Merge branch 'main' into fix/chromadb-version-constraint

.github/CODEOWNERS

@@ -0,0 +1,13 @@
+# Default owners for everything
+* @milla-jovovich @bensig @igorls
+
+# Core library
+mempalace/ @milla-jovovich @bensig
+
+# CI and workflows
+.github/ @bensig
+
+# Plugins and integrations
+.claude-plugin/ @bensig
+.codex-plugin/ @bensig
+integrations/ @bensig

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 3

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - run: pip install -e ".[dev]"
-      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80
+      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80 --durations=10
 
   test-windows:
     runs-on: windows-latest
@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: "3.9"
       - run: pip install -e ".[dev]"
-      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80
+      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80 --durations=10
 
   test-macos:
     runs-on: macos-latest
@@ -38,7 +38,7 @@ jobs:
         with:
           python-version: "3.9"
       - run: pip install -e ".[dev]"
-      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80
+      - run: python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing --cov-fail-under=80 --durations=10
   lint:
     runs-on: ubuntu-latest
     steps:

.gitignore

@@ -6,3 +6,30 @@ __pycache__/
 .pytest_cache/
 mempal.yaml
 .a5c/
+
+# Environment
+.env
+.env.*
+
+# OS
+.DS_Store
+Thumbs.db
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Coverage
+htmlcov/
+.coverage
+coverage.xml
+
+# Virtual environments
+.venv/
+venv/
+
+# ChromaDB local data
+*.sqlite3-journal

AGENTS.md

@@ -0,0 +1,78 @@
+# AGENTS.md
+
+> How to build, test, and contribute to MemPalace.
+
+## Setup
+
+```bash
+pip install -e ".[dev]"
+```
+
+## Commands
+
+```bash
+# Run tests
+python -m pytest tests/ -v --ignore=tests/benchmarks
+
+# Run tests with coverage
+python -m pytest tests/ -v --ignore=tests/benchmarks --cov=mempalace --cov-report=term-missing
+
+# Lint
+ruff check .
+
+# Format
+ruff format .
+
+# Format check (CI mode)
+ruff format --check .
+```
+
+## Project structure
+
+```
+mempalace/
+├── mcp_server.py        # MCP server — all read/write tools
+├── miner.py             # Project file miner
+├── convo_miner.py       # Conversation transcript miner
+├── searcher.py          # Semantic search
+├── knowledge_graph.py   # Temporal entity-relationship graph (SQLite)
+├── palace.py            # Shared palace operations (ChromaDB access)
+├── config.py            # Configuration + input validation
+├── normalize.py         # Transcript format detection + normalization
+├── cli.py               # CLI dispatcher
+├── dialect.py           # AAAK compression dialect
+├── palace_graph.py      # Room traversal + cross-wing tunnels
+├── hooks_cli.py         # Hook system for auto-save
+└── version.py           # Single source of truth for version
+```
+
+## Conventions
+
+- **Python style**: snake_case for functions/variables, PascalCase for classes
+- **Linter**: ruff with E/F/W rules
+- **Formatter**: ruff format, double quotes
+- **Commits**: conventional commits (`fix:`, `feat:`, `test:`, `docs:`, `ci:`)
+- **Tests**: `tests/test_*.py`, fixtures in `tests/conftest.py`
+- **Coverage**: 85% threshold (80% on Windows due to ChromaDB file lock cleanup)
+
+## Architecture
+
+```
+User → CLI / MCP Server → ChromaDB (vector store) + SQLite (knowledge graph)
+
+Palace structure:
+  WING (person/project)
+    └── ROOM (topic)
+          └── DRAWER (verbatim text chunk)
+
+Knowledge Graph:
+  ENTITY → PREDICATE → ENTITY (with valid_from / valid_to dates)
+```
+
+## Key files for common tasks
+
+- **Adding an MCP tool**: `mempalace/mcp_server.py` — add handler function + TOOLS dict entry
+- **Changing search**: `mempalace/searcher.py`
+- **Modifying mining**: `mempalace/miner.py` (project files) or `mempalace/convo_miner.py` (transcripts)
+- **Input validation**: `mempalace/config.py` — `sanitize_name()` / `sanitize_content()`
+- **Tests**: mirror source structure in `tests/test_<module>.py`

CONTRIBUTING.md

@@ -5,8 +5,11 @@ Thanks for wanting to help. MemPalace is open source and we welcome contribution
 ## Getting Started
 
 ```bash
-git clone https://github.com/milla-jovovich/mempalace.git
+# Fork the repo on GitHub first, then clone your fork
+git clone https://github.com/<your-username>/mempalace.git
 cd mempalace
+git remote add upstream https://github.com/milla-jovovich/mempalace.git
+
 pip install -e ".[dev]"    # installs with dev dependencies (pytest, build, twine)
 ```
 

README.md

@@ -84,6 +84,18 @@ Other memory systems try to fix this by letting AI decide what's worth rememberi
 
 ---
 
+## An important follow up note regarding fake MemPalace websites - April 11, 2026
+
+Several Community Members (#267, #326, #506) have pointed out there are fake MemPalace websites popping up, including ones with Malware.
+
+To be super clear, MemPalace *has no website* (at least for now), so anything claiming to be one is false.
+
+Thanks to our Community Members for letting us know about the problem.
+
+Stay safe out there.
+
+---
+
 ## Quick Start
 
 ```bash

docs/schema.sql

@@ -0,0 +1,36 @@
+-- MemPalace Knowledge Graph Schema
+-- SQLite database at ~/.mempalace/knowledge_graph.db
+
+CREATE TABLE IF NOT EXISTS entities (
+    id TEXT PRIMARY KEY,
+    name TEXT NOT NULL,
+    type TEXT DEFAULT 'unknown',
+    properties TEXT DEFAULT '{}'
+);
+
+CREATE TABLE IF NOT EXISTS triples (
+    id TEXT PRIMARY KEY,
+    subject TEXT NOT NULL,
+    predicate TEXT NOT NULL,
+    object TEXT NOT NULL,
+    valid_from TEXT,
+    valid_to TEXT,
+    confidence REAL DEFAULT 1.0,
+    source_closet TEXT,
+    source_file TEXT
+);
+
+CREATE TABLE IF NOT EXISTS attributes (
+    entity_id TEXT NOT NULL,
+    key TEXT NOT NULL,
+    value TEXT,
+    valid_from TEXT,
+    valid_to TEXT,
+    PRIMARY KEY (entity_id, key, valid_from)
+);
+
+-- Indexes
+CREATE INDEX IF NOT EXISTS idx_triples_subject ON triples(subject);
+CREATE INDEX IF NOT EXISTS idx_triples_object ON triples(object);
+CREATE INDEX IF NOT EXISTS idx_triples_predicate ON triples(predicate);
+CREATE INDEX IF NOT EXISTS idx_triples_valid ON triples(valid_from, valid_to);

hooks/mempal_precompact_hook.sh

@@ -72,6 +72,6 @@ fi
 cat << 'HOOKJSON'
 {
   "decision": "block",
-  "reason": "COMPACTION IMMINENT. Save ALL topics, decisions, quotes, code, and important context from this session to your memory system. Be thorough — after compaction, detailed context will be lost. Organize into appropriate categories. Use verbatim quotes where possible. Save everything, then allow compaction to proceed."
+  "reason": "COMPACTION IMMINENT (MemPalace). Save ALL session content before context is lost:\n1. mempalace_diary_write — thorough AAAK-compressed session summary\n2. mempalace_add_drawer — ALL verbatim quotes, decisions, code, context\n3. mempalace_kg_add — entity relationships (optional)\nBe thorough — after compaction, detailed context will be lost. Do NOT write to Claude Code's native auto-memory (.md files). Save everything to MemPalace, then allow compaction to proceed."
 }
 HOOKJSON

hooks/mempal_save_hook.sh

@@ -145,7 +145,7 @@ if [ "$SINCE_LAST" -ge "$SAVE_INTERVAL" ] && [ "$EXCHANGE_COUNT" -gt 0 ]; then
     cat << 'HOOKJSON'
 {
   "decision": "block",
-  "reason": "AUTO-SAVE checkpoint. Save key topics, decisions, quotes, and code from this session to your memory system. Organize into appropriate categories. Use verbatim quotes where possible. Continue conversation after saving."
+  "reason": "AUTO-SAVE checkpoint (MemPalace). Save this session's key content:\n1. mempalace_diary_write — AAAK-compressed session summary\n2. mempalace_add_drawer — verbatim quotes, decisions, code snippets\n3. mempalace_kg_add — entity relationships (optional)\nDo NOT write to Claude Code's native auto-memory (.md files). Continue conversation after saving."
 }
 HOOKJSON
 else

mempalace/cli.py

@@ -150,6 +150,14 @@ def cmd_split(args):
         sys.argv = old_argv
 
 
+def cmd_migrate(args):
+    """Migrate palace from a different ChromaDB version."""
+    from .migrate import migrate
+
+    palace_path = os.path.expanduser(args.palace) if args.palace else MempalaceConfig().palace_path
+    migrate(palace_path=palace_path, dry_run=args.dry_run)
+
+
 def cmd_status(args):
     from .miner import status
 
@@ -531,6 +539,17 @@ def main():
     )
 
     # status
+    # migrate
+    p_migrate = sub.add_parser(
+        "migrate",
+        help="Migrate palace from a different ChromaDB version (fixes 3.0.0 → 3.1.0 upgrade)",
+    )
+    p_migrate.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Show what would be migrated without changing anything",
+    )
+
     sub.add_parser("status", help="Show what's been filed")
 
     args = parser.parse_args()
@@ -565,6 +584,7 @@ def main():
         "compress": cmd_compress,
         "wake-up": cmd_wakeup,
         "repair": cmd_repair,
+        "migrate": cmd_migrate,
         "status": cmd_status,
     }
     dispatch[args.command](args)

mempalace/convo_miner.py

@@ -334,7 +334,7 @@ def mine_convos(
                 room_counts[chunk_room] += 1
             drawer_id = f"drawer_{wing}_{chunk_room}_{hashlib.sha256((source_file + str(chunk['chunk_index'])).encode()).hexdigest()[:24]}"
             try:
-                collection.add(
+                collection.upsert(
                     documents=[chunk["content"]],
                     ids=[drawer_id],
                     metadatas=[

mempalace/dedup.py

@@ -0,0 +1,239 @@
+"""
+dedup.py — Detect and remove near-duplicate drawers
+====================================================
+
+When the same files are mined multiple times, near-identical drawers
+accumulate. This module finds drawers from the same source_file that
+are too similar (cosine distance < threshold), keeps the longest/richest
+version, and deletes the rest.
+
+No API calls — uses ChromaDB's built-in embedding similarity.
+
+Usage (standalone):
+    python -m mempalace.dedup                          # dedup all
+    python -m mempalace.dedup --dry-run                # preview only
+    python -m mempalace.dedup --threshold 0.10         # stricter (near-identical only)
+    python -m mempalace.dedup --threshold 0.35         # looser (catches paraphrased content)
+    python -m mempalace.dedup --wing my_project        # scope to one wing
+    python -m mempalace.dedup --stats                  # stats only
+    python -m mempalace.dedup --source "my_project"    # filter by source
+
+Usage (from CLI):
+    mempalace dedup [--dry-run] [--threshold 0.15] [--stats]
+"""
+
+import argparse
+import os
+import time
+from collections import defaultdict
+
+import chromadb
+
+
+COLLECTION_NAME = "mempalace_drawers"
+# Cosine DISTANCE threshold (not similarity). Lower = stricter.
+# 0.15 = ~85% cosine similarity — catches near-identical chunks.
+# For looser dedup of paraphrased content, try 0.3–0.4.
+DEFAULT_THRESHOLD = 0.15
+MIN_DRAWERS_TO_CHECK = 5
+
+
+def _get_palace_path():
+    """Resolve palace path from config."""
+    try:
+        from .config import MempalaceConfig
+
+        return MempalaceConfig().palace_path
+    except Exception:
+        return os.path.join(os.path.expanduser("~"), ".mempalace", "palace")
+
+
+def get_source_groups(col, min_count=MIN_DRAWERS_TO_CHECK, source_pattern=None, wing=None):
+    """Group drawers by source_file, return groups with min_count+ entries.
+
+    If wing is specified, only considers drawers in that wing. This catches
+    cross-wing duplicates when the same source was mined into multiple wings.
+    """
+    total = col.count()
+    groups = defaultdict(list)
+
+    offset = 0
+    batch_size = 1000
+    while offset < total:
+        kwargs = {"limit": batch_size, "offset": offset, "include": ["metadatas"]}
+        if wing:
+            kwargs["where"] = {"wing": wing}
+        batch = col.get(**kwargs)
+        if not batch["ids"]:
+            break
+        for did, meta in zip(batch["ids"], batch["metadatas"]):
+            src = meta.get("source_file", "unknown")
+            if source_pattern and source_pattern.lower() not in src.lower():
+                continue
+            groups[src].append(did)
+        offset += len(batch["ids"])
+
+    return {src: ids for src, ids in groups.items() if len(ids) >= min_count}
+
+
+def dedup_source_group(col, drawer_ids, threshold=DEFAULT_THRESHOLD, dry_run=True):
+    """Dedup drawers within one source_file group.
+
+    Greedy: sort by doc length (longest first), keep if not too similar
+    to any already-kept drawer. Returns (kept_ids, deleted_ids).
+    """
+    data = col.get(ids=drawer_ids, include=["documents", "metadatas"])
+    items = list(zip(data["ids"], data["documents"], data["metadatas"]))
+    items.sort(key=lambda x: len(x[1] or ""), reverse=True)
+
+    kept = []
+    to_delete = []
+
+    for did, doc, meta in items:
+        if not doc or len(doc) < 20:
+            to_delete.append(did)
+            continue
+
+        if not kept:
+            kept.append((did, doc))
+            continue
+
+        try:
+            results = col.query(
+                query_texts=[doc],
+                n_results=min(len(kept), 5),
+                include=["distances"],
+            )
+            dists = results["distances"][0] if results["distances"] else []
+            kept_ids_set = {k[0] for k in kept}
+
+            is_dup = False
+            for rid, dist in zip(results["ids"][0], dists):
+                if rid in kept_ids_set and dist < threshold:
+                    is_dup = True
+                    break
+
+            if is_dup:
+                to_delete.append(did)
+            else:
+                kept.append((did, doc))
+        except Exception:
+            kept.append((did, doc))
+
+    if to_delete and not dry_run:
+        for i in range(0, len(to_delete), 500):
+            col.delete(ids=to_delete[i : i + 500])
+
+    return [k[0] for k in kept], to_delete
+
+
+def show_stats(palace_path=None):
+    """Show duplication statistics without making changes."""
+    palace_path = palace_path or _get_palace_path()
+    client = chromadb.PersistentClient(path=palace_path)
+    col = client.get_collection(COLLECTION_NAME)
+
+    groups = get_source_groups(col)
+
+    total_drawers = sum(len(ids) for ids in groups.values())
+    print(f"\n  Sources with {MIN_DRAWERS_TO_CHECK}+ drawers: {len(groups)}")
+    print(f"  Total drawers in those sources: {total_drawers:,}")
+
+    print("\n  Top 15 by drawer count:")
+    sorted_groups = sorted(groups.items(), key=lambda x: len(x[1]), reverse=True)
+    for src, ids in sorted_groups[:15]:
+        print(f"    {len(ids):4d}  {src[:65]}")
+
+    estimated_dups = sum(int(len(ids) * 0.4) for ids in groups.values() if len(ids) > 20)
+    print(f"\n  Estimated duplicates (groups > 20): ~{estimated_dups:,}")
+
+
+def dedup_palace(
+    palace_path=None,
+    threshold=DEFAULT_THRESHOLD,
+    dry_run=True,
+    source_pattern=None,
+    min_count=MIN_DRAWERS_TO_CHECK,
+    wing=None,
+):
+    """Main entry point: deduplicate near-identical drawers across the palace."""
+    palace_path = palace_path or _get_palace_path()
+
+    print(f"\n{'=' * 55}")
+    print("  MemPalace Deduplicator")
+    print(f"{'=' * 55}")
+
+    client = chromadb.PersistentClient(path=palace_path)
+    col = client.get_collection(COLLECTION_NAME)
+
+    print(f"  Palace: {palace_path}")
+    print(f"  Drawers: {col.count():,}")
+    print(f"  Threshold: {threshold}")
+    print(f"  Mode: {'DRY RUN' if dry_run else 'LIVE'}")
+    print(f"{'─' * 55}")
+
+    if wing:
+        print(f"  Wing: {wing}")
+    groups = get_source_groups(col, min_count, source_pattern, wing=wing)
+    print(f"\n  Sources to check: {len(groups)}")
+
+    t0 = time.time()
+    total_kept = 0
+    total_deleted = 0
+
+    sorted_groups = sorted(groups.items(), key=lambda x: len(x[1]), reverse=True)
+
+    for i, (src, drawer_ids) in enumerate(sorted_groups):
+        kept, deleted = dedup_source_group(col, drawer_ids, threshold, dry_run)
+        total_kept += len(kept)
+        total_deleted += len(deleted)
+
+        if deleted:
+            print(
+                f"  [{i + 1:3d}/{len(groups)}] "
+                f"{src[:50]:50s} {len(drawer_ids):4d} → {len(kept):4d}  "
+                f"(-{len(deleted)})"
+            )
+
+    elapsed = time.time() - t0
+
+    print(f"\n{'─' * 55}")
+    print(f"  Done in {elapsed:.1f}s")
+    print(
+        f"  Drawers: {total_kept + total_deleted:,} → {total_kept:,}  (-{total_deleted:,} removed)"
+    )
+    print(f"  Palace after: {col.count():,} drawers")
+
+    if dry_run:
+        print("\n  [DRY RUN] No changes written. Re-run without --dry-run to apply.")
+
+    print(f"{'=' * 55}\n")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Deduplicate near-identical drawers")
+    parser.add_argument("--palace", default=None, help="Palace directory path")
+    parser.add_argument(
+        "--threshold",
+        type=float,
+        default=DEFAULT_THRESHOLD,
+        help=f"Cosine distance threshold (default: {DEFAULT_THRESHOLD})",
+    )
+    parser.add_argument("--dry-run", action="store_true", help="Preview without deleting")
+    parser.add_argument("--stats", action="store_true", help="Show stats only")
+    parser.add_argument("--wing", default=None, help="Scope dedup to a single wing")
+    parser.add_argument("--source", default=None, help="Filter by source file pattern")
+    args = parser.parse_args()
+
+    path = os.path.expanduser(args.palace) if args.palace else None
+
+    if args.stats:
+        show_stats(palace_path=path)
+    else:
+        dedup_palace(
+            palace_path=path,
+            threshold=args.threshold,
+            dry_run=args.dry_run,
+            source_pattern=args.source,
+            wing=args.wing,
+        )

mempalace/hooks_cli.py

@@ -18,18 +18,22 @@ SAVE_INTERVAL = 15
 STATE_DIR = Path.home() / ".mempalace" / "hook_state"
 
 STOP_BLOCK_REASON = (
-    "AUTO-SAVE checkpoint. Save key topics, decisions, quotes, and code "
-    "from this session to your memory system. Organize into appropriate "
-    "categories. Use verbatim quotes where possible. Continue conversation "
-    "after saving."
+    "AUTO-SAVE checkpoint (MemPalace). Save this session's key content:\n"
+    "1. mempalace_diary_write — AAAK-compressed session summary\n"
+    "2. mempalace_add_drawer — verbatim quotes, decisions, code snippets\n"
+    "3. mempalace_kg_add — entity relationships (optional)\n"
+    "Do NOT write to Claude Code's native auto-memory (.md files). "
+    "Continue conversation after saving."
 )
 
 PRECOMPACT_BLOCK_REASON = (
-    "COMPACTION IMMINENT. Save ALL topics, decisions, quotes, code, and "
-    "important context from this session to your memory system. Be thorough "
-    "\u2014 after compaction, detailed context will be lost. Organize into "
-    "appropriate categories. Use verbatim quotes where possible. Save "
-    "everything, then allow compaction to proceed."
+    "COMPACTION IMMINENT (MemPalace). Save ALL session content before context is lost:\n"
+    "1. mempalace_diary_write — thorough AAAK-compressed session summary\n"
+    "2. mempalace_add_drawer — ALL verbatim quotes, decisions, code, context\n"
+    "3. mempalace_kg_add — entity relationships (optional)\n"
+    "Be thorough \u2014 after compaction, detailed context will be lost. "
+    "Do NOT write to Claude Code's native auto-memory (.md files). "
+    "Save everything to MemPalace, then allow compaction to proceed."
 )
 
 
@@ -63,6 +67,14 @@ def _count_human_messages(transcript_path: str) -> int:
                             if "<command-message>" in text:
                                 continue
                         count += 1
+                    # Also handle Codex CLI transcript format
+                    # {"type": "event_msg", "payload": {"type": "user_message", "message": "..."}}
+                    elif entry.get("type") == "event_msg":
+                        payload = entry.get("payload", {})
+                        if isinstance(payload, dict) and payload.get("type") == "user_message":
+                            msg_text = payload.get("message", "")
+                            if isinstance(msg_text, str) and "<command-message>" not in msg_text:
+                                count += 1
                 except (json.JSONDecodeError, AttributeError):
                     pass
     except OSError:

mempalace/mcp_server.py

@@ -28,6 +28,7 @@ from pathlib import Path
 
 from .config import MempalaceConfig, sanitize_name, sanitize_content
 from .version import __version__
+from .query_sanitizer import sanitize_query
 from .searcher import search_memories
 from .palace_graph import traverse, find_tunnels, graph_stats
 import chromadb
@@ -143,16 +144,25 @@ def tool_status():
     count = col.count()
     wings = {}
     rooms = {}
-    try:
-        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
-        for m in all_meta:
-            w = m.get("wing", "unknown")
-            r = m.get("room", "unknown")
-            wings[w] = wings.get(w, 0) + 1
-            rooms[r] = rooms.get(r, 0) + 1
-    except Exception:
-        pass
-    return {
+    batch_size = 5000
+    offset = 0
+    error_info = None
+    while True:
+        try:
+            batch = col.get(include=["metadatas"], limit=batch_size, offset=offset)
+            rows = batch["metadatas"]
+            for m in rows:
+                w = m.get("wing", "unknown")
+                r = m.get("room", "unknown")
+                wings[w] = wings.get(w, 0) + 1
+                rooms[r] = rooms.get(r, 0) + 1
+            offset += len(rows)
+            if len(rows) < batch_size:
+                break
+        except Exception as e:
+            error_info = f"Partial result, failed at offset {offset}: {str(e)}"
+            break
+    result = {
         "total_drawers": count,
         "wings": wings,
         "rooms": rooms,
@@ -160,6 +170,10 @@ def tool_status():
         "protocol": PALACE_PROTOCOL,
         "aaak_dialect": AAAK_SPEC,
     }
+    if error_info:
+        result["error"] = error_info
+        result["partial"] = True
+    return result
 
 
 # ── AAAK Dialect Spec ─────────────────────────────────────────────────────────
@@ -200,13 +214,28 @@ def tool_list_wings():
     if not col:
         return _no_palace()
     wings = {}
+    batch_size = 5000
+    offset = 0
     try:
-        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
-        for m in all_meta:
-            w = m.get("wing", "unknown")
-            wings[w] = wings.get(w, 0) + 1
-    except Exception:
-        pass
+        col.count()  # verify collection is accessible
+    except Exception as e:
+        return {"wings": {}, "error": str(e)}
+    while True:
+        try:
+            batch = col.get(include=["metadatas"], limit=batch_size, offset=offset)
+            rows = batch["metadatas"]
+            for m in rows:
+                w = m.get("wing", "unknown")
+                wings[w] = wings.get(w, 0) + 1
+            offset += len(rows)
+            if len(rows) < batch_size:
+                break
+        except Exception as e:
+            return {
+                "wings": wings,
+                "error": f"Partial result, failed at offset {offset}: {str(e)}",
+                "partial": True,
+            }
     return {"wings": wings}
 
 
@@ -215,16 +244,33 @@ def tool_list_rooms(wing: str = None):
     if not col:
         return _no_palace()
     rooms = {}
+    batch_size = 5000
+    offset = 0
+    where = {"wing": wing} if wing else None
     try:
-        kwargs = {"include": ["metadatas"], "limit": 10000}
-        if wing:
-            kwargs["where"] = {"wing": wing}
-        all_meta = col.get(**kwargs)["metadatas"]
-        for m in all_meta:
-            r = m.get("room", "unknown")
-            rooms[r] = rooms.get(r, 0) + 1
-    except Exception:
-        pass
+        col.count()  # verify collection is accessible
+    except Exception as e:
+        return {"wing": wing or "all", "rooms": {}, "error": str(e)}
+    while True:
+        try:
+            kwargs = {"include": ["metadatas"], "limit": batch_size, "offset": offset}
+            if where:
+                kwargs["where"] = where
+            batch = col.get(**kwargs)
+            rows = batch["metadatas"]
+            for m in rows:
+                r = m.get("room", "unknown")
+                rooms[r] = rooms.get(r, 0) + 1
+            offset += len(rows)
+            if len(rows) < batch_size:
+                break
+        except Exception as e:
+            return {
+                "wing": wing or "all",
+                "rooms": rooms,
+                "error": f"Partial result, failed at offset {offset}: {str(e)}",
+                "partial": True,
+            }
     return {"wing": wing or "all", "rooms": rooms}
 
 
@@ -233,27 +279,58 @@ def tool_get_taxonomy():
     if not col:
         return _no_palace()
     taxonomy = {}
+    batch_size = 5000
+    offset = 0
     try:
-        all_meta = col.get(include=["metadatas"], limit=10000)["metadatas"]
-        for m in all_meta:
-            w = m.get("wing", "unknown")
-            r = m.get("room", "unknown")
-            if w not in taxonomy:
-                taxonomy[w] = {}
-            taxonomy[w][r] = taxonomy[w].get(r, 0) + 1
-    except Exception:
-        pass
+        col.count()  # verify collection is accessible
+    except Exception as e:
+        return {"taxonomy": {}, "error": str(e)}
+    while True:
+        try:
+            batch = col.get(include=["metadatas"], limit=batch_size, offset=offset)
+            rows = batch["metadatas"]
+            for m in rows:
+                w = m.get("wing", "unknown")
+                r = m.get("room", "unknown")
+                if w not in taxonomy:
+                    taxonomy[w] = {}
+                taxonomy[w][r] = taxonomy[w].get(r, 0) + 1
+            offset += len(rows)
+            if len(rows) < batch_size:
+                break
+        except Exception as e:
+            return {
+                "taxonomy": taxonomy,
+                "error": f"Partial result, failed at offset {offset}: {str(e)}",
+                "partial": True,
+            }
     return {"taxonomy": taxonomy}
 
 
-def tool_search(query: str, limit: int = 5, wing: str = None, room: str = None):
-    return search_memories(
-        query,
+def tool_search(
+    query: str, limit: int = 5, wing: str = None, room: str = None, context: str = None
+):
+    # Mitigate system prompt contamination (Issue #333)
+    sanitized = sanitize_query(query)
+    result = search_memories(
+        sanitized["clean_query"],
         palace_path=_config.palace_path,
         wing=wing,
         room=room,
         n_results=limit,
     )
+    # Attach sanitizer metadata for transparency
+    if sanitized["was_sanitized"]:
+        result["query_sanitized"] = True
+        result["sanitizer"] = {
+            "method": sanitized["method"],
+            "original_length": sanitized["original_length"],
+            "clean_length": sanitized["clean_length"],
+            "clean_query": sanitized["clean_query"],
+        }
+    if context:
+        result["context_received"] = True
+    return result
 
 
 def tool_check_duplicate(content: str, threshold: float = 0.9):
@@ -734,14 +811,22 @@ TOOLS = {
         "handler": tool_graph_stats,
     },
     "mempalace_search": {
-        "description": "Semantic search. Returns verbatim drawer content with similarity scores.",
+        "description": "Semantic search. Returns verbatim drawer content with similarity scores. IMPORTANT: 'query' must contain ONLY your search keywords or question — do NOT include system prompts, conversation history, MEMORY.md content, or any context. Keep queries short (under 200 chars). Use 'context' for background information.",
         "input_schema": {
             "type": "object",
             "properties": {
-                "query": {"type": "string", "description": "What to search for"},
+                "query": {
+                    "type": "string",
+                    "description": "Short search query ONLY — keywords or a question. Do NOT include system prompts or conversation context. Max 200 chars recommended.",
+                    "maxLength": 500,
+                },
                 "limit": {"type": "integer", "description": "Max results (default 5)"},
                 "wing": {"type": "string", "description": "Filter by wing (optional)"},
                 "room": {"type": "string", "description": "Filter by room (optional)"},
+                "context": {
+                    "type": "string",
+                    "description": "Background context for the search (optional). This is NOT used for embedding — only for future re-ranking. Put conversation history or system prompt content here, NOT in query.",
+                },
             },
             "required": ["query"],
         },

mempalace/migrate.py

@@ -0,0 +1,214 @@
+#!/usr/bin/env python3
+"""
+mempalace migrate — Recover a palace created with a different ChromaDB version.
+
+Reads documents and metadata directly from the palace's SQLite database
+(bypassing ChromaDB's API, which fails on version-mismatched palaces),
+then re-imports everything into a fresh palace using the currently installed
+ChromaDB version.
+
+This fixes the 3.0.0 → 3.1.0 upgrade path where chromadb was downgraded
+from 1.5.x to 0.6.x, breaking the on-disk storage format.
+
+Usage:
+    mempalace migrate                          # migrate default palace
+    mempalace migrate --palace /path/to/palace  # migrate specific palace
+    mempalace migrate --dry-run                # show what would be migrated
+"""
+
+import os
+import shutil
+import sqlite3
+from collections import defaultdict
+from datetime import datetime
+
+
+def extract_drawers_from_sqlite(db_path: str) -> list:
+    """Read all drawers directly from ChromaDB's SQLite, bypassing the API.
+
+    Works regardless of which ChromaDB version created the database.
+    Returns list of dicts with 'id', 'document', and 'metadata' keys.
+    """
+    conn = sqlite3.connect(db_path)
+    conn.row_factory = sqlite3.Row
+
+    # Get all embedding IDs and their documents
+    rows = conn.execute("""
+        SELECT e.embedding_id,
+               MAX(CASE WHEN em.key = 'chroma:document' THEN em.string_value END) as document
+        FROM embeddings e
+        JOIN embedding_metadata em ON em.id = e.id
+        GROUP BY e.embedding_id
+    """).fetchall()
+
+    drawers = []
+    for row in rows:
+        embedding_id = row["embedding_id"]
+        document = row["document"]
+        if not document:
+            continue
+
+        # Get metadata for this embedding
+        meta_rows = conn.execute(
+            """
+            SELECT em.key, em.string_value, em.int_value, em.float_value, em.bool_value
+            FROM embedding_metadata em
+            JOIN embeddings e ON e.id = em.id
+            WHERE e.embedding_id = ?
+              AND em.key NOT LIKE 'chroma:%'
+        """,
+            (embedding_id,),
+        ).fetchall()
+
+        metadata = {}
+        for mr in meta_rows:
+            key = mr["key"]
+            if mr["string_value"] is not None:
+                metadata[key] = mr["string_value"]
+            elif mr["int_value"] is not None:
+                metadata[key] = mr["int_value"]
+            elif mr["float_value"] is not None:
+                metadata[key] = mr["float_value"]
+            elif mr["bool_value"] is not None:
+                metadata[key] = bool(mr["bool_value"])
+
+        drawers.append(
+            {
+                "id": embedding_id,
+                "document": document,
+                "metadata": metadata,
+            }
+        )
+
+    conn.close()
+    return drawers
+
+
+def detect_chromadb_version(db_path: str) -> str:
+    """Detect which ChromaDB version created the database by checking schema."""
+    conn = sqlite3.connect(db_path)
+    try:
+        # 1.x has schema_str column in collections table
+        cols = [r[1] for r in conn.execute("PRAGMA table_info(collections)").fetchall()]
+        if "schema_str" in cols:
+            return "1.x"
+        # 0.6.x has embeddings_queue but no schema_str
+        tables = [
+            r[0]
+            for r in conn.execute("SELECT name FROM sqlite_master WHERE type='table'").fetchall()
+        ]
+        if "embeddings_queue" in tables:
+            return "0.6.x"
+        return "unknown"
+    finally:
+        conn.close()
+
+
+def migrate(palace_path: str, dry_run: bool = False):
+    """Migrate a palace to the currently installed ChromaDB version."""
+    import chromadb
+
+    palace_path = os.path.expanduser(palace_path)
+    db_path = os.path.join(palace_path, "chroma.sqlite3")
+
+    if not os.path.isfile(db_path):
+        print(f"\n  No palace database found at {db_path}")
+        return False
+
+    print(f"\n{'=' * 60}")
+    print("  MemPalace Migrate")
+    print(f"{'=' * 60}\n")
+    print(f"  Palace:    {palace_path}")
+    print(f"  Database:  {db_path}")
+    print(f"  DB size:   {os.path.getsize(db_path) / 1024 / 1024:.1f} MB")
+
+    # Detect version
+    source_version = detect_chromadb_version(db_path)
+    print(f"  Source:    ChromaDB {source_version}")
+    print(f"  Target:    ChromaDB {chromadb.__version__}")
+
+    # Try reading with current chromadb first
+    try:
+        client = chromadb.PersistentClient(path=palace_path)
+        col = client.get_collection("mempalace_drawers")
+        count = col.count()
+        print(f"\n  Palace is already readable by chromadb {chromadb.__version__}.")
+        print(f"  {count} drawers found. No migration needed.")
+        return True
+    except Exception:
+        print(f"\n  Palace is NOT readable by chromadb {chromadb.__version__}.")
+        print("  Extracting from SQLite directly...")
+
+    # Extract all drawers via raw SQL
+    drawers = extract_drawers_from_sqlite(db_path)
+    print(f"  Extracted {len(drawers)} drawers from SQLite")
+
+    if not drawers:
+        print("  Nothing to migrate.")
+        return True
+
+    # Show summary
+    wings = defaultdict(lambda: defaultdict(int))
+    for d in drawers:
+        w = d["metadata"].get("wing", "?")
+        r = d["metadata"].get("room", "?")
+        wings[w][r] += 1
+
+    print("\n  Summary:")
+    for wing, rooms in sorted(wings.items()):
+        total = sum(rooms.values())
+        print(f"    WING: {wing} ({total} drawers)")
+        for room, count in sorted(rooms.items(), key=lambda x: -x[1]):
+            print(f"      ROOM: {room:30} {count:5}")
+
+    if dry_run:
+        print("\n  DRY RUN — no changes made.")
+        print(f"  Would migrate {len(drawers)} drawers.")
+        return True
+
+    # Backup the old palace
+    timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+    backup_path = f"{palace_path}.pre-migrate.{timestamp}"
+    print(f"\n  Backing up to {backup_path}...")
+    shutil.copytree(palace_path, backup_path)
+
+    # Build fresh palace in a temp directory (avoids chromadb reading old state)
+    import tempfile
+
+    temp_palace = tempfile.mkdtemp(prefix="mempalace_migrate_")
+    print(f"  Creating fresh palace in {temp_palace}...")
+    client = chromadb.PersistentClient(path=temp_palace)
+    col = client.get_or_create_collection("mempalace_drawers")
+
+    # Re-import in batches
+    batch_size = 500
+    imported = 0
+    for i in range(0, len(drawers), batch_size):
+        batch = drawers[i : i + batch_size]
+        col.add(
+            ids=[d["id"] for d in batch],
+            documents=[d["document"] for d in batch],
+            metadatas=[d["metadata"] for d in batch],
+        )
+        imported += len(batch)
+        print(f"  Imported {imported}/{len(drawers)} drawers...")
+
+    # Verify before swapping
+    final_count = col.count()
+    del col
+    del client
+
+    # Swap: remove old palace, move new one into place
+    print("  Swapping old palace for migrated version...")
+    shutil.rmtree(palace_path)
+    shutil.move(temp_palace, palace_path)
+
+    print("\n  Migration complete.")
+    print(f"  Drawers migrated: {final_count}")
+    print(f"  Backup at: {backup_path}")
+
+    if final_count != len(drawers):
+        print(f"  WARNING: Expected {len(drawers)}, got {final_count}")
+
+    print(f"\n{'=' * 60}\n")
+    return True

mempalace/miner.py

@@ -436,6 +436,16 @@ def process_file(
         print(f"    [DRY RUN] {filepath.name} → room:{room} ({len(chunks)} drawers)")
         return len(chunks), room
 
+    # Purge stale drawers for this file before re-inserting the fresh chunks.
+    # Converts modified-file re-mines from upsert-over-existing-IDs (which hits
+    # hnswlib's thread-unsafe updatePoint path and can segfault on macOS ARM
+    # with chromadb 0.6.3) into a clean delete+insert, bypassing the update
+    # path entirely.
+    try:
+        collection.delete(where={"source_file": source_file})
+    except Exception:
+        pass
+
     drawers_added = 0
     for chunk in chunks:
         added = add_drawer(

mempalace/query_sanitizer.py

@@ -0,0 +1,157 @@
+"""
+query_sanitizer.py — Mitigate system prompt contamination in search queries.
+
+Problem: AI agents sometimes prepend system prompts (2000+ chars) to search queries.
+Embedding models represent the concatenated string as a single vector where the
+system prompt overwhelms the actual question (typically 10-50 chars), causing
+near-total retrieval failure (89.8% → 1.0% R@10). See Issue #333.
+
+Approach: "Mitigation" (減災) — not perfect prevention, but prevents the cliff.
+
+Expected recovery:
+  Step 1 passthrough (≤200 chars)     → no degradation, ~89.8%
+  Step 2 question extraction (？found) → near-full recovery, ~85-89%
+  Step 3 tail sentence extraction      → moderate recovery, ~80-89%
+  Step 4 tail truncation (fallback)    → minimum viable, ~70-80%
+
+  Without sanitizer: 1.0% (catastrophic silent failure)
+  Worst case with sanitizer: ~70-80% (survivable)
+"""
+
+import re
+import logging
+
+logger = logging.getLogger("mempalace_mcp")
+
+# --- Constants ---
+MAX_QUERY_LENGTH = 500  # Above this, system prompt almost certainly dominates
+SAFE_QUERY_LENGTH = 200  # Below this, query is almost certainly clean
+MIN_QUERY_LENGTH = 10  # Extracted result shorter than this = extraction failed
+
+# Sentence splitter: split on . ! ? (including fullwidth) and newlines
+_SENTENCE_SPLIT = re.compile(r"[.!?。！？\n]+")
+
+# Question detector: ends with ? or ？ (possibly with trailing whitespace/quotes)
+_QUESTION_MARK = re.compile(r'[?？]\s*["\']?\s*$')
+
+
+def sanitize_query(raw_query: str) -> dict:
+    """
+    Extract the actual search intent from a potentially contaminated query.
+
+    Args:
+        raw_query: The raw query string from the AI agent, possibly containing
+                   system prompt content prepended to the actual question.
+
+    Returns:
+        dict with keys:
+            clean_query (str): The sanitized query to use for embedding search
+            was_sanitized (bool): Whether any sanitization was applied
+            original_length (int): Length of the raw input
+            clean_length (int): Length of the sanitized output
+            method (str): Which extraction method was used
+                - "passthrough": query was short enough, no action taken
+                - "question_extraction": found and extracted a question sentence
+                - "tail_sentence": extracted the last meaningful sentence
+                - "tail_truncation": fallback — took the last MAX_QUERY_LENGTH chars
+    """
+    if not raw_query or not raw_query.strip():
+        return {
+            "clean_query": raw_query or "",
+            "was_sanitized": False,
+            "original_length": len(raw_query) if raw_query else 0,
+            "clean_length": len(raw_query) if raw_query else 0,
+            "method": "passthrough",
+        }
+
+    raw_query = raw_query.strip()
+    original_length = len(raw_query)
+
+    # --- Step 1: Short query passthrough ---
+    if original_length <= SAFE_QUERY_LENGTH:
+        return {
+            "clean_query": raw_query,
+            "was_sanitized": False,
+            "original_length": original_length,
+            "clean_length": original_length,
+            "method": "passthrough",
+        }
+
+    # --- Step 2: Question extraction ---
+    # Split into sentences and find ones ending with ?
+    sentences = [s.strip() for s in _SENTENCE_SPLIT.split(raw_query) if s.strip()]
+
+    # Also split on newlines to catch questions on their own line
+    all_segments = []
+    for s in raw_query.split("\n"):
+        s = s.strip()
+        if s:
+            all_segments.append(s)
+
+    # Look for question marks in segments (prefer later ones = more likely the actual query)
+    question_sentences = []
+    for seg in reversed(all_segments):
+        if _QUESTION_MARK.search(seg):
+            question_sentences.append(seg)
+
+    if not question_sentences:
+        # Also check the sentence-split results
+        for sent in reversed(sentences):
+            if "?" in sent or "？" in sent:
+                question_sentences.append(sent)
+
+    if question_sentences:
+        # Take the last (most recent) question found
+        candidate = question_sentences[0].strip()
+        if len(candidate) >= MIN_QUERY_LENGTH:
+            # Apply length guard
+            if len(candidate) > MAX_QUERY_LENGTH:
+                candidate = candidate[-MAX_QUERY_LENGTH:]
+            logger.warning(
+                "Query sanitized: %d → %d chars (method=question_extraction)",
+                original_length,
+                len(candidate),
+            )
+            return {
+                "clean_query": candidate,
+                "was_sanitized": True,
+                "original_length": original_length,
+                "clean_length": len(candidate),
+                "method": "question_extraction",
+            }
+
+    # --- Step 3: Tail sentence extraction ---
+    # System prompts are prepended, so the actual query is near the end.
+    # Walk backwards through segments to find the last meaningful sentence.
+    for seg in reversed(all_segments):
+        seg = seg.strip()
+        if len(seg) >= MIN_QUERY_LENGTH:
+            candidate = seg
+            if len(candidate) > MAX_QUERY_LENGTH:
+                candidate = candidate[-MAX_QUERY_LENGTH:]
+            logger.warning(
+                "Query sanitized: %d → %d chars (method=tail_sentence)",
+                original_length,
+                len(candidate),
+            )
+            return {
+                "clean_query": candidate,
+                "was_sanitized": True,
+                "original_length": original_length,
+                "clean_length": len(candidate),
+                "method": "tail_sentence",
+            }
+
+    # --- Step 4: Tail truncation (fallback) ---
+    # Nothing worked — just take the last MAX_QUERY_LENGTH characters.
+    candidate = raw_query[-MAX_QUERY_LENGTH:].strip()
+    logger.warning(
+        "Query sanitized: %d → %d chars (method=tail_truncation)", original_length, len(candidate)
+    )
+    return {
+        "clean_query": candidate,
+        "was_sanitized": True,
+        "original_length": original_length,
+        "clean_length": len(candidate),
+        "method": "tail_truncation",
+    }

mempalace/repair.py

@@ -0,0 +1,299 @@
+"""
+repair.py — Scan, prune corrupt entries, and rebuild HNSW index
+================================================================
+
+When ChromaDB's HNSW index accumulates duplicate entries (from repeated
+add() calls with the same ID), link_lists.bin can grow unbounded —
+terabytes on large palaces — eventually causing segfaults.
+
+This module provides three operations:
+
+  scan    — find every corrupt/unfetchable ID in the palace
+  prune   — delete only the corrupt IDs (surgical)
+  rebuild — extract all drawers, delete the collection, recreate with
+            correct HNSW settings, and upsert everything back
+
+The rebuild backs up ONLY chroma.sqlite3 (the source of truth), not the
+full palace directory — so it works even when link_lists.bin is bloated.
+
+Usage (standalone):
+    python -m mempalace.repair scan [--wing X]
+    python -m mempalace.repair prune --confirm
+    python -m mempalace.repair rebuild
+
+Usage (from CLI):
+    mempalace repair
+    mempalace repair-scan [--wing X]
+    mempalace repair-prune --confirm
+"""
+
+import argparse
+import os
+import shutil
+import time
+
+import chromadb
+
+
+COLLECTION_NAME = "mempalace_drawers"
+
+
+def _get_palace_path():
+    """Resolve palace path from config."""
+    try:
+        from .config import MempalaceConfig
+
+        return MempalaceConfig().palace_path
+    except Exception:
+        default = os.path.join(os.path.expanduser("~"), ".mempalace", "palace")
+        return default
+
+
+def _paginate_ids(col, where=None):
+    """Pull all IDs in a collection using pagination."""
+    ids = []
+    page = 1000
+    offset = 0
+    while True:
+        try:
+            r = col.get(where=where, include=[], limit=page, offset=offset)
+        except Exception:
+            try:
+                r = col.get(where=where, include=[], limit=page)
+                new_ids = [i for i in r["ids"] if i not in set(ids)]
+                if not new_ids:
+                    break
+                ids.extend(new_ids)
+                offset += len(new_ids)
+                continue
+            except Exception:
+                break
+        n = len(r["ids"]) if r["ids"] else 0
+        if n == 0:
+            break
+        ids.extend(r["ids"])
+        offset += n
+        if n < page:
+            break
+    return ids
+
+
+def scan_palace(palace_path=None, only_wing=None):
+    """Scan the palace for corrupt/unfetchable IDs.
+
+    Probes in batches of 100, falls back to per-ID on failure.
+    Writes corrupt_ids.txt to the palace directory for the prune step.
+
+    Returns (good_set, bad_set).
+    """
+    palace_path = palace_path or _get_palace_path()
+    print(f"\n  Palace: {palace_path}")
+    print("  Loading...")
+
+    client = chromadb.PersistentClient(path=palace_path)
+    col = client.get_collection(COLLECTION_NAME)
+
+    where = {"wing": only_wing} if only_wing else None
+    total = col.count()
+    print(f"  Collection: {COLLECTION_NAME}, total: {total:,}")
+    if only_wing:
+        print(f"  Scanning wing: {only_wing}")
+
+    print("\n  Step 1: listing all IDs...")
+    t0 = time.time()
+    all_ids = _paginate_ids(col, where=where)
+    print(f"  Found {len(all_ids):,} IDs in {time.time() - t0:.1f}s\n")
+
+    if not all_ids:
+        print("  Nothing to scan.")
+        return set(), set()
+
+    print("  Step 2: probing each ID (batches of 100)...")
+    t0 = time.time()
+    good_set = set()
+    bad_set = set()
+    batch = 100
+
+    for i in range(0, len(all_ids), batch):
+        chunk = all_ids[i : i + batch]
+        try:
+            r = col.get(ids=chunk, include=["documents"])
+            for got in r["ids"]:
+                good_set.add(got)
+            for mid in chunk:
+                if mid not in good_set:
+                    bad_set.add(mid)
+        except Exception:
+            for sid in chunk:
+                try:
+                    r = col.get(ids=[sid], include=["documents"])
+                    if r["ids"]:
+                        good_set.add(sid)
+                    else:
+                        bad_set.add(sid)
+                except Exception:
+                    bad_set.add(sid)
+
+        if (i // batch) % 50 == 0:
+            elapsed = time.time() - t0
+            rate = (i + batch) / max(elapsed, 0.01)
+            eta = (len(all_ids) - i - batch) / max(rate, 0.01)
+            print(
+                f"    {i + batch:>6}/{len(all_ids):>6}  "
+                f"good={len(good_set):>6}  bad={len(bad_set):>6}  "
+                f"eta={eta:.0f}s"
+            )
+
+    print(f"\n  Scan complete in {time.time() - t0:.1f}s")
+    print(f"  GOOD: {len(good_set):,}")
+    print(f"  BAD:  {len(bad_set):,}  ({len(bad_set) / max(len(all_ids), 1) * 100:.1f}%)")
+
+    bad_file = os.path.join(palace_path, "corrupt_ids.txt")
+    with open(bad_file, "w") as f:
+        for bid in sorted(bad_set):
+            f.write(bid + "\n")
+    print(f"\n  Bad IDs written to: {bad_file}")
+    return good_set, bad_set
+
+
+def prune_corrupt(palace_path=None, confirm=False):
+    """Delete corrupt IDs listed in corrupt_ids.txt."""
+    palace_path = palace_path or _get_palace_path()
+    bad_file = os.path.join(palace_path, "corrupt_ids.txt")
+
+    if not os.path.exists(bad_file):
+        print("  No corrupt_ids.txt found — run scan first.")
+        return
+
+    with open(bad_file) as f:
+        bad_ids = [line.strip() for line in f if line.strip()]
+    print(f"  {len(bad_ids):,} corrupt IDs queued for deletion")
+
+    if not confirm:
+        print("\n  DRY RUN — no deletions performed.")
+        print("  Re-run with --confirm to actually delete.")
+        return
+
+    client = chromadb.PersistentClient(path=palace_path)
+    col = client.get_collection(COLLECTION_NAME)
+    before = col.count()
+    print(f"  Collection size before: {before:,}")
+
+    batch = 100
+    deleted = 0
+    failed = 0
+    for i in range(0, len(bad_ids), batch):
+        chunk = bad_ids[i : i + batch]
+        try:
+            col.delete(ids=chunk)
+            deleted += len(chunk)
+        except Exception:
+            for sid in chunk:
+                try:
+                    col.delete(ids=[sid])
+                    deleted += 1
+                except Exception:
+                    failed += 1
+        if (i // batch) % 20 == 0:
+            print(f"    deleted {deleted}/{len(bad_ids)}  (failed: {failed})")
+
+    after = col.count()
+    print(f"\n  Deleted: {deleted:,}")
+    print(f"  Failed:  {failed:,}")
+    print(f"  Collection size: {before:,} → {after:,}")
+
+
+def rebuild_index(palace_path=None):
+    """Rebuild the HNSW index from scratch.
+
+    1. Extract all drawers via ChromaDB get()
+    2. Back up ONLY chroma.sqlite3 (not the bloated HNSW files)
+    3. Delete and recreate the collection with hnsw:space=cosine
+    4. Upsert all drawers back
+    """
+    palace_path = palace_path or _get_palace_path()
+
+    if not os.path.isdir(palace_path):
+        print(f"\n  No palace found at {palace_path}")
+        return
+
+    print(f"\n{'=' * 55}")
+    print("  MemPalace Repair — Index Rebuild")
+    print(f"{'=' * 55}\n")
+    print(f"  Palace: {palace_path}")
+
+    client = chromadb.PersistentClient(path=palace_path)
+    try:
+        col = client.get_collection(COLLECTION_NAME)
+        total = col.count()
+    except Exception as e:
+        print(f"  Error reading palace: {e}")
+        print("  Palace may need to be re-mined from source files.")
+        return
+
+    print(f"  Drawers found: {total}")
+
+    if total == 0:
+        print("  Nothing to repair.")
+        return
+
+    # Extract all drawers in batches
+    print("\n  Extracting drawers...")
+    batch_size = 5000
+    all_ids = []
+    all_docs = []
+    all_metas = []
+    offset = 0
+    while offset < total:
+        batch = col.get(limit=batch_size, offset=offset, include=["documents", "metadatas"])
+        if not batch["ids"]:
+            break
+        all_ids.extend(batch["ids"])
+        all_docs.extend(batch["documents"])
+        all_metas.extend(batch["metadatas"])
+        offset += len(batch["ids"])
+    print(f"  Extracted {len(all_ids)} drawers")
+
+    # Back up ONLY the SQLite database, not the bloated HNSW files
+    sqlite_path = os.path.join(palace_path, "chroma.sqlite3")
+    if os.path.exists(sqlite_path):
+        backup_path = sqlite_path + ".backup"
+        print(f"  Backing up chroma.sqlite3 ({os.path.getsize(sqlite_path) / 1e6:.0f} MB)...")
+        shutil.copy2(sqlite_path, backup_path)
+        print(f"  Backup: {backup_path}")
+
+    # Rebuild with correct HNSW settings
+    print("  Rebuilding collection with hnsw:space=cosine...")
+    client.delete_collection(COLLECTION_NAME)
+    new_col = client.create_collection(COLLECTION_NAME, metadata={"hnsw:space": "cosine"})
+
+    filed = 0
+    for i in range(0, len(all_ids), batch_size):
+        batch_ids = all_ids[i : i + batch_size]
+        batch_docs = all_docs[i : i + batch_size]
+        batch_metas = all_metas[i : i + batch_size]
+        new_col.upsert(documents=batch_docs, ids=batch_ids, metadatas=batch_metas)
+        filed += len(batch_ids)
+        print(f"  Re-filed {filed}/{len(all_ids)} drawers...")
+
+    print(f"\n  Repair complete. {filed} drawers rebuilt.")
+    print("  HNSW index is now clean with cosine distance metric.")
+    print(f"\n{'=' * 55}\n")
+
+
+if __name__ == "__main__":
+    p = argparse.ArgumentParser(description="MemPalace repair tools")
+    p.add_argument("command", choices=["scan", "prune", "rebuild"])
+    p.add_argument("--palace", default=None, help="Palace directory path")
+    p.add_argument("--wing", default=None, help="Scan only this wing")
+    p.add_argument("--confirm", action="store_true", help="Actually delete corrupt IDs")
+    args = p.parse_args()
+
+    path = os.path.expanduser(args.palace) if args.palace else None
+
+    if args.command == "scan":
+        scan_palace(palace_path=path, only_wing=args.wing)
+    elif args.command == "prune":
+        prune_corrupt(palace_path=path, confirm=args.confirm)
+    elif args.command == "rebuild":
+        rebuild_index(palace_path=path)

pyproject.toml

@@ -54,11 +54,15 @@ packages = ["mempalace"]
 [tool.ruff]
 line-length = 100
 target-version = "py39"
+extend-exclude = ["benchmarks"]
 
 [tool.ruff.lint]
-select = ["E", "F", "W"]
+select = ["E", "F", "W", "C901"]
 ignore = ["E501"]
 
+[tool.ruff.lint.mccabe]
+max-complexity = 25
+
 [tool.ruff.format]
 quote-style = "double"
 

tests/test_dedup.py

@@ -0,0 +1,272 @@
+"""Tests for mempalace.dedup — near-duplicate drawer detection and removal."""
+
+from unittest.mock import MagicMock, patch
+
+
+from mempalace import dedup
+
+
+# ── get_source_groups ─────────────────────────────────────────────────
+
+
+def test_get_source_groups_basic():
+    col = MagicMock()
+    col.count.return_value = 5
+    col.get.side_effect = [
+        {
+            "ids": ["d1", "d2", "d3", "d4", "d5"],
+            "metadatas": [
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+            ],
+        },
+        {"ids": []},
+    ]
+    groups = dedup.get_source_groups(col, min_count=5)
+    assert "a.txt" in groups
+    assert len(groups["a.txt"]) == 5
+
+
+def test_get_source_groups_below_min():
+    col = MagicMock()
+    col.count.return_value = 2
+    col.get.side_effect = [
+        {
+            "ids": ["d1", "d2"],
+            "metadatas": [
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+            ],
+        },
+        {"ids": []},
+    ]
+    groups = dedup.get_source_groups(col, min_count=5)
+    assert len(groups) == 0
+
+
+def test_get_source_groups_source_filter():
+    col = MagicMock()
+    col.count.return_value = 6
+    col.get.side_effect = [
+        {
+            "ids": ["d1", "d2", "d3", "d4", "d5", "d6"],
+            "metadatas": [
+                {"source_file": "project_a.txt"},
+                {"source_file": "project_a.txt"},
+                {"source_file": "project_a.txt"},
+                {"source_file": "project_a.txt"},
+                {"source_file": "project_a.txt"},
+                {"source_file": "other.txt"},
+            ],
+        },
+        {"ids": []},
+    ]
+    groups = dedup.get_source_groups(col, min_count=5, source_pattern="project_a")
+    assert "project_a.txt" in groups
+    assert "other.txt" not in groups
+
+
+def test_get_source_groups_wing_filter():
+    col = MagicMock()
+    col.count.return_value = 5
+    col.get.side_effect = [
+        {
+            "ids": ["d1", "d2", "d3", "d4", "d5"],
+            "metadatas": [
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+            ],
+        },
+        {"ids": []},
+    ]
+    dedup.get_source_groups(col, min_count=5, wing="my_wing")
+    # Verify where filter was passed
+    first_call = col.get.call_args_list[0]
+    assert first_call.kwargs.get("where") == {"wing": "my_wing"}
+
+
+def test_get_source_groups_missing_source_file():
+    col = MagicMock()
+    col.count.return_value = 5
+    col.get.side_effect = [
+        {
+            "ids": ["d1", "d2", "d3", "d4", "d5"],
+            "metadatas": [{}, {}, {}, {}, {}],
+        },
+        {"ids": []},
+    ]
+    groups = dedup.get_source_groups(col, min_count=5)
+    assert "unknown" in groups
+
+
+# ── dedup_source_group ────────────────────────────────────────────────
+
+
+def test_dedup_source_group_all_unique():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": ["long document one content here", "different document two here"],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    col.query.return_value = {
+        "ids": [["d1"]],
+        "distances": [[0.8]],  # far apart = unique
+    }
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=True)
+    assert len(kept) == 2
+    assert len(deleted) == 0
+
+
+def test_dedup_source_group_with_duplicate():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": [
+            "long document content that is fairly long",
+            "long document content that is fairly long",
+        ],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    col.query.return_value = {
+        "ids": [["d1"]],
+        "distances": [[0.05]],  # very close = duplicate
+    }
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=True)
+    assert len(kept) == 1
+    assert len(deleted) == 1
+
+
+def test_dedup_source_group_short_docs_deleted():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": ["long enough document to keep in the palace", "tiny"],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=True)
+    assert "d2" in deleted  # too short
+
+
+def test_dedup_source_group_empty_doc_deleted():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": ["real document content here that is long enough", None],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=True)
+    assert "d2" in deleted
+
+
+def test_dedup_source_group_live_deletes():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": ["long document content here enough", "long document content here enough"],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    col.query.return_value = {
+        "ids": [["d1"]],
+        "distances": [[0.05]],
+    }
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=False)
+    col.delete.assert_called_once()
+
+
+def test_dedup_source_group_query_failure_keeps():
+    col = MagicMock()
+    col.get.return_value = {
+        "ids": ["d1", "d2"],
+        "documents": [
+            "long document one content here enough",
+            "long document two content here enough",
+        ],
+        "metadatas": [{"wing": "a"}, {"wing": "a"}],
+    }
+    col.query.side_effect = Exception("query failed")
+    kept, deleted = dedup.dedup_source_group(col, ["d1", "d2"], threshold=0.15, dry_run=True)
+    assert len(kept) == 2  # both kept on error
+
+
+# ── show_stats ────────────────────────────────────────────────────────
+
+
+@patch("mempalace.dedup.chromadb")
+def test_show_stats(mock_chromadb, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 5
+    mock_col.get.side_effect = [
+        {
+            "ids": ["d1", "d2", "d3", "d4", "d5"],
+            "metadatas": [
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+                {"source_file": "a.txt"},
+            ],
+        },
+        {"ids": []},
+    ]
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    dedup.show_stats(palace_path=str(tmp_path))  # should not raise
+
+
+# ── dedup_palace ──────────────────────────────────────────────────────
+
+
+@patch("mempalace.dedup.dedup_source_group")
+@patch("mempalace.dedup.get_source_groups")
+@patch("mempalace.dedup.chromadb")
+def test_dedup_palace_dry_run(mock_chromadb, mock_groups, mock_dedup_group, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 10
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    mock_groups.return_value = {"a.txt": ["d1", "d2", "d3", "d4", "d5"]}
+    mock_dedup_group.return_value = (["d1", "d2", "d3"], ["d4", "d5"])
+
+    dedup.dedup_palace(palace_path=str(tmp_path), dry_run=True)
+    mock_dedup_group.assert_called_once()
+
+
+@patch("mempalace.dedup.dedup_source_group")
+@patch("mempalace.dedup.get_source_groups")
+@patch("mempalace.dedup.chromadb")
+def test_dedup_palace_with_wing(mock_chromadb, mock_groups, mock_dedup_group, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 10
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    mock_groups.return_value = {}
+    dedup.dedup_palace(palace_path=str(tmp_path), wing="test_wing", dry_run=True)
+    mock_groups.assert_called_once_with(mock_col, 5, None, wing="test_wing")
+
+
+@patch("mempalace.dedup.dedup_source_group")
+@patch("mempalace.dedup.get_source_groups")
+@patch("mempalace.dedup.chromadb")
+def test_dedup_palace_no_groups(mock_chromadb, mock_groups, mock_dedup_group, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 3
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    mock_groups.return_value = {}
+    dedup.dedup_palace(palace_path=str(tmp_path), dry_run=True)
+    mock_dedup_group.assert_not_called()

tests/test_query_sanitizer.py

@@ -0,0 +1,212 @@
+"""
+Tests for query_sanitizer.py — system prompt contamination mitigation (#333).
+
+Tests cover all 4 pipeline stages:
+  Step 1: passthrough (short queries)
+  Step 2: question extraction
+  Step 3: tail sentence extraction
+  Step 4: tail truncation (fallback)
+"""
+
+from mempalace.query_sanitizer import (
+    MAX_QUERY_LENGTH,
+    MIN_QUERY_LENGTH,
+    SAFE_QUERY_LENGTH,
+    sanitize_query,
+)
+
+
+class TestPassthrough:
+    """Step 1: Queries under SAFE_QUERY_LENGTH pass through unchanged."""
+
+    def test_short_query_unchanged(self):
+        result = sanitize_query("What is Rust error handling?")
+        assert result["clean_query"] == "What is Rust error handling?"
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_empty_query(self):
+        result = sanitize_query("")
+        assert result["clean_query"] == ""
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_none_query(self):
+        result = sanitize_query(None)
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_exactly_safe_length(self):
+        query = "a" * SAFE_QUERY_LENGTH
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is False
+        assert result["method"] == "passthrough"
+
+    def test_one_over_safe_length_triggers_sanitization(self):
+        query = "a" * (SAFE_QUERY_LENGTH + 1)
+        result = sanitize_query(query)
+        # Will go through sanitization pipeline (may or may not change the query)
+        assert result["original_length"] == SAFE_QUERY_LENGTH + 1
+
+
+class TestQuestionExtraction:
+    """Step 2: Extract question sentences (ending with ?)."""
+
+    def test_question_at_end_of_long_text(self):
+        system_prompt = "You are a helpful assistant. " * 50  # ~1400 chars
+        query = system_prompt + "What is the best way to handle errors in Rust?"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "error" in result["clean_query"].lower() or "Rust" in result["clean_query"]
+        assert result["method"] == "question_extraction"
+
+    def test_japanese_question_mark(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "Rustのエラーハンドリング方法は？"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "Rust" in result["clean_query"] or "エラー" in result["clean_query"]
+        assert result["method"] == "question_extraction"
+
+    def test_multiple_questions_takes_last(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Python?\nHow does Rust handle errors?"
+        result = sanitize_query(query)
+        assert "Rust" in result["clean_query"] or "error" in result["clean_query"].lower()
+
+    def test_question_in_system_prompt_ignored_when_real_question_exists(self):
+        # System prompt contains a question, but real query also has one
+        system_prompt = "Are you ready to help? " * 30 + "\n"
+        real_query = "What databases does MemPalace support?"
+        query = system_prompt + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "MemPalace" in result["clean_query"] or "database" in result["clean_query"].lower()
+
+
+class TestTailSentence:
+    """Step 3: Extract the last meaningful sentence when no question mark found."""
+
+    def test_command_style_query(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "Show me all Rust error handling patterns"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "Rust" in result["clean_query"] or "error" in result["clean_query"].lower()
+        assert result["method"] in ("tail_sentence", "question_extraction")
+
+    def test_keyword_style_query(self):
+        system_prompt = "System configuration loaded. " * 60
+        query = system_prompt + "\nMemPalace ChromaDB integration setup"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert "MemPalace" in result["clean_query"] or "ChromaDB" in result["clean_query"]
+
+
+class TestTailTruncation:
+    """Step 4: Fallback — take the last MAX_QUERY_LENGTH characters."""
+
+    def test_single_long_line_no_sentences(self):
+        # Short lines only — no segment reaches MIN_QUERY_LENGTH; fallback truncates tail
+        filler = "\n".join(["ab"] * 200)
+        result = sanitize_query(filler)
+        assert result["was_sanitized"] is True
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+        assert result["method"] == "tail_truncation"
+
+    def test_truncation_preserves_tail(self):
+        filler = "x" * 1000 + "IMPORTANT_QUERY_CONTENT"
+        result = sanitize_query(filler)
+        assert "IMPORTANT_QUERY_CONTENT" in result["clean_query"]
+
+
+class TestLengthGuards:
+    """Verify output length constraints."""
+
+    def test_output_never_exceeds_max(self):
+        # Very long question sentence
+        long_question = "a" * 1000 + "?"
+        system_prompt = "Context. " * 100
+        query = system_prompt + long_question
+        result = sanitize_query(query)
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+
+    def test_extraction_too_short_falls_through(self):
+        # Question mark found but the sentence is too short
+        system_prompt = "You are helpful. " * 50
+        query = system_prompt + "\nOK?"
+        result = sanitize_query(query)
+        # "OK?" is only 3 chars < MIN_QUERY_LENGTH, should fall through
+        assert result["was_sanitized"] is True
+
+
+class TestMetadata:
+    """Verify sanitizer metadata is correct."""
+
+    def test_original_length_preserved(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["original_length"] == len(query.strip())
+
+    def test_clean_length_matches_clean_query(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["clean_length"] == len(result["clean_query"])
+
+    def test_sanitized_flag_true_when_changed(self):
+        system_prompt = "You are a helpful assistant. " * 50
+        query = system_prompt + "What is Rust?"
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+
+    def test_sanitized_flag_false_when_unchanged(self):
+        result = sanitize_query("Short query")
+        assert result["was_sanitized"] is False
+
+
+class TestRealWorldScenarios:
+    """Simulate realistic system prompt contamination patterns."""
+
+    def test_mempalace_wakeup_prepended(self):
+        """Simulates mempalace wake-up output prepended to a query."""
+        wakeup = (
+            "MemPalace loaded. Wings: technical, emotions, identity. "
+            "Rooms: chromadb-setup, error-handling, project-planning. "
+            "Total drawers: 234. Knowledge graph: 89 entities, 156 triples. "
+            "AAAK dialect active. Protocol: verify before responding. "
+        ) * 5  # ~1000 chars
+        real_query = "How did we decide on the database architecture?"
+        query = wakeup + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert len(result["clean_query"]) <= MAX_QUERY_LENGTH
+        # Should recover something meaningful
+        assert len(result["clean_query"]) >= MIN_QUERY_LENGTH
+
+    def test_memory_md_prepended(self):
+        """Simulates MEMORY.md content prepended to a query."""
+        memory_md = (
+            "# Project Memory\n"
+            "## Architecture Decisions\n"
+            "- Use ChromaDB for vector storage\n"
+            "- MCP protocol for tool integration\n"
+            "- AAAK compression for efficient storage\n"
+        ) * 10  # ~750 chars
+        real_query = "What were the performance benchmarks for the search system?"
+        query = memory_md + "\n" + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert result["method"] in ("question_extraction", "tail_sentence")
+
+    def test_2000_char_system_prompt_with_question(self):
+        """The exact scenario from Issue #333 — 2000 chars prepended."""
+        system_prompt = "You are an AI assistant with access to tools. " * 45  # ~2000 chars
+        real_query = "What is the status of the MemPalace project?"
+        query = system_prompt + real_query
+        result = sanitize_query(query)
+        assert result["was_sanitized"] is True
+        assert result["original_length"] > 2000
+        assert result["clean_length"] <= MAX_QUERY_LENGTH
+        assert result["method"] == "question_extraction"

tests/test_repair.py

@@ -0,0 +1,266 @@
+"""Tests for mempalace.repair — scan, prune, and rebuild HNSW index."""
+
+import os
+from unittest.mock import MagicMock, patch
+
+
+from mempalace import repair
+
+
+# ── _get_palace_path ──────────────────────────────────────────────────
+
+
+@patch("mempalace.repair.MempalaceConfig", create=True)
+def test_get_palace_path_from_config(mock_config_cls):
+    mock_config_cls.return_value.palace_path = "/configured/palace"
+    with patch.dict("sys.modules", {}):
+        # Force reimport to pick up the mock
+        result = repair._get_palace_path()
+    assert isinstance(result, str)
+
+
+def test_get_palace_path_fallback():
+    with patch("mempalace.repair._get_palace_path") as mock_get:
+        mock_get.return_value = os.path.join(os.path.expanduser("~"), ".mempalace", "palace")
+        result = mock_get()
+        assert ".mempalace" in result
+
+
+# ── _paginate_ids ─────────────────────────────────────────────────────
+
+
+def test_paginate_ids_single_batch():
+    col = MagicMock()
+    col.get.return_value = {"ids": ["id1", "id2", "id3"]}
+    ids = repair._paginate_ids(col)
+    assert ids == ["id1", "id2", "id3"]
+
+
+def test_paginate_ids_empty():
+    col = MagicMock()
+    col.get.return_value = {"ids": []}
+    ids = repair._paginate_ids(col)
+    assert ids == []
+
+
+def test_paginate_ids_with_where():
+    col = MagicMock()
+    col.get.return_value = {"ids": ["id1"]}
+    repair._paginate_ids(col, where={"wing": "test"})
+    col.get.assert_called_with(where={"wing": "test"}, include=[], limit=1000, offset=0)
+
+
+def test_paginate_ids_offset_exception_fallback():
+    col = MagicMock()
+    # First call raises, fallback returns ids, second fallback returns empty
+    col.get.side_effect = [
+        Exception("offset bug"),
+        {"ids": ["id1", "id2"]},
+        Exception("offset bug"),
+        {"ids": ["id1", "id2"]},  # same ids = no new = break
+    ]
+    ids = repair._paginate_ids(col)
+    assert "id1" in ids
+
+
+# ── scan_palace ───────────────────────────────────────────────────────
+
+
+@patch("mempalace.repair.chromadb")
+def test_scan_palace_no_ids(mock_chromadb, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 0
+    mock_col.get.return_value = {"ids": []}
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    good, bad = repair.scan_palace(palace_path=str(tmp_path))
+    assert good == set()
+    assert bad == set()
+
+
+@patch("mempalace.repair.chromadb")
+def test_scan_palace_all_good(mock_chromadb, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 2
+    # _paginate_ids call
+    mock_col.get.side_effect = [
+        {"ids": ["id1", "id2"]},  # paginate
+        {"ids": ["id1", "id2"]},  # probe batch — both returned
+    ]
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    good, bad = repair.scan_palace(palace_path=str(tmp_path))
+    assert "id1" in good
+    assert "id2" in good
+    assert len(bad) == 0
+
+
+@patch("mempalace.repair.chromadb")
+def test_scan_palace_with_bad_ids(mock_chromadb, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 2
+
+    def get_side_effect(**kwargs):
+        ids = kwargs.get("ids", None)
+        if ids is None:
+            # paginate call
+            return {"ids": ["good1", "bad1"]}
+        if "bad1" in ids and len(ids) == 1:
+            raise Exception("corrupt")
+        if "good1" in ids and len(ids) == 1:
+            return {"ids": ["good1"]}
+        # batch probe — raise to force per-id
+        raise Exception("batch fail")
+
+    mock_col.get.side_effect = get_side_effect
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    good, bad = repair.scan_palace(palace_path=str(tmp_path))
+    assert "good1" in good
+    assert "bad1" in bad
+
+
+@patch("mempalace.repair.chromadb")
+def test_scan_palace_with_wing_filter(mock_chromadb, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 1
+    mock_col.get.side_effect = [
+        {"ids": ["id1"]},  # paginate
+        {"ids": ["id1"]},  # probe
+    ]
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.scan_palace(palace_path=str(tmp_path), only_wing="test_wing")
+    # Verify where filter was passed
+    first_call = mock_col.get.call_args_list[0]
+    assert first_call.kwargs.get("where") == {"wing": "test_wing"}
+
+
+# ── prune_corrupt ─────────────────────────────────────────────────────
+
+
+@patch("mempalace.repair.chromadb")
+def test_prune_corrupt_no_file(mock_chromadb, tmp_path):
+    # Should print message and return without error
+    repair.prune_corrupt(palace_path=str(tmp_path))
+
+
+@patch("mempalace.repair.chromadb")
+def test_prune_corrupt_dry_run(mock_chromadb, tmp_path):
+    bad_file = tmp_path / "corrupt_ids.txt"
+    bad_file.write_text("bad1\nbad2\n")
+    repair.prune_corrupt(palace_path=str(tmp_path), confirm=False)
+    # No chromadb calls in dry run
+    mock_chromadb.PersistentClient.assert_not_called()
+
+
+@patch("mempalace.repair.chromadb")
+def test_prune_corrupt_confirmed(mock_chromadb, tmp_path):
+    bad_file = tmp_path / "corrupt_ids.txt"
+    bad_file.write_text("bad1\nbad2\n")
+
+    mock_col = MagicMock()
+    mock_col.count.side_effect = [10, 8]
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.prune_corrupt(palace_path=str(tmp_path), confirm=True)
+    mock_col.delete.assert_called_once()
+
+
+@patch("mempalace.repair.chromadb")
+def test_prune_corrupt_delete_failure_fallback(mock_chromadb, tmp_path):
+    bad_file = tmp_path / "corrupt_ids.txt"
+    bad_file.write_text("bad1\nbad2\n")
+
+    mock_col = MagicMock()
+    mock_col.count.side_effect = [10, 8]
+    # Batch delete fails, per-id succeeds
+    mock_col.delete.side_effect = [Exception("batch fail"), None, None]
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.prune_corrupt(palace_path=str(tmp_path), confirm=True)
+    assert mock_col.delete.call_count == 3  # 1 batch + 2 individual
+
+
+# ── rebuild_index ─────────────────────────────────────────────────────
+
+
+@patch("mempalace.repair.chromadb")
+def test_rebuild_index_no_palace(mock_chromadb, tmp_path):
+    nonexistent = str(tmp_path / "nope")
+    repair.rebuild_index(palace_path=nonexistent)
+    mock_chromadb.PersistentClient.assert_not_called()
+
+
+@patch("mempalace.repair.shutil")
+@patch("mempalace.repair.chromadb")
+def test_rebuild_index_empty_palace(mock_chromadb, mock_shutil, tmp_path):
+    mock_col = MagicMock()
+    mock_col.count.return_value = 0
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.rebuild_index(palace_path=str(tmp_path))
+    mock_client.delete_collection.assert_not_called()
+
+
+@patch("mempalace.repair.shutil")
+@patch("mempalace.repair.chromadb")
+def test_rebuild_index_success(mock_chromadb, mock_shutil, tmp_path):
+    # Create a fake sqlite file
+    sqlite_path = tmp_path / "chroma.sqlite3"
+    sqlite_path.write_text("fake")
+
+    mock_col = MagicMock()
+    mock_col.count.return_value = 2
+    mock_col.get.return_value = {
+        "ids": ["id1", "id2"],
+        "documents": ["doc1", "doc2"],
+        "metadatas": [{"wing": "a"}, {"wing": "b"}],
+    }
+
+    mock_new_col = MagicMock()
+    mock_client = MagicMock()
+    mock_client.get_collection.return_value = mock_col
+    mock_client.create_collection.return_value = mock_new_col
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.rebuild_index(palace_path=str(tmp_path))
+
+    # Verify: backed up sqlite only (not copytree)
+    mock_shutil.copy2.assert_called_once()
+    assert "chroma.sqlite3" in str(mock_shutil.copy2.call_args)
+
+    # Verify: deleted and recreated with cosine
+    mock_client.delete_collection.assert_called_once_with("mempalace_drawers")
+    mock_client.create_collection.assert_called_once_with(
+        "mempalace_drawers", metadata={"hnsw:space": "cosine"}
+    )
+
+    # Verify: used upsert not add
+    mock_new_col.upsert.assert_called_once()
+    mock_new_col.add.assert_not_called()
+
+
+@patch("mempalace.repair.shutil")
+@patch("mempalace.repair.chromadb")
+def test_rebuild_index_error_reading(mock_chromadb, mock_shutil, tmp_path):
+    mock_client = MagicMock()
+    mock_client.get_collection.side_effect = Exception("corrupt")
+    mock_chromadb.PersistentClient.return_value = mock_client
+
+    repair.rebuild_index(palace_path=str(tmp_path))
+    mock_client.delete_collection.assert_not_called()