CLI Reference

All commands, flags, and options available in the ctxe CLI.

Global options

All commands support these output formats via -f or --format:

  • human — readable output (default)
  • json — structured JSON for scripting
  • compact — minimal output

ctxe index

Index a project directory. Parses source into AST chunks, generates vector embeddings, and builds the knowledge graph.

ctxe index [path] [options]
pathProject root (defaults to .)
--forceFull reindex, ignore cached hashes
--retry-errorsRetry chunks stuck in error state (embedding, summary, doc expansion)

Indexing is incremental by default — only changed files are reprocessed.

ctxe status

Show index status for a workspace: file count, chunk count, embedding coverage, and capabilities.

ctxe status [path]
pathProject root (defaults to .)

ctxe ask

Goal-driven semantic search with LLM evidence planner. Performs multi-round retrieval (vector search, FTS5, graph expansion) and returns synthesized evidence.

ctxe ask <query> [options]
queryNatural language question or objective
--fullEmit full diagnostics in JSON output (planner history, scoring metadata)

ctxe summarize

Generate or update LLM-powered chunk summaries for improved search relevance.

ctxe summarize [path] [options]
pathProject root (defaults to .)
--forceRe-summarize all chunks (ignore existing)
--retry-errorsRetry chunks stuck in error state
--chunk-ids <ids>Comma-separated list of specific chunk IDs
--limit <n>Maximum number of chunks to process

ctxe config

Manage CtxE configuration.

config init

Create default config at ~/.ctxe/config.toml.

ctxe config init

config show

Show the active (merged) configuration. Secret-bearing fields are redacted.

ctxe config show

config path

Show config file paths and their status (exists / not found).

ctxe config path

ctxe daemon

Background daemon for multi-workspace indexing. Manages workspace registry and keeps indexes fresh automatically.

daemon run

Start the daemon in foreground.

ctxe daemon run [paths...]
pathsInitial workspace paths to register

daemon add

ctxe daemon add <path>

daemon remove

ctxe daemon remove <path>

daemon list

ctxe daemon list

daemon status

ctxe daemon status

daemon stop

ctxe daemon stop

ctxe serve

Start a local HTTP server for non-MCP clients.

ctxe serve [options]
--host <addr>Bind address (default: 127.0.0.1)
--port <port>Listen port (default: 4590)

ctxe mcp

Start the MCP server on stdio. This is what AI clients (Claude Code, Cursor, etc.) invoke to communicate with CtxE.

ctxe mcp

Typically invoked automatically by the MCP client — you rarely need to run this manually.

ctxe tool

Inspect and invoke tools from the unified tool registry (same tools exposed via MCP).

tool list

List all available tools.

ctxe tool list [--category <name>]

tool describe

Show detailed info about a tool (parameters, description).

ctxe tool describe <name>

tool run

Run a tool with JSON input.

ctxe tool run <name> --json '{"query": "..."}'

Graph inspection

Debug and inspect the knowledge graph. These are advanced commands for understanding code relationships.

graph-neighbors

Query graph neighbors of a chunk.

ctxe graph-neighbors --chunk-id <id> [--edges <kinds>] [--direction <dir>] [--limit <n>]
--edgesComma-separated edge kinds (calls, called_by, references, etc.)
--directionincoming, outgoing, or both (default: both)
--limitMaximum results (default: 20)

graph-expand

Expand graph neighborhood from seed chunks.

ctxe graph-expand --chunk-id <ids> [--edges <kinds>] [--hops <n>] [--limit <n>]
--chunk-idComma-separated seed chunk IDs
--hopsMaximum hops (default: 2)
--limitMaximum nodes to return (default: 50)

graph-path

Find paths between two chunks in the graph.

ctxe graph-path --from <id> --to <id> [--edges <kinds>] [--max-hops <n>] [--max-paths <n>] [--strategy <s>]
--max-hopsMaximum hops (default: 5)
--max-pathsMaximum paths to return (default: 3)
--strategyshortest or all_simple (default: shortest)

graph-container

Show structural container metadata for a chunk (file, module, package).

ctxe graph-container --chunk-id <id>

ctxe classify-chunks

Classify chunk embeddings using chunk-type exemplars (e.g., function, type definition, test, config).

ctxe classify-chunks [path] [--all] [--limit <n>]
--allClassify all embedded chunks (default: stale/missing only)
--limitMaximum chunks to classify

ctxe classify-report

Show chunk-type classification distribution report.

ctxe classify-report [path]

ctxe version

Show version and build info.

ctxe version