Indexing a repo

codehub analyze is the full indexing pipeline: parse with tree-sitter (and SCIP for every language with a pinned indexer — TypeScript, Python, Go, Rust, Java, C#, C/C++, Kotlin, Ruby), resolve imports and inheritance, detect processes and clusters, build BM25 and vector indexes, and write everything to .codehub/ under the repo root.

The whole index lives in one store.sqlite file (WAL mode) under .codehub/, via Node’s built-in node:sqlite. It holds graph nodes, edges, embeddings, and the temporal tables, and it is written on every analyze. There is no backend knob and no native storage binding (ADR 0019). See Storage backend.

Basic indexing

codehub analyze

Re-run after significant changes. A no-op short-circuit skips work if the index already matches HEAD; pass --force to rebuild.

Add semantic vectors

codehub analyze --embeddings

--embeddings computes symbol and optional file/community vectors and writes them to the embeddings table. After this, codehub query fuses BM25 and vector results via reciprocal-rank fusion (RRF).

Memory-constrained machines can use --embeddings-int8 for quantised vectors, --embeddings-workers auto to tune the worker pool, or --embeddings-batch-size 32 (default) to tune batch throughput.

Zero-network indexing

codehub analyze --offline

--offline disables every code path that would open a socket. Combine with cached embedder weights (see codehub setup --embeddings --model-dir <path>) to index fully air-gapped.

Staleness and status

codehub status

status compares the index against the working tree and reports staleness. MCP responses also carry an envelope field _meta["codehub/staleness"] whenever the index lags HEAD, so agents can detect drift without polling.

Resetting the index

codehub clean

codehub clean --all deletes every index registered on the machine and wipes ~/.codehub/registry.json.

Granularity

codehub analyze --granularity symbol,file,community

The pipeline produces hierarchical embeddings so a single query can surface a symbol, the file that contains it, and the community the symbol participates in. The default granularity is symbol.

What lives in `.codehub/`

Every index writes the same single-file layout: one store.sqlite via Node’s built-in node:sqlite:

Path	Purpose
`store.sqlite`	The whole index (WAL mode) — symbols, edges, embeddings, the FTS5 search index, and the temporal tables (cochanges).
`store.sqlite-wal` / `store.sqlite-shm`	WAL companions present while a writer is open; collapse into `store.sqlite` at close.
`meta.json`	Index metadata (graph hash, node counts, CLI version, toolchain pins, embedder modelId).
`scan.sarif`	SARIF scan output when `codehub scan` has run.
`sbom.cyclonedx.json` / `sbom.spdx.json`	SBOMs when `codehub analyze --sbom` has run.

What runs by default

A bare codehub analyze produces a production-grade .codehub/ folder in one command:

Graph pipeline (tree-sitter parse + SCIP resolution + communities + processes + cochanges + ownership + dependencies + detectors).
SBOM emission (CycloneDX + SPDX) — default on; suppress with --no-sbom.
Priority-1 scanners → .codehub/scan.sarif + findings ingested into the graph — default on; suppress with --no-scan. Network-backed scanners (osv-scanner, grype, npm/pip audit) self-skip under --offline, so the on-default stays honest.
Coverage overlay — default auto: runs only when a report is present at coverage/lcov.info, lcov.info, coverage.xml, build/reports/jacoco/test/jacocoTestReport.xml, or coverage.json. Silent no-op otherwise. Force with --coverage; force off with --no-coverage.

Everything else — embeddings, skills — is opt-in.

Opt-in flags

--embeddings — compute semantic vectors for queries by meaning. Requires codehub setup --embeddings first.
--skills — generate Claude Code skills from the graph.
--strict-detectors — fail the build if a detector (DET-O-001) regresses.
--verbose — noisier logs.

See CLI reference: analyze for the complete flag list.