Addresses Issue #333: AI agents prepending system prompts to search queries
causes embedding retrieval to collapse (89.8% → 1.0% R@10).
Mitigation approach (減災):
- New query_sanitizer.py with 4-stage pipeline:
Step 1: passthrough for short queries (≤200 chars)
Step 2: question extraction (finds ? sentences) → ~85-89% recovery
Step 3: tail sentence extraction → ~80-89% recovery
Step 4: tail truncation fallback → ~70-80% recovery
Worst case without sanitizer: 1.0% (catastrophic)
Worst case with sanitizer: ~70-80% (survivable)
- mcp_server.py: tool_search applies sanitizer before ChromaDB query
- MCP schema: query description warns agents not to include prompts
- New 'context' parameter separates background info from search intent
- Sanitizer metadata included in response when triggered
22 new tests covering all pipeline stages and real-world scenarios.
Made-with: Cursor
The _count_human_messages() function previously only handled Claude Code
transcript format: {"message": {"role": "user", "content": "..."}}
Codex CLI transcripts use a different schema:
{"type": "event_msg", "payload": {"type": "user_message", "message": "..."}}
This meant the stop-hook auto-save threshold never triggered for Codex
sessions because the count always returned 0.
Added detection for the Codex format so both Claude Code and Codex CLI
transcripts are counted correctly.
The initialize handler hardcoded protocolVersion "2024-11-05", which
causes newer MCP clients (e.g. Claude Code) to reject the connection
when they negotiate "2025-11-25" or later.
Echo the client's requested version if it is in the supported set,
otherwise fall back to the latest supported version. This keeps
backwards compatibility with older clients while allowing newer ones
to connect.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Merged both the PR's benchmark suite additions (psutil dep, pytest
markers, --ignore=tests/benchmarks) and upstream's coverage changes
(pytest-cov, --cov-fail-under=30, coverage config) so both coexist.
Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
_patch_mcp_server had palace_path removed from its signature but the
assertion body still referenced it, causing NameError at runtime and
F821 from ruff.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
CI was installing latest ruff (0.15.x) which has different formatting
rules than our local 0.4.x. Pin to ruff>=0.4.0,<0.5 for consistency.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add tests for config, convo_miner, spellcheck, knowledge_graph
- Fix Windows PermissionError in test cleanup (chromadb file locks)
- Add UTF-8 encoding to split_mega_files, entity_registry, hooks_cli
- Fix mcp_server parse_known_args logging for unknown args
- Set coverage threshold to 85 in pyproject.toml and CI
- Reset all version files to 3.0.11
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
MCP tool_add_drawer:
- Make drawer_id content-based: hash full content instead of
content[:100] + timestamp. Same content → same ID, eliminating
TOCTOU race conditions
- Switch from col.add() to col.upsert() so re-filing with updated
content updates the existing drawer
miner.add_drawer:
- Switch from collection.add() to collection.upsert() so re-mining
a modified file updates instead of silently failing
- Remove the try/except catching 'already exists' — upsert handles
this naturally
Findings: #11 (HIGH — add ignores updates), #6 (MEDIUM — TOCTOU),
#13 (MEDIUM — non-deterministic IDs)
Includes test infrastructure from PR #131.
92 tests pass.
Add/expand tests for normalize (39%→97%), searcher (39%→100%),
layers (28%→97%), split_mega_files (34%→72%).
Fix mcp_server.py parse_args→parse_known_args to prevent SystemExit
when imported during pytest (CI was crashing on all test jobs).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
When --palace is not explicitly provided, fall back to KnowledgeGraph()
which uses DEFAULT_KG_PATH (~/.mempalace/knowledge_graph.sqlite3),
preserving backward compatibility for existing users.
Ben Sigman