Reference — CLI (noezis)

Ingests a file, a recursive folder, or raw text

Usage: noezis ingest [OPTIONS] [SOURCE]

Arguments:
  [SOURCE]
          Source to ingest: file path, folder (recursive), or ignored if `--text`

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)

      --text <TEXT>
          Ingests raw text directly (alternative to `<SOURCE>`)

      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`)
          
          [env: NOEZIS_CONFIG=]

      --summary <SUMMARY>
          Explicit summary — otherwise generated automatically

      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly
          
          [env: NOEZIS_PROFILE=]

      --resume
          Resumes an interrupted batch from the last checkpoint. Files already processed in the last run are skipped

      --batch-id <BATCH_ID>
          Explicit batch identifier (to resume a specific batch). Without this argument, `--resume` resumes the directory's last batch

      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)

      --force
          Bypasses content deduplication: re-ingests even the documents already indexed (upsert on the same LID). Use it to repopulate the `content` field of a store predating full-text persistence, without losing the Decisions/OpEvents (which are not re-ingested). See RB-06

      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`)
          
          [env: NOEZIS_STORE=]

      --async
          Asynchronous ingestion (ADR-0004 D3): launches a job on the daemon and tracks its progress by polling instead of holding the RPC connection open during the whole embedding. No effect in embedded mode (`--ephemeral`/`--resume`) where ingestion is already local synchronous. Reserved for ingesting a single file or text (not a directory, which already iterates file by file).
          
          `--wait` is the agent-first alias (T211): same behavior, flag name aligned with the standards (HeyGen). Blocks until `done`/`failed`, returns the full job report (not the `job_id`). Exit: `0` done, `1` failed, `124` timeout (see `--wait-timeout`). **CLI only**: the MCP tools stay atomic/non-blocking (maintainer decision).
          
          [aliases: --wait]

      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests

      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`)
          
          [env: NOEZIS_MOCK_EMBEDDER=]
          [default: false]
          [possible values: true, false]

      --wait-timeout <WAIT_TIMEOUT>
          Max wait time for the async/`--wait` job, in seconds (T211). Beyond → exit 124 (`ExitCode::Timeout`). Default 600, aligned with the hooks timeout
          
          [default: 600]

  -h, --help
          Print help (see a summary with '-h')

Ingests a session transcript (closes the learning loop)

Usage: noezis ingest-session [OPTIONS] [FILE]

Arguments:
  [FILE]  Transcript file to ingest (stdin if absent)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --session-id <SESSION_ID>
          Session identifier (generated if absent)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --extract-skills
          Extracts and indexes the skills detected in the session
      --min-ingest-delta <MIN_INGEST_DELTA>
          Idempotence: re-ingests the full transcript (costly embedding) only if it has grown by at least N bytes since this session's last successful ingestion. The delta's decisions are always asserted. `0` disables the threshold (re-ingests on every call — old behavior) [default: 4096]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --no-checkpoint
          Ignores the session checkpoint (re-processes the whole transcript)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Watches a folder (start/stop/list)

Usage: noezis watch [OPTIONS] <COMMAND>

Commands:
  start  Starts a watch
  stop   Stops a watch
  list   Lists the currently watched paths
  help   Print this message or the help of the given subcommand(s)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Management of the skills indexed in the graph

Usage: noezis skill [OPTIONS] <COMMAND>

Commands:
  list      Lists the indexed skills with status and last-use date
  feedback  Records feedback on the use of a skill
  show      Displays the full content of a skill
  prune     Removes obsolete or contradictory skills
  help      Print this message or the help of the given subcommand(s)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Sends product feedback (opt-in, T217) — local spool + central send if `[feedback].enabled`. Store-free

Usage: noezis feedback [OPTIONS] [MESSAGE]

Arguments:
  [MESSAGE]  Feedback message (read from stdin if absent)

Options:
      --category <CATEGORY>
          Free-form category (e.g. `bug`, `idea`, `praise`) [default: general]
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --send
          Attempts the central send (requires the `[feedback].enabled` opt-in + endpoint)
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --status
          Displays the central feedback opt-in state without sending anything
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Inventory of the available CLI commands and MCP tools (agent discovery)

Usage: noezis inspect [OPTIONS]

Options:
      --include-mcp
          Includes the MCP tools with their JSON schema in the output
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --check-parity
          CLI↔MCP parity gate (T210a): verifies that every MCP tool and every CLI command is classified (paired or exempted) and that the enum values of the paired commands do not diverge. Exit 1 on drift. No runtime
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --skill
          Prints the workflows manifest (embedded SKILL.md, T212) — introspection level "how to chain the commands", above the plain list. Human or machine reading (markdown)
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Displays the version and the compiled features

Usage: noezis version [OPTIONS]

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Structural children of a LID

Usage: noezis children [OPTIONS] <LID>

Arguments:
  <LID>  LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

All members of the community containing the LID

Usage: noezis community [OPTIONS] <LID>

Arguments:
  <LID>  LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Structural parent of a LID (or null if root)

Usage: noezis parent [OPTIONS] <LID>

Arguments:
  <LID>  LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

A* path between two LIDs

Usage: noezis path [OPTIONS] <FROM> <TO>

Arguments:
  <FROM>  Source LID (hex 64 chars)
  <TO>    Target LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --max-hops <MAX_HOPS>
          Maximum A* depth
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Semantic search (MCTS over the snapshot)

Usage: noezis search [OPTIONS] <QUERY>

Arguments:
  <QUERY>  Text query

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --scope <SCOPE>
          Search scope (V1: only `local` is wired) [default: local] [possible values: local, cloud, both]
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --max-hops <MAX_HOPS>
          Maximum MCTS traversal depth
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --simulations <SIMULATIONS>
          Number of MCTS simulations
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --min-score <MIN_SCORE>
          Floor score (inclusive) applied after MCTS — `f32` in `[0, 1]`. Enables adaptive exploration (broad with `0.3`, targeted with `0.85`)
      --max-results <MAX_RESULTS>
          Maximum number of nodes returned (post-MCTS truncation)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mode <MODE>
          Search leg (parity with the `noezis_search` MCP tool): `semantic` (default, MCTS over embeddings), `lexical` (pure BM25 — exact tokens/symbols, zero embed, answers even when ONNX is saturated), `hybrid` (both in parallel, sections + per-LID vote — never a combined score, decision `lexical_index_b_fusion_arbitration`) [default: semantic] [possible values: semantic, lexical, hybrid]
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
      --path-prefix <PREFIX>
          R5 — restrict results to documents whose source_path starts with this prefix (e.g. `--path-prefix DOCS/`). Semantic leg only
      --community-id <ID>
          R6 — restrict results to a Leiden community (id from graph_report). Semantic leg only
  -h, --help
          Print help

Neighbors of the node within its community

Usage: noezis siblings [OPTIONS] <LID>

Arguments:
  <LID>  LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Public summary of a LID (without centroid)

Usage: noezis summary [OPTIONS] <LID>

Arguments:
  <LID>  LID (hex 64 chars)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Formatted structural report (god nodes, communities, entropy)

Usage: noezis status [OPTIONS]

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

K-RITIK statistics and verification of the store

Usage: noezis store [OPTIONS] <COMMAND>

Commands:
  stats             Store statistics (nodes by state, edges by kind, etc.)
  verify            Verifies the K-RITIK invariants on the full snapshot (INV_N1-N7 via `verify_all`). With `--full`, additionally re-applies the 4 deterministic checks of the `IngestValidator` node by node (Merkle, Versioning, Centroid, NoEdgeToTransient), without rollback. The global `--json` then produces a structured `VerifyReport` usable in CI
  migrate           Applies the V1→V2 schema migrations (idempotent). Reads the current version in `<store_root>/_migrations/`, applies only the migrations not yet played
  gc                Purges dead nodes: `Failed` tombstones (K-RITIK rollback) + `Indexing` orphans (lost embedding/hash). WRITE — routed to the daemon (never steals the single-writer LOCK, ADR-0004). Run it outside active ingestion: any `Indexing` node is treated as an orphan
  merge-entities    `merge-entities` (G3) — retroactively merges historical duplicate entities sharing one canonical identity AND the same kind (no fuzzy matching; type-conflicts skipped). Surfaced by the entity-health audit. Dry-run by default — pass `--apply` to write. WRITE — routed to the daemon (ADR-0004); tombstones finalized by `store gc`
  retype-entities   `retype-entities` (gazetteer A4/B2/B5) — applies the curated project gazetteer to existing entities: authoritative re-typing of known project entities + tombstoning of project-garbage fragments D2 misses. Dry-run by default — pass `--apply` to write. WRITE — routed to the daemon (ADR-0004)
  purge-superseded  Purges old document versions (chained `SUPERSEDED_BY`). Safeguard: a document is purged only if the end of its version chain exists and is `Ready` (the live successor guarantees no content is lost). WRITE — routed to the daemon (ADR-0004)
  purge-uncited     Opt-in KM-4 purge of Documents uncited for more than `--days` days (default 90). Tombstones the document + its chunks to `Failed` (reversible until a later `store gc` finalizes them — never a hard delete). SAFE BY DEFAULT: simulates unless `--confirm` is passed (double-confirmation guard). WRITE — routed to the daemon (ADR-0004)
  relation-replay   Replays relation extraction for the chunks spooled after a Groq 429 rate-limit (decision `relation_spool_replay`). WRITE — routed to the daemon (ADR-0004)
  help              Print this message or the help of the given subcommand(s)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Verifies the full installation: store, embedder, triggers, version

Usage: noezis doctor [OPTIONS]

Options:
      --cpu
          CPU self-test: samples the CPU of the `noezis-mcp-server` daemons bound to this store and alerts if one exceeds `--cpu-threshold` **at rest** (leak symptom — see 2026-06-02 audit: orphan resident at ~1.2 core). Does not open the store; reads `/proc`
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --cpu-threshold <CPU_THRESHOLD>
          CPU alert threshold as a percentage of a core (default 20.0). Above, `--cpu` emits a warning and exits with code 1 [default: 20]
      --fix
          Automatically repairs the missing links by running `noezis onboard` (idempotent) on the current repo, then re-verifies. Without this flag, doctor only STATES the remediation command per link (agent-first)
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Initializes the store and the TOML configuration

Usage: noezis init [OPTIONS]

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)

      --store <STORE>
          Path to the RocksDB store

      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`)
          
          [env: NOEZIS_CONFIG=]

      --mode <MODE>
          Operating mode (V1: local only)
          
          [default: local]
          [possible values: local, cloud, hybrid]

      --embedder <EMBEDDER>
          Embedder to pre-configure
          
          [default: nomic-multi]
          [possible values: jina-v2, siglip-base, nomic-multi, mock]

      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly
          
          [env: NOEZIS_PROFILE=]

      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)

      --download
          Downloads the configured ONNX model into ~/.noezis/models/ after init. Required before any startup of the MCP server or the CLI in Onnx mode

      --force
          Rewrites the configuration even if it already exists

      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests

      --ingest-path [<PATH>]
          Immediately ingests all files in the folder after init. Without an argument: ingests the current directory. Example: `noezis init --ingest-path` → ingests `.` `noezis init --ingest-path /root/lumis` → ingests /root/lumis

      --cpu-profile <PROFILE>
          CPU consumption level during indexing and the watcher.
          
          turbo      — all cores, 0 ms/chunk  (first install, dedicated machine) balanced   — half the cores, 50 ms/chunk (active desktop) background — 1 core, 200 ms/chunk, nice 19 (default — invisible in the background) minimal    — 1 core, 500 ms/chunk, nice 19 (laptop in a meeting)
          
          [default: background]

      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`)
          
          [env: NOEZIS_MOCK_EMBEDDER=]
          [default: false]
          [possible values: true, false]

      --with-degraded-ner
          Downloads the SUB-GATE local entity models (DistilBERT NER ONNX + Qwen-0.5B relation GGUF + llama-server). OFF by default: the entity layer is gated on a capable model (cloud ≥ ~8B, BYOK) and these local backends fall below the quality bar (NER F1≈0.24) — decision `ner_quality_gate_skip_degraded`. Enable ONLY to experiment with the degraded local path (`NOEZIS_NER_ALLOW_DEGRADED=1`). The embedder, NLI and ORT runtime are always downloaded (hard deps, unaffected)

      --models-dir <DIR>
          Override the models root (default `~/.noezis/models`). Point it at a pre-populated directory (e.g. from `make bundle`) to install offline / air-gapped: models already present there are detected and NOT re-downloaded (decision `airgapped_offline_install`)

  -h, --help
          Print help (see a summary with '-h')

Lists the Noezis stores configured on this machine

Usage: noezis ls [OPTIONS]

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Progress of the ongoing indexing (INDEXING vs READY)

Usage: noezis progress [OPTIONS]

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --wait
          Blocks until indexing finishes (no INDEXING/PENDING node) instead of returning a snapshot. Designed for scripts/CI that launch an async job (`noezis ingest --async`) then wait for its completion. Exit codes: 0 = finished without failure, 1 = finished with `failed` nodes, 124 = timeout exceeded (`--timeout`). Internal polling, no LLM dependency
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --timeout <TIMEOUT>
          Maximum wait time in seconds (with `--wait`). Beyond → exit 124 [default: 300]
      --poll-interval <POLL_INTERVAL>
          Polling interval in seconds (with `--wait`) [default: 2]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

Configures the triggers for the closed learning loop

Usage: noezis setup [OPTIONS]

Options:
      --agent <AGENT>
          Target agent for hook generation [default: claude-code] [possible values: claude-code, hermes, generic]
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --dry-run
          Displays the generated configuration without applying it
      --config-path <PATH>
          Path to the agent config (auto-detected if absent)
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help

MCP JSON-RPC 2.0 stdio transport (mode 2)

Usage: noezis mcp [OPTIONS] <COMMAND>

Commands:
  serve         Launches the stdio MCP server (mode 2 — external agents)
  inspect       Lists the 12 MCP tools with their JSON schemas
  schema        Exports the full catalog of MCP tools (name, description, tier, use_when, inputSchema) as JSON on stdout — single source for SDK generation or third-party agent documentation
  generate-sdk  Generates a thin SDK (~10 lines per tool) emitting the corresponding `tools/call` JSON-RPC calls over stdio, from the descriptors
  help          Print this message or the help of the given subcommand(s)

Options:
      --json
          Line-delimited JSON output (eases `jq`, scripts, CI)
      --config <CONFIG>
          Path to the TOML configuration (default: `~/.noezis/config.toml`) [env: NOEZIS_CONFIG=]
      --profile <NAME>
          Named configuration profile (T215) — loads `~/.noezis/profiles/<NAME>.toml` instead of the default config. Ignored if `--config` is passed explicitly [env: NOEZIS_PROFILE=]
      --deliver <TARGET>
          Delivers JSON output somewhere other than stdout (T216): `file:<path>` or `webhook:<url>`. Opt-in: the target must match a prefix of `[delivery] allow` in the config (otherwise refused)
      --store <STORE>
          Path to the SurrealDB store (overrides the config's `[store].path`) [env: NOEZIS_STORE=]
      --ephemeral
          Uses an in-memory (non-persistent) store — handy for tests
      --mock-embedder [<MOCK_EMBEDDER>]
          Forces the use of MockEmbedder (deterministic SHA-256) regardless of the configuration. Useful for tests without a downloaded ONNX model. Equivalent to `NOEZIS_MOCK_EMBEDDER=1` (also accepts `true`/`yes`/`on`) [env: NOEZIS_MOCK_EMBEDDER=] [default: false] [possible values: true, false]
  -h, --help
          Print help