second-brain MCP

Show vault index statistics: total notes, breakdown by type, DB location.

Initialize or repair vault directory structure and default templates. Safe to re-run: only creates missing items, never overwrites existing files. Call this after cloning the repo or setting up on a new machine.

Answer a literature question as a fixed-format, CITED synthesis note (retrieve → synthesize). Retrieves grounded material via query_graph (LitNet 正本 edges + full-text net), then Claude writes a cited summary. GENERATED prose (not raw literature): every claim is anchored to a source note in the retrieval; tagged type: synthesis; a synthesis is NEVER re-extracted into the 正本 (saved outside 20-areas/research/). Args: entity: comma-separated entities to look up; if empty, extracted from the question (auto-extraction caps at _LA_MAX_AUTO_ENTITIES=3 entities — pass entity explicitly …

Manage API keys for multi-user access (admin only). action: "register" | "revoke" | "list" raw_key: the plaintext API key (register/revoke). Never stored; only its SHA-256 hash is persisted. user_id: human-readable owner label (register/list filter). role: "reader" | "member" | "writer" | "admin" (register only, default "reader"). 'member' (lab-open plan) requires user_uuid — it is how the key's private 90-personal/<uuid>/ area is derived (see visibility.py). user_uuid: canonical UUID from EP lab-access (register only). Required for role='member'; optional for other roles. e…

Update the frontmatter status field of a note and sync to DB. Use this to track note lifecycle without rewriting the whole file — including a decision note's proposed → accepted → superseded progression. Args: path: Relative path from vault root, e.g. '30-resources/my-note.md' status: active | completed | archived (general / project notes), proposed | accepted | superseded (decision / ADR), or consolidated | archive_backup (normally written by consolidate_tool / vault_sleep, accepted here for repairs).

Create a new note in the vault using the correct folder and template. If the title or tags contain a known project slug (from PROJECT_REGISTRY.md), the note is automatically routed into that project's subfolder: coding → {project}/phases/, research/paper/finding → {project}/research/, resource/reference/tool → {project}/docs/ decision/adr always go to decisions/; project always goes to 10-projects/. A coding-type note whose title slug starts with "fix-" routes to {project}/fixes/ instead of phases/ — a postmortem isn't an in-flight phase plan. Args: note_type: Type of note — decision…

Delete archived originals older than min_age_days that have a snapshot. Safe to run: only deletes when a PNG snapshot exists as long-term memory. Default dry_run=True — set to False to actually delete. Args: min_age_days: Minimum age of archived file to consider (default 365) dry_run: If True, only report what would be deleted (default True)

Query the write-action audit log (admin only). user_id: filter by actor (optional). tool_name: filter by tool (optional). limit: max rows to return (default 50).

Dual-path knowledge-graph query for an entity (gene / factor / phenotype / …). Path 1 — structured typed edges (ACTIVATES / INHIBITS / PROMOTES / CAUSES / PREVENTS / ASSOCIATED_WITH) mentioning the entity, aggregated ACROSS papers with verbatim evidence + source note. Cross-paper agreement = stronger (shown as ×N). Path 2 — full-text verbatim snippet recall net (same engine as search_snippets), so a relation the edge extractor missed is still surfaced (goal: 無遺漏). Args: entity: e.g. 'TXNDC5', 'TGF-beta', 'pulmonary fibrosis'. mode: 'edges' | 'snippets' | 'both' (default 'both'). …

Load ONE extracted figure as a down-scaled image (the cheap rung of the recall ladder — between text search and rendering a whole page). Use this only when search_figures' text proxy (caption + OCR + description) can't answer the question. Returns a thumbnail (long edge ~768px, ~256-400 tokens) rather than the full-resolution image or the whole page. Args: note_path: Vault-relative path of the source note, e.g. '20-areas/research/paper.md' fig_index: 0-based figure index as shown by search_figures

Read a specific note by its relative path within the vault. Args: path: Relative path from vault root, e.g. 'decisions/my-decision.md'

Read a note as a PNG snapshot (direct image for VLM agents) or text fallback. Returns the PNG image directly so the calling agent (Claude, Gemini, etc.) reads it with its own vision model — cheaper and faster than routing through an intermediary. Args: path: Relative path from vault root

Reconcile figure files and index rows without Vision-model calls. Only deterministic evidence is applied: a unique canonical local file, a unique same-stem replacement for a missing path, or a guarded public image URL with an existing text proxy. Ambiguous cases remain in the manual queue. Research Markdown is never modified. Args: note_paths: Explicit vault-relative Markdown paths; at most 20. dry_run: Report actions without downloading files or updating rows. limit: Maximum notes to inspect from the supplied list; 1 through 20.

Restore missing legacy embedded-image files from their original PDFs. Restoration is fail-closed: the reconstructed PDF sequence must match every database row and every surviving file byte-for-byte before any file is written. The call never changes research Markdown or figure database rows. Args: note_paths: Explicit vault-relative article paths; at most 20. dry_run: Validate and list the next bounded restore batch without writes. note_limit: Maximum supplied notes to inspect; 1 through 20. image_limit: Maximum missing image files to restore; 1 through 20. source_pdfs: Op…

Convert a web article or PDF into a markdown note and save it to the vault. Args: source: URL of a web article, or absolute path to a local PDF/DOCX file. title: Optional title override. If empty, inferred from the source filename or URL. tags: Comma-separated tags to add to frontmatter, e.g. 'bioinformatics,clustering'. dest_folder: Vault-relative folder to save into. Defaults to '30-resources'. Use '20-areas/research' for academic papers with DOI/journal. filename: Filename stem (without .md). If empty, auto-generated from title as kebab-slug. …

Search article-only structured bibliography fields. Use this instead of search_notes when asking for papers by an author. Author matching is based only on article frontmatter, never body text or references. Full names, surname-first initials and ORCID are supported. A surname-only result is marked ambiguous and must not be treated as identity resolution.

Search figures by OCR text or semantic description across all saved articles. Args: query: Search term, e.g. 'UMAP', 'TYRP1', 'cluster', 'p < 0.001'

Hybrid search that returns results split into two groups in one call: - **knowledge**: permanent notes, project notes, literature (excludes cnyes_archive) - **news**: cnyes morning briefs from the last 7 days Useful for finance research (get stock report + morning brief context together) and general knowledge work (see both deep notes and recent news at once). Args: query: Search terms, e.g. "NVDA" or "transformer architecture" limit: Max results per group (default 10) Returns: Markdown with two sections: Knowledge and News.

Search recent cnyes daily news archives. Only searches cnyes_archive notes within the last N days. Use search_notes for knowledge base search. Args: query: Stock ticker, keyword, or company name (e.g. '2317', 'TSMC', 'AI') days: How many days back to search (default 7)

Hybrid semantic + full-text search across knowledge notes (excludes daily news archives). Uses BM25 + cosine similarity (bge-m3, 1024d) when embedding server is available, falls back to BM25-only, then file scan. To search news specifically, use search_news_tool. Args: query: Search term — supports natural language and keywords

Precise localization: return the VERBATIM source sentence from each of the most relevant notes, with its citation. The sentence is quoted exactly from the paper, never rewritten — ideal for 'what does the literature say about X' or 'a factor's role': jumps to the passage. Args: query: keyword or phrase, e.g. 'TGF-beta fibrosis', 'hair follicle stem cell niche'. top_k: how many notes to pull snippets from (default 8).

Check current sleep triggers and list candidates without compressing.

Render a markdown note to PNG snapshot for token-efficient storage. Args: note_path: Relative path within vault, e.g. 'decisions/my-note.md' tier: Resolution tier — 'large' (400 tokens), 'base' (256), 'small' (100)

Backfill note_chunks for notes whose chunks are missing or stale — the dedicated tool for draining a large backlog (sync_index()'s own chunk backfill is capped small so it stays fast; see its docstring). limit: max notes to process this call (default 200). Call repeatedly (the response says how many remain) until "remaining" reaches 0 — each call is its own bounded unit of work rather than one unbounded one, so a big backlog never turns a single call into an hours-long block (see PostgresStore.sync_chunks's docstring for the architecture debt this replaced, fixed 2026-09-04).

Rebuild the DuckDB index by scanning all vault markdown files. Run this after adding notes manually, or when setting up on a new machine. Also backfills note_chunks for up to _SYNC_INDEX_CHUNK_LIMIT notes that predate chunking or whose chunks failed previously. If more than that are outstanding, run sync_chunks_tool() separately to drain the rest — this tool intentionally does not attempt the whole backlog in one call.

Reindex only the explicitly requested vault notes.

Return your most important notes ranked by engagement. Two ranking modes: - **score** (default): Ebbinghaus decay score = access_count / time_decay. High score = frequently accessed AND recently accessed. Best for finding your core knowledge nodes and most-researched stocks. - **recency**: Last accessed time. Best for resuming recent work. Use cases: - Finance: find your most-researched tickers (= notes with highest score) - Knowledge: find Evergreen note candidates (high score = worth refining) - Weekly review: top 20 notes you've engaged with most this week Args: by: "score" or…

Replace the contents of memory/goals.md with new content. Args: new_content: Full new content for goals.md (markdown format)

Refresh auto-generated related wikilinks in one note or all notes. Uses semantic similarity (bge-m3, 1024d) to find related notes and writes them into the frontmatter `related` field. Args: note_path: Relative path within vault (e.g. 'decisions/my-note.md'). Leave empty to update ALL notes that have embeddings.

Overwrite an existing note with new content. Use when rewriting or restructuring a note. For adding content without losing existing text, use append_to_note instead. Args: path: Relative path from vault root, e.g. 'decisions/my-decision.md' content: Full new content to write (replaces the entire file)

Compress old low-activity notes to slim down the vault. Thresholds are read from vault/.sleep-config.json (per-folder): - cnyes_archive: 7 days - finance: 30 days - everything else: 90 days Notes with Ebbinghaus score > 0.5 are skipped. Args: dry_run: If True, show candidates without making changes.