Engram

⚠️ Breaking change. The pre-vault TOML memory-record storage layer (~/.local/share/engram/memory/) was removed. Engram now writes only to an agent-memory Obsidian vault. Migration from the old layout is not automated. An LLM should be able to migrate easily.

Overview

Engram gives Claude Code and Pi agents persistent memory via a zettelkasten-style vault. All six skills — recall, learn, please, route, curate, and write-memory — ship as SKILL.md installed by engram update. Each skill may additionally carry a companion skill-claude-<name> vault runbook note (key claude:<name>) offered by engram update/engram register-skills and curated like any other pending offer. Registration also offers runbook notes for every other skill, command and Pi prompt template the harnesses load by default: user, synced, plugin, Pi-configured, and project-local sources, namespaced by source (e.g. skill-superpowers-brainstorming, skill-project-github-com-toejough-engram-cmd-opsx-apply). please orchestrates end-to-end work by sequencing recall, learn, and other skills around a user's <ask> (matched by the literal triggers /please, take this end-to-end, please), route encodes the delegate-everything doctrine please draws on to staff its subagents, curate judges engram serve's pending-offer notes against the host vault (matched by the literal triggers curate, /curate, pending offers, pending offer), and write-memory executes the vault-write commands recall/learn invoke natively at their write sites (parents judge, the worker writes). The please and route skills are pure meta-orchestration.

engram update installs the skills into Claude Code and Pi, and the vault is harness-agnostic — so recall and learn work the same on each. Automatic sweeping of raw session transcripts into the chunk index reads Claude Code JSONL and Pi session files.

After a few months of use, the vault's wikilink graph looks like this in Obsidian — each dot is a note, each line a [[wikilink]]; dense clusters are groups of related notes, and the connective tissue reflects thematic proximity:

Screenshot pre-dates the 2026-07-10 vocab→tags migration (#678): the ~25 vocab term-note hubs visible here no longer exist — vocab membership now rides tags: [vocab/<term>], not wikilinks, so a fresh graph view no longer shows these hubs.

Installing

Requires Go 1.25+, git and git-lfs on PATH: engram update builds the binary from the engram checkout it runs in, or from a fresh clone when there is none, and refuses a clone whose embedded model is a git-lfs pointer.

1. Install the binary:

   go install github.com/toejough/engram/cmd/engram@latest

   Make sure $GOBIN (or $GOPATH/bin, default ~/go/bin) is on your PATH. This proxy-built binary is only a bootstrap: its embedded model is a git-lfs pointer (#645), and step 2 replaces it with a build from a clone.

2. Deploy the skills to every detected harness (Claude Code, Pi):

   engram update                 # install / refresh
   engram update --with-guidance # also sync guidance docs (recall.md, delegate.md, learn.md, shim.md) to engram-owned roots; --with-guidance is a one-time opt-in: once any guidance file is imported, plain `engram update` keeps all of them current
   engram update --dry-run       # show what would change, without writing
   engram update --allow-downgrade # override the local-mode refusal to install an older revision than what's installed

   engram update syncs engram artifacts to engram-owned roots per harness (~/.claude/engram/, ~/.pi/agent/engram/) and materializes them as symlinks in each harness's discovery paths (~/.claude/skills/, ~/.pi/agent/skills/, etc.). Removals from the source propagate on every update. First update performs a dark migration of pre-existing copies to symlinks. Run it again any time to upgrade — it also reinstalls the binary via go install, then re-execs the fresh binary so the sync itself runs with the new logic (792a11e The rest of the update runs in the new binary). --with-guidance additionally syncs guidance docs to the root's guidance/ subtree (canonical paths) and materializes symlinks; compat symlinks at flat paths (~/.claude/engram/*.md) keep existing @import lines in CLAUDE.md and AGENTS.md resolving (Claude Code + Pi; opt-in). It's a one-time opt-in per file — once your CLAUDE.md (or AGENTS.md) imports a guidance file, plain engram update keeps it current. Until then, plain engram update prints a one-line hint. See install-and-update for the deployment-as-sync behavior.

Skills

Skill	What it does
recall	Surfaces relevant notes and raw chunks via a single engram query call: a clustered relevance channel (recency-biased per-phrase cosine over notes+chunks → bounded matched set → one unified chunk+note clustering that builds candidate_l2s from within-cluster top-5 only) plus an explore channel (notes sampled from vocab-term centroids by proximity to the query, budgeted to the matched-note count, delivered as top-level items tagged provenance: explore) plus an un-clustered recency channel (the newest chunks, tagged recent). For each cluster (and the explore items) it judges coverage inline (covered/near/absent) and crystallizes via engram amend (update an existing note) or a handoff to the write-memory skill (create one) in its default deep mode (a glance pass is read-only), activates only the notes it actually used, then reports whether the surfaced memory changed the agent's plan.
learn	Captures the session's explicit lessons — corrections, explicit save-requests, self-discovered reversals, and confirmed approaches (positive reinforcement, user-praised or self-validated) — as permanent vault notes via write-memory handoffs. Along the way it mechanically sweeps every conversation and doc into the searchable chunk index (engram ingest --auto) and checks vocab liveness (engram vocab stats, auto-refitting when due), so raw event memory stays current even when no explicit lesson exists.

See agent-instructions/skills/{recall,learn,please,route,curate,write-memory}/SKILL.md for the full skill definitions.

All six ship with a SKILL.md (see skill-runbook-registration for the mechanism). please drives an ask end-to-end through a fixed seven-step workflow (capture, orient, plan, execute (TDD), document, complete, capture), tracked on the task list, with four adversarial review gates dispatching fresh per-angle reviewer subagents over the plan, each refactor, touched docs, and outward prose, plus a step-7 lessons audit; it is one skill and runbook note (its former three sub-runbooks merged into the single note/skill body), triggered by /please <ask> and the literal phrases take this end-to-end and please. route guides subagent selection (agent type, model, effort): easy work goes to a cheap model, complex work is decomposed before dispatch, and every dispatched subagent recalls first; please consults it when staffing gate reviewers. curate judges pending-offer notes (a child's served learn, a note pulled down from the parent) against the host vault using the same covered/near/absent reasoning recall documents, authors the runbook fields of pending skill notes instead of judging them, and composes and executes engram amend directly (an offer's content already exists as a note file, so it does not hand off to write-memory); it runs host-local only and is triggered by the literal words curate, /curate, pending offers, and pending offer. write-memory is invoked natively as a skill by recall/learn at their write sites, not reached via basename/wikilink.

Vault location

Engram reads and writes a zettelkasten vault. Resolution order:

1. --vault <path> flag
2. ENGRAM_VAULT_PATH environment variable
3. $XDG_DATA_HOME/engram/vault (fallback: ~/.local/share/engram/vault)

Every vault-resolving command (not only engram learn) creates a missing vault on first use: the directory is bootstrapped with a minimal .obsidian/ config so Obsidian recognizes it, a .gitignore, a starter README.md, a .engram/ state directory and a vault ID, and one stderr line (engram: created new vault at <path>) announces it so a mistyped --vault path is visible. An existing vault is left untouched by read-only use. See 792a2f Existing vaults are left alone.

Vault layout (flat since the 2026-06-12 flat-vault migration — notes live at the vault root; the Permanent/ and MOCs/ subdirectories are retired and ignored by the scanner):

<vault>/
  <luhmann-id>.<YYYY-MM-DD>.<slug>.md   atomic notes at the root
  <luhmann-id>.<YYYY-MM-DD>.<slug>.vec.json   sibling embedding sidecar

Binary commands

engram learn feedback --slug ... --source ... --situation ... --behavior ... --impact ... --action ... [--tag <family>[/<value>] ...] [--project <slug>] [--issue <id>]
engram learn fact     --slug ... --source ... --situation ... --subject ... --predicate ... --object ... [--tag <family>[/<value>] ...] [--project <slug>] [--issue <id>]
engram learn qa       --slug ... --source ... [--question <text>] [--answer <text>|--answer-file <path>] [--contributors <basename>...] [--certainty high|medium|low]   Write a QA pair (Q+A notes) to the vault. --slug and --source required; --answer and --answer-file are mutually exclusive; --contributors repeatable, validated against the vault; --certainty defaults to medium.
engram learn runbook  --slug ... --source ... --situation ... --done-when ... [--body <numbered steps>] [--red-flag <text> ...] [--trigger <text> ...] [--tag <family>[/<value>] ...] [--project <slug>] [--issue <id>]   Write a runbook note. `--trigger` (repeatable, each ≥ 3 chars) declares literal cues — a slash form or multi-word phrase, never a lone common word — that surface the runbook first when they appear in `engram query --text`; `engram amend --trigger` replaces the list.
engram embed apply [--all|--missing|--stale|--force|--dry-run]   (Re-)embed notes per selection (default: missing)
engram embed status                    Report counts per state (total / with-embeddings / without / stale / incompatible / broken)
engram query --phrase <p> [--phrase <p>...] [--text <user message>] [--limit N] [--project <slug>] [--chunks-dir <dir>] [--content-budget N] [--recent-fill N] [--lazy-chunks]   Semantic search over vault notes + chunk index; YAML output. `--limit` (default 20) caps the returned `items[]` count — a real, enforced cap, not report-only metadata — except runbook trigger hits, which do not count against it. (A runbook can only be a trigger hit if it has a compatible embedding sidecar.) `--text` takes the user's message verbatim (never embedded; at least one of `--phrase`/`--text` is required): a runbook whose `triggers:` list has an entry appearing in it (case-insensitive whole-word match, whitespace collapsed: `curate` hits "curate!" and "/curate" but not "accurate") is a trigger hit and leads `items[]` with provenance `trigger`, regardless of similarity. With `ENGRAM_PARENT` set, merges local + parent results into one payload — see [Parent sync](#parent-sync-engram_parent). Recency-weights chunks AND notes. Builds a bounded matched set (per-phrase top-30, union/dedup, relevance floor 0.25, cap ~300), clusters it in one pass (AutoK k-means), emits `candidate_l2s: [{path, cosine, content}]` per cluster — within-cluster top-5 notes only — plus superseded-note ride-alongs at the next rank. Separately samples an **explore** half from vocab-term centroids by proximity to the query (softmax allocation, budgeted to the matched-note count, δ=0.05 match-evidence bonus for terms with an exploit-half member, core-first within-term selection, dedupe+backfill), delivered as top-level `items[]` entries (`provenance: explore`, `source_term`; budget reported in `explore_allocated`, a term → delivered-count map, always present — `{}` on missing/unreadable centroid data). Appends the newest chunks un-clustered (tagged `recent`; default 25, controlled by `--recent-fill`). `--content-budget` caps how many chunk items render with full content (default 15; later chunks get a snippet). `--lazy-chunks` renders matched chunk items path/score only — the agent fetches evidence on demand via `engram show-chunk`. Activation is agent-driven — the binary emits no `activated` flag. --project restricts items to notes whose frontmatter `project:` matches.
engram query-chunks --phrase <p> [--phrase <p>...] [--limit N] [--chunks-dir <dir>]   Semantic search over the chunk index only (YAML output). Scores chunks by max cosine across phrases; clusters results with AutoK k-means. No vault notes, no recency channel — chunk-space search only.
engram resituate --note <ref> --situation <text>   Rewrite a note's situation field in sync: frontmatter, body opener, and sidecar situation_vector (D4/INV-S2). Both flags required; no --dry-run.
engram check   Run vault-invariant checks (G0 and G3 links, M5 situation, S1 sidecars); a PASS/WARN/FAIL line each, exit non-zero only on FAIL
engram ingest [--auto]   Merge-append session transcripts + markdown into the per-source chunk index — re-chunks/re-embeds only changed content; within one source this is append-only (a re-chunk never drops a prior record). Across sources, byte-identical content is deduplicated by content hash: only one canonical copy per hash group is indexed, and a duplicate's index file is removed only once its retained twin's index file is verified to cover every one of its own records — never on hash-match alone. `--auto` sweeps all known sources, skips session-log directories whose slugified project path starts with a non-persistent-workspace prefix (slugified forms of `/private/tmp`, `/tmp`, and macOS `$TMPDIR`), and additionally drops any resolved sweep root whose own path sits under `/tmp`, `/private/tmp`, `/var/folders`, or `/private/var/folders` — preventing eval/test runs from bloating the main index. An ancestor `.claude` dir's sweep also now excludes its `jobs/` subdirectory (agent-harness scratch, including whole snapshot copies of the vault) — matching the exclude the `.pi` ancestor sweep already had; `.claude/jobs` was previously swept and indexed. Configurable via `.engram/sweep.json` (`non_persistent_prefixes` / `non_persistent_path_prefixes` keys); bypassed by explicit `--sweep`/`--transcript`/`--markdown`/`--pi-sessions` or an isolated index via `ENGRAM_CHUNKS_DIR`. Used by /learn and /recall.
engram prune [--empty [--dry-run]] [--duplicates [--dry-run]]   Detach chunk index entries whose source file no longer exists (GC). Operator-run; reads the manifest and drops the stale per-source manifest entry, keeping the embedded chunks on disk (still searchable). `--empty` instead removes existing 0-byte `.jsonl` chunk-index files left by zero-record sources (ranking-neutral — empties hold zero records); `--duplicates` retroactively collapses every exact-content-hash group down to one canonical member, removing the rest's index files + manifest entries — safe by construction (a duplicate is removed only once its retained twin's index file is verified to cover its records; otherwise refused, not removed) and convergent (a second run removes nothing); `--dry-run` previews the count without deleting or removing. Not part of the recall/learn flows.
engram count [--group-by <attr> [--filter <attr=value>...]] [--backlinks-of <basename>]   Read-only vault aggregation, off the query/similarity path. `--group-by` counts distinct note membership per frontmatter attribute value (list attrs count one per distinct element; a value listed twice in one note still counts once), optionally restricted by repeatable AND-ed `--filter attr=value` predicates (scalar equality or list-contains); output is `value<TAB>count` lines sorted count-desc then value-asc, an `(attr absent): N` bucket when any in-set note lacks the attribute, then `total: N` (empty result prints nothing). `--backlinks-of <basename>` prints a vault-graph node's wikilink in-degree plus its sorted linkers. The two modes are mutually exclusive and each independently Obsidian-verifiable (group-by against a property/tag filter, backlinks-of against the backlinks panel) — they are NOT equal to each other: backlinks-of counts every linker (e.g. an index/MOC page) while group-by counts only frontmatter members, so the two diverge by the count of non-member linkers.
engram show <ref> [--parent]   Print a note (frontmatter + body) and its outbound wikilink targets, read-only. One required positional; no --ref flag. (candidate_l2s carry content inline, so /recall no longer shows candidates.) `--parent` resolves the ref against `ENGRAM_PARENT` instead of the local vault — errors if unset. On a local miss, with `--parent` not passed, `engram show` falls back to `ENGRAM_PARENT` automatically if configured, prefixing output with `# from_parent: true`; a local hit never contacts the parent, and with no `ENGRAM_PARENT` configured the same not-found error surfaces as before.
engram show-chunk <source#anchor> [--chunks-dir <dir>]   Print a chunk's text by its source#anchor id (read-only). Used by /recall with `--lazy-chunks` to fetch a specific chunk's evidence on demand. Local only — chunks never cross vaults, so there is no `--parent` flag and no parent fallback.
engram amend --target <ref> [--activate] [--clear-pending] [--supersedes "<basename>|<type>|<claim>"] [--chunk-source <source#anchor>...] [--situation/--subject/--predicate/--object | --behavior/--impact/--action | --done-when/--body ...] [--red-flag <text>...] [--trigger <text>...] [--discard [--into <existing>]] [--expect-hash <exchange hash>]   Amend a note in place: merge chunk-source provenance (idempotent), overwrite only supplied content fields, re-embed only on a content change; `--activate` bumps `LastUsed`; `--clear-pending` clears the pending-offer marker a served write or a pull-down set, accepting it as a normal live note; `--supersedes` writes typed supersession frontmatter + inverse + body line. `--discard` deletes the target note and its sidecar; with `--into <existing>` it folds the target's basename, aliases and parent links into `<existing>` first (curation's covered/near fold), instead of a bare delete. `--expect-hash` is required for `--clear-pending`, `--discard` and `--discard --into` on a note carrying `offer.origin`: the command fails without changing anything unless the note's current exchange hash equals the expected one (any hash that is not equal to the current one — including one from another hash version, which compares as unknown — fails), so a curator's judgment can never be silently overtaken by an in-place offer update. The /recall update path: covered link-enriches, near re-synthesizes content.
engram activate --note <ref> [--note <ref>...] [--parent]   Mark note(s) as recently used — bumps `LastUsed` in the sidecar so usefulness keeps useful notes fresh (called by /recall on only the notes the agent actually used). `--note` paths are vault-relative (resolved against the vault root / `ENGRAM_VAULT_PATH`); absolute paths are used as-is. On a local miss, a basename or `<basename>.md` ref is a parent candidate when `ENGRAM_PARENT` is set: it is fetched and written as a new local pending offer instead of failing (a bare Luhmann id never goes to the parent — ids are minted per vault). `--parent` forces parent resolution even when a local file of that name exists, and errors if `ENGRAM_PARENT` is unset; a path ref with `--parent` is refused as "not sent to the parent" rather than looked up locally. Either way, activating a parent note also bumps its use on the parent, best-effort (a failure there is not fatal). With `ENGRAM_PARENT` set, a local hit on a note linked to a parent note (a previously pulled or offered copy) also re-checks that parent note: when its exchange hash has changed since the link was recorded, and that version was not declined, the new version is pulled down as another local pending offer; an unchanged note, a declined version or an unreachable parent writes nothing and never fails the local activate. The re-check does not bump the parent note's use. A served `POST /activate` resolves refs only against the vault's note names and refuses an absolute path, a path separator or `..` with a 400.
engram vocab bootstrap --seed <yaml> [--floor <f>]     Seed vocab definition fact notes (bare `vocab` tag plus their own `vocab/<term>` self-tag per term — one family note stays bare-only) from the validated term set (--seed, required); embed them; tag all existing notes with `vocab/<term>` entries in the shared `tags:` list (no separate index file — the index is emergent via `engram count`). --floor sets the minimum cosine similarity for vocab assignment (default 0.35). Idempotent.
engram vocab tag-definitions [--vault <dir>]  Idempotent backfill: adds the missing `vocab/<term>` self-tag to every existing per-term definition note (skips the family note). Tags are not content-hash inputs so no re-embed occurs. `--vault` overrides the vault root.
engram vocab propose --term <t> --description <d>  LLM-gated: create a new vocab definition note if no existing term covers it and projected attachment ≤ 20% of vault (~$0.05/proposal). Both flags required.
engram vocab stats                     Per-term member counts, vault untagged-rate, hub terms (> 25% of vault), orphan terms (< 2 members), version staleness.
engram vocab refit [--dry-run] [--names <file>]  Derivational: derives the vocabulary from the vault's note embeddings; matches clusters to existing terms, retires unmatched derived terms (proposed terms are never auto-retired), and emits naming requests for new clusters — answer via --names <file>. --dry-run previews the matched/new/retired diff. Rewrites member `tags:` entries in the `vocab/<term>` namespace; major version bump on the family definition note (no index to regenerate — the index is emergent). Triggered growth-only (≥40 new notes AND ≥14 days).
engram update [--with-guidance]        Refresh binary, re-exec the fresh binary for the sync phase (792a11e in docs/specs/product/install-and-update.md); sync agents-instructions/{skills,guidance} to engram-owned roots and materialize as symlinks; removals propagate; dark migration on first sync ([--dry-run] previews, never installs/re-execs); --with-guidance includes guidance (canonical paths in guidance/, compat symlinks at flat paths) (Claude Code + Pi; opt-in; see 792a11 in docs/specs/product/install-and-update.md). Local-mode installs refuse a provable downgrade (installed binary's revision not an ancestor of the module root's HEAD); override with --allow-downgrade

engram serve & the two-doors model

One vault is one node, and one node has exactly one brain — but it has two doors. The local door is the CLI running directly against the vault: every command, including the host-only ones (ingest, vocab refit, prune, check, update, resituate), lives here and commits immediately. It is never served over HTTP. The network door is engram serve — the same node's HTTP surface for remote callers, exposing only a fixed subset (query, show, activate, learn). /amend, /query-chunks and /show-chunk are not served — chunks never cross vaults, and offers use /learn for both new notes and amend-offers. Both doors run the exact same Run* code paths and share the exact same vault flocks (vault-write-lock), so a local write and a served write racing the same vault never lose an update — there is no separate server-side implementation to keep in sync.

The two doors differ in write semantics, not in code path: a local learn/amend commits as a normal, immediately-live note. A served learn (a child's offer) lands as a pending offer — a normal note carrying a pending marker, excluded from query results until a curation pass (the curate runbook) judges it covered/near/absent against the existing vault and folds it in or discards it; so does a note a child pulls down from its parent (engram activate, see Parent sync below). This is deliberate: an offer is a caller outside the host's own act of record asking to contribute, not the vault owner's own write.

ENGRAM_SERVER is no longer supported: setting it is a hard error for every command; set ENGRAM_PARENT to the same URL. A served learn stamps the note's user: field from whatever identity the calling instance declares in the request body (client-detected, the same way repo: already works) — no external authentication service is required or consulted; the server rejects only an empty declared identity, nothing else. Trust for a served write rests on network reachability of the server itself, not on edge-authenticated SSO.

Parent sync: ENGRAM_PARENT

Every environment always has its own local vault — the first command that resolves a vault path creates one, with a one-line stderr notice. ENGRAM_PARENT=http://host:port names this node's single parent vault (the vault-graph is a tree — personal → team → org — never a mesh, so a node has at most one parent) and turns on symmetric, local-first exchange: this node keeps every note it writes locally, and offers/pulls notes with the parent, never chunks. Each vault has a stable random vault ID, stored in the tracked .engram-vault-id file; links to a parent's notes are keyed by that ID, not by URL, so a hostname or IP change breaks nothing. engram vault-id prints the ID and a location check; --regenerate/--claim resolve a copy or a moved vault.

Upward: offers. engram learn writes locally, then offers the note to the parent. A content-changing engram amend or engram resituate is offered too, as an amend targeting the linked parent counterpart when one exists, otherwise as a new note. Bookkeeping (--activate, --clear-pending of most notes, --discard, identity backfill, learn qa) stays local and is never offered — except that accepting a served offer (--clear-pending on a note carrying offer.origin) is itself offered onward to this vault's own parent, so an accepted note keeps propagating up the tree. Offers that the parent can't take queue in a local outbox (<vault>/.engram/outbox.json) and drain after the next successful parent contact; the parent is backed off (skipped) for a while after a failure. Nothing is lost offline, and retries never duplicate an offer.

Downward: pull-down. engram query runs locally and fetches the parent's /query, then merges the two result sets into one payload — runbook trigger hits first (local, then parent), then the direct items from both sides by descending score, then the explore picks by descending score, with --limit capping the direct and explore items and a note floor keeping enough notes among them — deduping so only the local copy of a note that exists on both sides shows. Parent chunks never travel — the parent's chunk items (including its recency channel) are dropped before the merge, chunk content budgets are local-only, and show-chunk reads only the local chunk index; only notes cross vaults. Each item carries its source's model_id as a visible, non-gating signal (the merge never refuses on a model mismatch) and a from_parent boolean so an agent knows where an item came from. engram activate on a ref that misses locally pulls the parent's note down as a new local pending offer — curation judges it like any other offer before it counts as live knowledge — and best-effort bumps the note's use on the parent too. Because the merged query shows the local copy in place of a linked parent note, activating that local copy is where a later parent-side change comes back down: activate re-checks the linked parent note and pulls a changed version down as another pending offer. If the parent is unreachable, engram query degrades to local-only results (which still include every accepted — i.e. live, non-pending — copy of a previously pulled or offered note) with a warning rather than failing, and repeated failures back off further parent contact for a while.

Fleet impact. Every environment that already sets ENGRAM_PARENT starts offering all of its learns and content amends on upgrade, so the host's curation queue (pending_offers) grows by the fleet's write rate; curating it is expected upkeep, not a bug.

BREAKING: --limit is now a real, enforced cap on engram query's returned items[] count, in every mode — local and ENGRAM_PARENT-merged alike — except that runbook trigger hits do not count against it. It was previously report-only metadata; actual item count was governed by clustering/candidate-nomination sizing with no hard ceiling. Existing callers will see at most 20 items by default where they previously saw more.

Semantic search & the embed-on-write pipeline

Engram bundles all-MiniLM-L6-v2 (384-d) inside the binary via go:embed; inference is pure Go through Hugot + GoMLX's simplego backend — no CGO, no daemon, no API key. Every note (<id>.<date>.<slug>.md) gets a sibling .vec.json sidecar written on engram learn.

For the sidecar shape and the dual-vector / recency-decay / content_hash mechanics, see docs/GLOSSARY.md (the sidecar entry) and embedding-sidecar and text-embedder. For the engram query matched-set + clustering pipeline, see the engram query line under Binary commands above (and query-engine) — the algorithm is not restated here.

engram embed CLI reference:

• engram embed status — a total and per-state counts: with-embeddings / without / stale / incompatible / broken.
• engram embed apply [--missing|--stale|--force|--all|--dry-run] — (re-)embed notes per selection: --missing (default) notes without sidecars; --stale notes whose content changed; --force notes whose sidecar is from another model or an older schema; --all every note; mode flags combine, a broken sidecar is always re-embedded, and --dry-run reports without writing.

Inputs longer than 1500 chars are truncated to MiniLM-L6's 512-token limit — a non-issue for engram's 200–500-word notes.

Project structure

cmd/engram/          CLI entry point: wiring-only single-statement main() composing cli.Primitives from checker-thin per-capability-group functions of raw capability references (all adapter composition lives in internal/cli via cli.NewDeps; enforced by targ check-thin-api)
internal/            Business logic (DI boundaries)
  chunk/             Splits transcripts/markdown into embedding-sized chunks for the chunk index (pure string logic, no I/O)
  cli/               CLI command wiring (targ targets)
  cluster/           k-means clustering with silhouette-based auto-K, for recall clustering
  context/           Transcript processing
  debuglog/          Structured debug logging
  embed/             Embedder interface + Hugot/GoMLX backend, sidecar I/O, state classification
  luhmann/           Luhmann-ID allocation under file lock
  transcript/        Session transcript reading (Claude Code + Pi JSONL), read by engram ingest
  update/            Self-refresh subcommand
  vaultgraph/        Vault traversal (wikilink graph, note scanning)
agent-instructions/
  skills/            Source for all six skills — recall, learn, please, route, curate, write-memory
  guidance/          Source for the deployable ambient guidance docs — recall-firing (recall.md), delegation-firing (delegate.md), learn-firing (learn.md), and runbook-follow-frame (shim.md)

Development

• go install ./cmd/engram — install the binary (targ has no build target; it covers check/test/lint only)
• targ test — run unit + integration tests
• targ check-full — lint + coverage (use this to see ALL errors at once)
• Never run go test / go build / go vet directly — use targ

Design principles

Design principles are summarized in AGENTS.md, and their rationale lives with the requirements they justify in the behavior record; this README covers orientation and the CLI reference only.

Documentation

See docs/AGENTS.md for the documentation conventions and the index of guides, docs/GLOSSARY.md for terms, docs/ROADMAP.md for planned and parked work, and dev/eval/LEDGER.md for proven results.