Create or update one graph node. Prefer this for curated nodes (feature:, ext:, note: ids, or a manual correction to a code node) -- code nodes (file:/fn:) are normally written by index_repo instead, so a later reindex does not immediately overwrite what you just wrote.

Create or update several nodes at once, in the (id, kind, label) shape (each entry may also set repo/path/status/confidence/etc).

Create or update one edge. weight/origin default from the edge type (see graph.weights) when omitted -- pass origin='manual' explicitly when in doubt; that is the one origin a reindex never overwrites.

Create or update several edges at once, in the (src, dst, type) shape from starter_edges (each entry may also set weight/origin/etc).

Remove a node. Soft delete (default) hides it from reads but keeps the row; hard=True also deletes every edge touching it, irreversibly.

Remove one edge by its (src, dst, type) key.

Move a node to a new id, carrying every edge with it (e.g. after a file move index_repo would otherwise treat as delete-then-create, losing manual/git edges attached to the old id).

Update a node's status (verified/probable/assumed/outdated/refuted) and optionally its confidence, without touching anything else.

Fetch one node by its exact id.

One-hop neighbors of a node. direction is 'out', 'in', or 'both'.

Full-text search over node id/label/path/curated-note body. If query is itself a valid node id, that exact node is included first.

The main entry point: FTS5-seeded, PageRank-expanded context for a natural-language description of a task. Read MUST_READ first, note DANGER, expect MAY_CHANGE/MUST_TEST before you consider a change done.

Impact analysis for one specific node: what it needs (MUST_READ), what depends on it (MAY_CHANGE), what exercises it (MUST_TEST), the knowledge that documents it, and anything flagged DANGER.

Shortest connection between two nodes through the graph (either direction), for "how are these two things related" questions.

Node/edge counts by kind and type.

Full (re)index of one configured repo: wipes and rewrites every scanner-origin node/edge for it, leaving manual/git-origin rows alone.

Incremental reindex of just these relpaths within a repo -- call this after editing files so the graph does not drift from the code.

Derive co_edit edges from this repo's git history: files that keep changing together, even without an import connecting them.

Find nodes/notes pointing at paths that no longer exist, and manual/git edges whose endpoint node vanished -- read-only, reports only; nothing here is deleted automatically.

Wipe every node and edge for a vault. Irreversible; requires confirm=True.

Read one note's frontmatter and body.

Create or update a note. Enforces the vault's note contract (id, type, area, status, confidence, source, ...) when the vault's profile requires it, and refuses content that looks like a live secret unless allow_secrets=True.

Merge updates into a note's existing frontmatter, leaving the body untouched. created is preserved; updated is bumped automatically.

Materialize a graph node (file/symbol/feature) as a curated note under 20-Knowledge/codebase/{files,symbols,features}, pre-filled with its neighbors from the graph. Written as status:"assumed" (it is a skeleton, not verified prose) -- promote sparingly, per Instructions.md Sec.12: not every file earns a note.

List note paths under the vault (or under subdir).

Substring search over every note's id/body, with a short snippet per hit.

Move a note to 99-Archive/ with a dated filename and a header recording why -- nothing in the vault is ever hard-deleted.

The Instructions.md Sec.7 consolidation ritual, as a read-only report: decayed notes, isolated graph nodes, and divergence issues. Run this every ~10 sessions, or when asked to 'consolida'.

Add wikilinks to curated notes for graph neighbors that also have a note (documents/decided_by/depends_on/dangerous/test edges). Additive only -- never removes a link you added by hand.

Report which vaults are configured and whether the requested (or default) vault's graph store is reachable.