': COLLECTION_NAME,
-            'total_fragments': collection.count()
+            'total_fragments': total
         }
 
     except Exception as e:
@@ -660,11 +667,13 @@ def store_llm_fragments_batch(
             metadatas=frag_metas
         )
 
+        total = collection.count()
+        log_operation("symbolic_store_llm_batch", {"stored": len(frag_ids), "total": total, "success": True})
         return {
             'success': True,
             'stored': len(frag_ids),
             'collection': COLLECTION_NAME,
-            'total_fragments': collection.count()
+            'total_fragments': total
         }
 
     except Exception as e:
@@ -703,10 +712,12 @@ def delete_fragment(
 
         collection.delete(ids=[fragment_id])
 
+        total = collection.count()
+        log_operation("symbolic_delete_fragment", {"deleted_id": fragment_id, "total": total, "success": True})
         return {
             'success': True,
             'deleted_id': fragment_id,
-            'total_fragments': collection.count()
+            'total_fragments': total
         }
 
     except Exception as e:

src/aipass/memory/apps/handlers/templates/differ.py

@@ -28,6 +28,7 @@ from pathlib import Path
 from typing import Dict, Any, List, Optional
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # =============================================================================
 # PATH SETUP
@@ -65,7 +66,7 @@ def _replace_placeholders(template: dict, branch_name: str) -> dict:
     today = datetime.now().strftime("%Y-%m-%d")
     result = copy.deepcopy(template)
 
-    def _replace_in_value(val):
+    def _replace_in_value(val: Any) -> Any:
         if isinstance(val, str):
             return val.replace("{{BRANCHNAME}}", branch_name).replace("{{DATE}}", today)
         elif isinstance(val, list):
@@ -74,7 +75,9 @@ def _replace_placeholders(template: dict, branch_name: str) -> dict:
             return {k: _replace_in_value(v) for k, v in val.items()}
         return val
 
-    return _replace_in_value(result)
+    replaced = _replace_in_value(result)
+    assert isinstance(replaced, dict)
+    return replaced
 
 
 # =============================================================================
@@ -295,6 +298,7 @@ def diff_template_vs_branch(branch_path: str | Path) -> dict:
         if file_diff["additions"] or file_diff["removals"] or file_diff["modifications"]:
             result["observations"].append(file_diff)
 
+    log_operation("template_diff", {"branch": branch_name, "local_diffs": len(result["local"]), "obs_diffs": len(result["observations"]), "success": True})
     return result
 
 

src/aipass/memory/apps/handlers/templates/pusher.py

@@ -30,9 +30,10 @@ from typing import Dict, Any, List, Tuple, Optional
 from datetime import datetime
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # Handler imports (same-branch allowed per handler boundaries)
-from aipass.memory.apps.handlers.json.json_handler import (
+from aipass.memory.apps.handlers.json.memory_files import (
     read_memory_file_data,
     write_memory_file_simple
 )
@@ -81,7 +82,7 @@ def _replace_placeholders(template: dict, branch_name: str) -> dict:
     """Replace {{BRANCHNAME}} and {{DATE}} in template values. Returns new dict."""
     today = datetime.now().strftime("%Y-%m-%d")
 
-    def _walk(val):
+    def _walk(val: Any) -> Any:
         if isinstance(val, str):
             return val.replace("{{BRANCHNAME}}", branch_name).replace("{{DATE}}", today)
         elif isinstance(val, list):
@@ -90,7 +91,9 @@ def _replace_placeholders(template: dict, branch_name: str) -> dict:
             return {k: _walk(v) for k, v in val.items()}
         return val
 
-    return _walk(copy.deepcopy(template))
+    result = _walk(copy.deepcopy(template))
+    assert isinstance(result, dict)
+    return result
 
 
 # =============================================================================
@@ -417,6 +420,7 @@ def push_templates(dry_run: bool = False) -> dict:
         if not _update_version_file(result["branches_list"]):
             result["errors"].append("Failed to update template version file")
 
+    log_operation("template_push", {"branches": result["branches_updated"], "files": result["files_modified"], "dry_run": dry_run, "success": True})
     return result
 
 

src/aipass/memory/apps/handlers/templates/spawn_pusher.py

@@ -29,6 +29,7 @@ from pathlib import Path
 from typing import Any, Dict, List
 
 from aipass.prax import logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # =============================================================================
 # PATH SETUP
@@ -229,6 +230,7 @@ def push_to_spawn_templates(dry_run: bool = False) -> dict:
         f"{result['files_modified']} files modified"
     )
 
+    log_operation("spawn_template_push", {"sets_updated": result["template_sets_updated"], "files": result["files_modified"], "dry_run": dry_run, "success": True})
     return result
 
 

src/aipass/memory/apps/handlers/tracking/line_counter.py

@@ -26,8 +26,9 @@ from typing import Dict, Any
 from datetime import datetime
 
 # Handler imports (relative within package)
-from aipass.memory.apps.handlers.json.json_handler import update_metadata
+from aipass.memory.apps.handlers.json.memory_files import update_metadata
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -91,6 +92,8 @@ def update_line_count(file_path: Path) -> Dict[str, Any]:
             'error': f"Failed to update metadata: {result['error']}"
         }
 
+    log_operation("update_line_count", {"file": file_path.name, "lines": line_count, "success": True})
+
     return {
         'success': True,
         'file': str(file_path),

src/aipass/memory/apps/handlers/vector/embedder.py

@@ -33,6 +33,7 @@ from typing import List, Dict, Any
 from pathlib import Path
 
 from aipass.prax.apps.modules.logger import get_system_logger
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 logger = get_system_logger()
 
@@ -117,11 +118,12 @@ class EmbeddingService:
 
         # Pre-sort by length (reduces padding waste by 30%)
         sorted_pairs = sorted(enumerate(texts), key=lambda x: len(x[1]))
-        sorted_indices, sorted_texts = zip(*sorted_pairs)
+        sorted_indices: list[int] = [p[0] for p in sorted_pairs]
+        sorted_text_list: list[str] = [p[1] for p in sorted_pairs]
 
         # Encode with optimal settings
         embeddings = self.model.encode(
-            sorted_texts,
+            sorted_text_list,
             batch_size=self.batch_size,
             convert_to_tensor=False,  # Return numpy for Chroma
             normalize_embeddings=True,  # Critical for L2 distance
@@ -195,6 +197,7 @@ def encode_batch(texts: List[str]) -> Dict[str, Any]:
         service = _get_service()
         result = service.encode_batch(texts)
 
+        log_operation("vector_encode_batch", {"count": result.get('count', 0), "dimension": result.get('dimension', 0), "success": True})
         return {
             'success': True,
             **result

src/aipass/memory/apps/modules/rollover.py

@@ -29,6 +29,7 @@ from rich import box
 
 from aipass.prax import logger
 from aipass.cli.apps.modules import console, error, warning
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # =============================================================================
 # INFRASTRUCTURE SETUP
@@ -221,6 +222,7 @@ def run_rollover() -> bool:
         for fail in failed:
             error(f"{fail['trigger']} - {fail['stage']}: {fail['error']}")
 
+    log_operation("rollover_execute", {"triggers": triggers_count, "success_count": success_count})
     return success_count > 0
 
 
@@ -253,6 +255,7 @@ def sync_line_counts() -> None:
             warning(f"{result['failed']} files failed")
             for branch, mem_type, err_msg in result.get('failures', []):
                 error(f"{branch}.{mem_type}: {err_msg}")
+        log_operation("rollover_sync_lines", {"updated": result['updated'], "failed": result['failed']})
     else:
         error("Failed to sync line counts")
 
@@ -325,6 +328,8 @@ def show_status() -> None:
 
             console.print()
 
+    log_operation("rollover_status", {"branches_checked": stats['total_branches'], "files_ready": stats['files_ready']})
+
 
 def check_triggers() -> None:
     """
@@ -351,6 +356,7 @@ def check_triggers() -> None:
 
     if not triggers:
         console.print("[green]>[/green] No files need rollover")
+        log_operation("rollover_check", {"files_needing_rollover": 0})
         return
 
     console.print(f"[bold cyan]Found {len(triggers)} files ready for rollover:[/bold cyan]")
@@ -362,6 +368,7 @@ def check_triggers() -> None:
     console.print()
     console.print("[dim]Run 'drone @memory rollover' to process these files[/dim]")
     console.print()
+    log_operation("rollover_check", {"files_needing_rollover": len(triggers)})
 
 
 # =============================================================================

src/aipass/memory/apps/modules/search.py

@@ -28,6 +28,7 @@ from rich import box
 
 from aipass.prax import logger
 from aipass.cli.apps.modules import console, error, warning
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # =============================================================================
 # INFRASTRUCTURE SETUP
@@ -256,6 +257,7 @@ def show_search_results(
         ))
 
     console.print()
+    log_operation("search_query", {"query": query, "results": len(filtered_results)})
     return True
 
 

src/aipass/memory/apps/modules/symbolic.py

@@ -35,6 +35,7 @@ from typing import List, Dict, Any
 # Service imports
 from aipass.prax import logger
 from aipass.cli.apps.modules import console, header
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # Handler imports (domain-organized)
 from aipass.memory.apps.handlers.symbolic import extractor
@@ -980,6 +981,7 @@ def run_demo() -> None:
 
     console.print("[dim]Note: Run 'symbolic extract <file>' to use the real LLM pipeline[/dim]")
     console.print()
+    log_operation("symbolic_demo", {"success": True})
 
 
 def search_fragments_cli(args: List[str]) -> None:
@@ -1137,6 +1139,7 @@ def search_fragments_cli(args: List[str]) -> None:
 
     console.print()
     logger.info(f"[symbolic] Displayed {len(results)} fragment results")
+    log_operation("symbolic_fragments", {"query": query or "", "results": len(results)})
 
 
 def run_hook_test(args: List[str]) -> None:
@@ -1267,18 +1270,19 @@ def run_hook_test(args: List[str]) -> None:
     console.print(f"  [dim]Fragments surfaced:[/dim] {state.get('fragments_surfaced', 0)}")
     console.print(f"  [dim]Messages since last:[/dim] {state.get('messages_since_last', 0)}")
     console.print()
+    log_operation("symbolic_hook_test", {"surfaced": result.get('surfaced', False), "success": result.get('success', False)})
 
 
 def analyze_file(file_path: str) -> None:
     """Analyze a conversation JSON file"""
-    from aipass.memory.apps.handlers.json import json_handler
+    from aipass.memory.apps.handlers.json import memory_files
 
     path = Path(file_path)
     if not path.exists():
         console.print(f"[red]Error:[/red] File not found: {file_path}")
         return
 
-    read_result = json_handler.read_memory_file(path)
+    read_result = memory_files.read_memory_file(path)
     if not read_result.get('success'):
         console.print(f"[red]Error:[/red] {read_result.get('error', 'Failed to read JSON')}")
         return
@@ -1315,6 +1319,7 @@ def analyze_file(file_path: str) -> None:
         console.print(f"  [dim]Words:[/dim]    {meta.get('total_words', 0)}")
         console.print(f"  [dim]Depth:[/dim]    {meta.get('depth', 'unknown')}")
         console.print()
+        log_operation("symbolic_analyze", {"file": path.name, "messages": result['message_count']})
     else:
         console.print(f"[red]✗[/red] Analysis failed: {result.get('error', 'Unknown error')}")
 
@@ -1330,14 +1335,14 @@ def extract_file(file_path: str, source_branch: str | None = None) -> None:
         file_path: Path to JSON conversation file
         source_branch: Optional branch name tag for stored fragments
     """
-    from aipass.memory.apps.handlers.json import json_handler
+    from aipass.memory.apps.handlers.json import memory_files
 
     path = Path(file_path)
     if not path.exists():
         console.print(f"[red]Error:[/red] File not found: {file_path}")
         return
 
-    read_result = json_handler.read_memory_file(path)
+    read_result = memory_files.read_memory_file(path)
     if not read_result.get('success'):
         console.print(f"[red]Error:[/red] {read_result.get('error', 'Failed to read JSON')}")
         return
@@ -1380,6 +1385,8 @@ def extract_file(file_path: str, source_branch: str | None = None) -> None:
 
     console.print()
     logger.info(f"[symbolic] extract_file complete: {result}")
+    if result.get('success'):
+        log_operation("symbolic_extract", {"file": path.name, "added": result.get('added', 0), "updated": result.get('updated', 0)})
 
 
 # =============================================================================
@@ -1650,6 +1657,7 @@ def bootstrap_from_jsonl(max_sessions: int = 8) -> None:
         f"{total_added} added, {total_updated} updated, "
         f"{total_skipped} skipped, {total_errors} errors"
     )
+    log_operation("symbolic_bootstrap", {"sessions": processed_count, "added": total_added, "errors": total_errors})
 
 
 # =============================================================================

src/aipass/memory/apps/modules/templates.py

@@ -28,6 +28,7 @@ from rich import box
 
 from aipass.prax import logger
 from aipass.cli.apps.modules import console, error, warning
+from aipass.memory.apps.handlers.json.json_handler import log_operation
 
 # =============================================================================
 # INFRASTRUCTURE SETUP
@@ -37,7 +38,7 @@ from aipass.cli.apps.modules import console, error, warning
 from aipass.memory.apps.handlers.templates.pusher import push_templates, get_template_status
 from aipass.memory.apps.handlers.templates.differ import diff_template_vs_branch
 from aipass.memory.apps.handlers.templates.spawn_pusher import push_to_spawn_templates
-from aipass.memory.apps.handlers.json.json_handler import read_memory_file_data
+from aipass.memory.apps.handlers.json.memory_files import read_memory_file_data
 
 
 def _find_repo_root() -> Path:
@@ -286,6 +287,7 @@ def _display_push_results(result: dict, dry_run: bool) -> None:
         f"{result['branches_updated']}/{result['branches_scanned']} branches, "
         f"{result['files_modified']} files"
     )
+    log_operation("templates_push", {"branches_updated": result['branches_updated'], "files_modified": result['files_modified']})
     console.print()
 
 
@@ -424,6 +426,7 @@ def _display_diff_results(branch_name: str | None = None) -> None:
             console.print(f"[red]{total_errors} errors encountered[/red]")
 
     logger.info(f"[templates] Diff complete: {total_diffs} branches with diffs, {total_errors} errors")
+    log_operation("templates_diff", {"branches_compared": len(branches), "branches_with_diffs": total_diffs})
     console.print()
 
 
@@ -481,6 +484,7 @@ def _display_status(status: dict) -> None:
         console.print("[cyan]Branches pushed:[/cyan]    none")
 
     logger.info(f"[templates] Status checked - version: {version}, last push: {last_push}")
+    log_operation("templates_status", {"version": version, "branches_pushed": len(pushed)})
     console.print()
 
 

src/aipass/memory/config/.plans_processed.json

@@ -1,3 +1,11 @@
 {
-  "FPLAN-0025_build_status_board_per_branch_statusloca_2026-03-10.md": "2026-03-12T16:49:45.098626"
+  "FPLAN-0025_build_status_board_per_branch_statusloca_2026-03-10.md": "2026-03-12T16:49:45.098626",
+  "FPLAN-0033_cli_stderr_migration_phase_3_remaining_1_2026-03-13.md": "2026-03-17T17:03:38.975570",
+  "FPLAN-0040_phase_1_dashboard_cleanup_remove_devpuls_2026-03-14.md": "2026-03-17T17:03:49.794023",
+  "FPLAN-0049_memory_search_introspection_2026-03-15.md": "2026-03-17T17:04:00.894613",
+  "FPLAN-0041_migrate_init_projectpy_to_cli_branch_2026-03-14.md": "2026-03-17T17:04:11.390219",
+  "FPLAN-0032_cli_stderr_standardization_phase_1_add_e_2026-03-13.md": "2026-03-17T17:04:20.978306",
+  "FPLAN-0034_fplan_0033_wave_1_stderr_migration_api_s_2026-03-14.md": "2026-03-17T17:04:31.760541",
+  "FPLAN-0031_drone_stderr_and_error_propagation_inves_2026-03-13.md": "2026-03-17T17:04:42.782966",
+  "FPLAN-0047_memory_rollover_introspection_2026-03-15.md": "2026-03-17T17:04:54.278205"
 }

src/aipass/seedgo/apps/handlers/audit/branch_audit.py

@@ -9,11 +9,11 @@
 
 import importlib.util
 from pathlib import Path
-from typing import Dict, List
+from typing import Any, Dict, List
 from aipass.seedgo.apps.handlers.bypass import ignore_handler
 from aipass.seedgo.apps.handlers.json import json_handler
 
-def discover_checkers(pack_path: Path = None) -> Dict[str, object]:
+def discover_checkers(pack_path: Path | None = None) -> Dict[str, Any]:
     """Auto-discover all *_check.py modules from a pack directory.
 
     Args:
@@ -76,35 +76,14 @@ def _log_structure_post_checks(branch_path: Path) -> tuple:
       - ``system_logs/`` at repo root is managed by prax (runtime dispatch).
         Having many system logs and few local logs is *normal*.
       - ``logs/`` at branch root holds local-only logs. Flat placement is
-        fine -- hierarchical sub-directories are only expected when there
-        are enough logs to warrant organisation (>5).
+        fine — the standard does not prescribe internal organisation.
     """
     violations: list[dict] = []
     scores: list[int] = []
 
-    root_logs_dir = branch_path / "logs"
     in_dirs = [f for f in branch_path.rglob("*.log") if f.parent.name == "logs"]
 
-    # Check 1: If the branch has a logs/ directory, verify it is not empty
-    # and only flag flat placement when there are enough files to warrant
-    # hierarchical organisation.
-    if root_logs_dir.is_dir():
-        root_only = [f for f in in_dirs if f.parent == root_logs_dir]
-        has_subdirs = any(f.parent != root_logs_dir for f in in_dirs)
-        if not root_only and not has_subdirs:
-            # logs/ exists but is empty -- acceptable (no violation)
-            scores.append(100)
-        elif len(root_only) > 5 and not has_subdirs:
-            # Many logs piled at root with no subdirectories
-            scores.append(50)
-            violations.append({
-                "file": "(branch-level)", "path": str(root_logs_dir), "score": 50,
-                "issues": [f"{len(root_only)} logs at branch root with no sub-directories — consider hierarchical placement"],
-            })
-        else:
-            scores.append(100)
-
-    # Check 2: Verify system_logs/ exists when the branch produces logs.
+    # Check: Verify system_logs/ exists when the branch produces logs.
     # The two-tier model expects prax to dispatch runtime logs to
     # system_logs/.  A mismatch only matters when the branch has NO
     # system logs at all despite having local logs (potential prax
@@ -146,7 +125,7 @@ def _load_diagnostics_checker():
     return mod
 
 
-def audit_branch(branch: Dict[str, str], bypass_rules: list, pack_path: Path = None) -> Dict:
+def audit_branch(branch: Dict[str, str], bypass_rules: list, pack_path: Path | None = None) -> Dict:
     """Audit a branch for standards compliance. Returns backward-compatible dict."""
     entry_file, branch_path = branch["entry_file"], Path(branch["path"])
     checkers, all_files = discover_checkers(pack_path), _collect_py_files(branch_path)