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 HNSW indexes, and write everything to .codehub/ under the repo root.

The default backend is LadybugDB for the graph half + DuckDB for the temporal sibling. Set CODEHUB_STORE=duck to force the single-file DuckDB layout. See Storage backend.

Basic indexing

index the current repo

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

full index with embeddings

codehub analyze --embeddings

--embeddings computes symbol and optional file/community vectors and writes them to the HNSW index. 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

offline mode — no sockets

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

check index freshness

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

delete the .codehub/ directory

codehub clean

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

Granularity

index at symbol, file, and community level

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/

The contents depend on the storage backend selected at index time. On the default LadybugDB layout:

Path	Purpose
graph.lbug	LadybugDB graph store — symbols, edges, embeddings, BM25 + HNSW indexes.
temporal.duckdb	DuckDB sibling — cochanges, symbol-summary cache.
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.

On the single-file DuckDB fallback, graph.duckdb replaces both graph.lbug and temporal.duckdb.

Other useful flags

• --sbom — emit a CycloneDX SBOM alongside the index.
• --coverage — bridge coverage data into the graph.
• --summaries / --no-summaries — LLM-generated symbol summaries (default on; capped by --max-summaries, default auto = 10% of callables, hard cap 500).
• --skills — generate Claude Code skills from the graph.
• --native-parser — opt into the native tree-sitter N-API addon on Node 22 (the default runtime is web-tree-sitter / WASM).
• --strict-detectors — fail the build if a detector (DET-O-001) regresses.
• --verbose — noisier logs.

See CLI reference: analyze for the complete flag list.