akm-cli 0.9.30 → 0.9.32

package/docs/architecture/specs/stash-organization-conventions.md

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+# Design: bundle organization & back-linking conventions
+
+Status: accepted (conventions shipped in the bundle skeleton)
+Author: akm
+Date: 2026-07-11
+
+> **Amended by the 0.9.0 surface decisions.** Two mechanisms this document
+> records as closed are superseded; the sections below that narrate the
+> 2026-07-12 amendments are kept as a historical record, not current guidance:
+> - **A tooled rename** (`akm mv`, SPEC-7) — the command still ships, but only
+>   as an **Experimental** surface outside the stability contract: its
+>   inbound-ref rewriting is inverted relative to the body-ref grammar. A rename
+>   is delete plus create: the destination is a new identity and learned state
+>   does not follow it. The recommended forced-rename procedure is the manual
+>   one (move, fix inbound refs, `akm index`, `akm lint`). See
+>   [0.9.0-decisions.md D3](0.9.0-decisions.md#d3--renames-are-delete--create-akm-mv-ships-experimental).
+> - **The ref-prefix filter** (SPEC-4) — the `<type>:<prefix>/` spelling is
+>   retired in favour of conceptId prefixes (`memories/projecta/`,
+>   `bundle//skills/`). See
+>   [0.9.0-decisions.md D4](0.9.0-decisions.md#d4--browse-uses-conceptid-prefixes-not-type).
+>
+> The no-rename default this document argues for is therefore *stronger* under
+> 0.9.0, not weaker: no tool you may rely on makes a rename cheap.
+
+## Problem
+
+The bundle skeleton already ships per-type authoring conventions
+(`facts/conventions/assets/<type>.md`) that tell an agent **how to write** each
+asset type. Nothing told an agent **where to place** an asset (which
+subdirectory) or **how to cross-link** it. Yet placement and linking are exactly
+what determine whether the same knowledge is *retrievable* two sessions later, or
+re-derived from scratch — and whether cross-project reuse happens or duplicates
+accumulate.
+
+The request that drove this: define conventions that instruct agents how to
+organize assets under their type directories (subdirectories for projects,
+domains, etc.) and how to back-link them to improve retrieval during agentic
+tasks. This document records the analysis, a structured debate, and the resulting
+conventions.
+
+## What AKM's mechanics dictate (the ground truth)
+
+Any organization scheme has to fit how AKM actually stores and retrieves. The
+load-bearing facts, each verified in code:
+
+1. **Path becomes the ref.** A file's subpath under its type dir is part of its
+   ref name — `memories/projectA/auth-tip.md` → `memory:projectA/auth-tip`. Works
+   for every type. A ref-prefix query syntax exists since SPEC-4 landed
+   (amended 2026-07-11): `akm search "memory:projectA/"` enumerates exactly
+   that subtree (typed, recursive, `/`-boundary exact) and a bare `memory:`
+   enumerates the whole type. At review time the idiom was false —
+   `sanitizeFtsQuery` strips `:` and `/` and `entry_type` is not an FTS
+   column, so the query degenerated to token noise (empirically tested; see
+   the Review round). `akm search "projectA" --type memory` remains the
+   token-match alternative. The path is
+   therefore the one facet you cannot express twice and cannot change without
+   breaking the ref (and every inbound reference to it).
+2. **Retrieval is search, not browse — and folders are highly visible to the
+   ranker.** There is no folder walk at query time — agents `akm search`/
+   `akm curate`, then `akm show <ref>`. A subdirectory's real payoff: its tokens
+   join the FTS `name` column at the highest bm25 weight (10.0), always merge
+   into `tags` (since SPEC-2 landed; see fact 6), and match the cwd
+   project-context boost (`projectContextRankingContributor`, +0.2/token,
+   cap 0.5). No "indexing-confidence bump" for subdirectories exists in code.
+3. **The FTS surface is `name`, `description`, `tags`, `hints`, `content`**
+   (`entries_fts`, `src/storage/repositories/index-schema.ts`). There is **no `project` field** —
+   a bare `project:` frontmatter value is invisible to search. Off-axis facets
+   must be `tags` to be retrievable.
+4. **`xrefs:` fold into the FTS `hints` field for all types**
+   (`src/indexer/search/search-fields.ts:58`). Back-links are a *retrieval*
+   signal, not decoration — which means both too few and too many degrade
+   ranking.
+5. **Project relevance is recovered at query time.** Ranking blends
+   a per-project usage signal — `scopedUtility * 0.7 + globalUtility * 0.3`
+   (`SCOPED_UTILITY_BLEND_SCOPED`, `src/indexer/search/ranking-contributors.ts`),
+   keyed by a cwd-anchor (a hash of the querying project root), not the asset's
+   path. It is NOT rename-proof for the asset: `entry_key` includes the full
+   name, so renaming a file mints a new entry row and orphans its accumulated
+   global + scoped utility history. As of 0.9.0 that is the defined semantics —
+   a rename is delete plus create, and no command preserves learned state
+   across one (see 0.9.0-decisions.md D3). A
+   reusable asset does not need the *project* baked into its path to rank well
+   inside a project — and a manual rename costs learned ranking.
+6. **Directory (scope/domain) tokens always merge into `tags`** — since SPEC-2
+   landed (`extractDirTagsFromName`, `src/indexer/passes/metadata.ts`) they are
+   derived from the canonical ref subpath, so explicit `tags` no longer
+   suppress the scope token, both indexing walks agree, and the exact-tag
+   ranking boost fires for the path token without restating it. Filename
+   tokens are still auto-derived only when `tags` is empty (they already live
+   in the FTS `name` column and in aliases). The old explicit-tags footgun is
+   gone; existing installs pick the merged tags up on the next reindex.
+7. **The entity/relation graph boost extracts from body content, not the path**
+   (`graph-extraction.ts`). Canonical entity naming must live in the prose.
+8. **`category: convention|meta` facts are surfaced to every non-wiki authoring
+   flow** (`resolveStashStandards`); `facts/conventions/assets/<type>.md` is
+   surfaced type-scoped (`resolveTypeConventions`). This is the only channel that
+   reaches a browse-blind agent mid-task — so conventions must ship as facts.
+9. **Non-wiki xref breakage is caught by `akm lint`, not at write time.** The
+   deterministic `missing-ref` check covers body refs, the `refs:` frontmatter
+   array, and (since SPEC-1 landed) the `xrefs:`/`supersededBy:`/
+   `contradictedBy:` frontmatter channels. A rename dangles inbound links
+   silently — nothing catches them until the next `akm lint` run flags them, so
+   run `akm lint` as the last step of any rename. (`akm mv` automates this, but
+   its rewriting is inverted relative to the body-ref grammar, so it ships
+   Experimental in 0.9.0 and does not substitute for the lint run — see
+   0.9.0-decisions.md D3.) Wikis are excluded from
+   `akm lint`'s directory sweep; the equivalent
+   orphan/broken-xref/broken-source/stale-index/uncited-raw structural checks
+   are implemented in the LLM Wiki adapter
+   (`core/adapter/adapters/llm-wiki-adapter.ts`, ported from the pre-0.9.0
+   `akm wiki lint`). **Amendment:** the `akm wiki` command family, including
+   `akm wiki lint`, was removed in the 0.9.0 bundle-adapter cutover (see
+   [wikis.md](../../guides/wikis.md)) — there is currently no CLI surface that
+   invokes these checks.
+
+## Research inputs
+
+Three parallel research briefs (Karpathy's LLM wiki; agent memory / RAG /
+GraphRAG; PKM taxonomies — Zettelkasten, PARA, Johnny.Decimal) converged on a few
+transferable principles:
+
+- **Separate raw from synthesized, and keep raw immutable.** Karpathy's core
+  invariant: interpret and correct in a synthesized layer that *cites* the raw
+  source; never edit the source. Gives every claim an auditable provenance chain.
+- **The index is the catalog — don't hand-maintain one.** Karpathy's `index.md`
+  exists because a filesystem has no ranker. AKM already has one (plus a utility
+  signal), so effort should go into per-asset *retrievability* (strong title,
+  accurate first paragraph, tags, xrefs), not a hand-kept catalog.
+- **Metadata/facets beat folder depth for retrieval.** The literature repeatedly
+  measures metadata-enriched and "contextual"/self-situating retrieval as
+  materially better (e.g. contextual headers cutting failed retrievals by a large
+  margin) — because the reader is a ranker, not a browser.
+- **Atomicity + sparse, real links (Zettelkasten), not dense mandatory links.**
+  Backlinks help multi-hop recall, but forced density produces junk edges.
+- **Controlled vocabulary prevents bucket drift**, but deep hierarchies and
+  opaque codes (Johnny.Decimal) fail when nobody browses.
+
+## The debate
+
+Four positions were argued and adversarially critiqued:
+
+| Position | Thesis | Verdict |
+|---|---|---|
+| **Domain-first taxonomy** | Path = stable subject domain; lowest rename rate, highest lexical signal. | reject-keep-ideas |
+| **Scope-first namespacing** | Path = project/client/team; scope is the dominant retrieval filter. | reject-keep-ideas |
+| **Flat + faceted + dense backlinks** | Minimal folders; organizing signal lives in frontmatter + a dense link graph the index can read. | adopt-with-changes |
+| **Hybrid "narrowest stable scope" ladder** | One folder = the narrowest stable boundary (client > project > domain > root), rest in facets. | adopt-with-changes |
+
+The critiques were decisive:
+
+- **A single global axis fails both ways.** Domain-first makes project scope
+  invisible (no `project` FTS field; agents that write `project:` frontmatter get
+  zero retrieval benefit) and splits "everything about project A's auth" across
+  three query idioms. Scope-first strands reusable assets behind an arbitrary
+  project home and creates a `shared/` dumping ground.
+- **The per-asset "narrowest scope" ladder is non-deterministic.** Two agents run
+  the delete/archive test on equivalent insights and pick different rungs,
+  fragmenting a topic across `memory:projectA/` and `knowledge/auth/` with no
+  reconciliation pass — and the wrong guess is baked into an immutable ref.
+- **Mandatory dense xrefs actively hurt.** Because ref strings fold into the FTS
+  `hints` field, a link quota smears a popular source's ref token across dozens of
+  citers (destroying its ranking signal) and fills the entity graph with
+  plausible-but-wrong edges.
+- **Per-namespace hub wikis rot.** As an obligation they contend on concurrent
+  writes, generate stale-index lint noise, and flatten the multi-hop graph into a
+  namespace-wide star.
+
+## Decision
+
+**Resolve the project-vs-domain tension by asset TYPE, not per-asset judgment.**
+This is the one rule that is both deterministic mid-task and mechanically
+justified:
+
+- **Scope-born types** (`memory`, `lesson`, `task`, `env`, `secret`) → the
+  current **project/client** slug. They are born bound to the work in front of
+  the agent, so the working context *is* the answer — zero counterfactual
+  reasoning, and `akm search "projectA" --type memory` reconstructs the project.
+- **Reuse-born types** (`knowledge`, `skill`, `wiki`, `fact`, `script`) → a
+  stable **domain** from a short closed vocabulary. Project relevance is already
+  recovered by scoped-utility ranking (fact 5), so spending the path on the
+  project axis is redundant; the domain prefix is the only handle that
+  co-locates cross-project reuse. For a wiki, the domain names the wiki itself.
+- **Global-by-nature types** (`command`, `agent`, `workflow`, bundle-wide `env`) →
+  type root or a tool slug.
+
+Supporting rules, all shipped as convention facts:
+
+- One path axis; depth 1 (2 max for strict containment); lowercase-hyphen
+  semantic segments; **no volatile facets in the path** (status/date/version/…);
+  flat type-root fallback instead of inventing a one-off domain.
+- Off-axis facets go in `tags` (never a bare `project:` field); the path
+  scope/domain token merges into `tags` automatically, so it never needs
+  restating (fact 6).
+- **A provenance xref is mandatory when the asset derives from another** (never
+  invented for original observations). Associative xrefs are discretionary and
+  capped (~5, a heuristic). Corrections are new assets that xref what they
+  correct, paired with `beliefState: superseded`/`supersededBy` on the stale
+  asset; immutability applies to ingested material (wiki `raw/`, vendored docs,
+  transcripts) — synthesized knowledge pages are the rewritable layer (Karpathy
+  immutability inside AKM's flat model).
+- **Self-situating text on every asset** — the orientation line goes in
+  `description:`/`when_to_use:` (the higher-weight indexed fields; bounded
+  body prose also enters the lowest-weight `content` field). The body header feeds the
+  entity graph (extracted from body prose) and human readers at `akm show`.
+  Anthropic's Contextual Retrieval figures (35%/49%/67% top-20 failure-rate
+  reduction) were measured on chunk-prepended context in a chunked RAG pipeline —
+  an analogy motivating the description-field placement, not a measurement of it.
+- Hubs are optional wiki assets for a few high-traffic domains, never a per-write
+  obligation. The FTS index is the catalog.
+- A ref is an address chosen once: **default to not renaming**; if unavoidable,
+  move the file, grep the bundle for the old ref and fix inbound xrefs in the
+  same pass, then `akm index` and `akm lint`. The destination is a new identity
+  and starts with fresh learned state.
+
+Rejected over-builds: mandatory dense/bidirectional xrefs, per-namespace hub
+wikis, the per-asset scope ladder, and any hand-maintained catalog.
+
+## What shipped
+
+Convention facts in the bundle skeleton (`src/assets/stash-skeleton/facts/conventions/`):
+
+- `organization.md` (`category: convention`) — the partition-by-type placement
+  rules. Surfaced to every non-wiki author.
+- `backlinks.md` (`category: convention`) — the cross-linking / provenance /
+  canonical-naming rules. Surfaced to every non-wiki author.
+- `domains.md` (`category: convention`) — the editable domain vocabulary and
+  canonical entity spellings for reuse-born assets.
+- A short **Placement & linking** section added to each
+  `facts/conventions/assets/<type>.md`, stating that type's default axis
+  (surfaced type-scoped).
+
+Because these are `category: convention` facts, `resolveStashStandards` injects
+them into the authoring context automatically — no code change was required to
+enforce the surfacing. They are soft guidance; a bundle owner edits them to match
+how their bundle is queried.
+
+The code changes the finalized conventions imply are specced separately in
+[stash-conventions-code-spec.md](stash-conventions-code-spec.md) (8 specs,
+prioritized and sequenced; nothing implemented in this change).
+
+## Review round
+
+A two-reviewer adversarial review (retrieval mechanics / IR + KM methodology /
+agent usability), with cross-rebuttals, tuned the shipped conventions. Decisive
+corrections, each code-verified or empirically tested:
+
+- **The ref-prefix search idiom was false.** `akm search "<type>:<prefix>/"`
+  never worked (`sanitizeFtsQuery` strips `:` and `/`; `entry_type` is not an
+  FTS column) — live-tested at zero hits. All convention text now uses
+  `akm search "<slug>" --type <type>`. *Amendment (2026-07-11): SPEC-4 has
+  since made the idiom real — `<type>:<prefix>/` (and bare `<type>:`) queries
+  now translate to a typed subtree enumeration (`parseRefPrefixQuery`). The
+  finding was correct at review time; the shipped convention facts keep the
+  `--type` idiom for now (re-adoption deferred one release — see open
+  questions).*
+- **"Folders are invisible to the ranker" was backwards.** Subpath tokens are
+  indexed in the FTS `name` column at the highest weight and earn the cwd
+  project-context boost; the claimed "indexing-confidence bump" does not exist.
+- **xrefs never feed the entity graph** — extraction reads body prose
+  (memory + knowledge) with frontmatter stripped, so graph-relevant
+  relationships must be stated in the body.
+- **Body prose is not FTS/embedding-indexed** — self-situating orientation
+  belongs in `description:`/`when_to_use:`; the body header serves the graph
+  and human readers.
+- **"Rename-proof" was misleading** — a rename orphans the asset's utility
+  history (new `entry_key` row), strengthening the no-rename rule.
+  *Amendment (2026-07-12): SPEC-7 (`akm mv`) made a tooled rename preserve that
+  history.* **Superseded (0.9.0): a rename is delete plus create and orphans
+  the utility history. `akm mv`'s in-place re-key still ships, but it is
+  Experimental and nothing may be built on it, so the original finding stands
+  unqualified.**
+- **Corrections now pair with `beliefState: superseded`/`supersededBy`**
+  (parsed for all markdown types, demoted at rank time), and immutability was
+  rescoped to ingested material only, resolving a contradiction with the
+  knowledge type conventions.
+- Completeness: `script` joined the reuse-born bucket; wikis take the domain as
+  the wiki NAME; `env` got a decision test; a `conventions` domain entered the
+  vocabulary (the shipped facts had violated their own list); a two-domain
+  tie-break was added; and duplicated pointer text was trimmed from the nine
+  co-injected per-type files.
+
+## Open questions / future work
+
+Items with an implementation path were specced in
+[stash-conventions-code-spec.md](stash-conventions-code-spec.md), and all
+eight specs have since landed (amended 2026-07-12): the lint frontmatter
+channels (SPEC-1), the tag merge (SPEC-2), `--xref` (SPEC-3), the ref-prefix
+filter (SPEC-4), `--supersedes` demotion (SPEC-5), category capture (SPEC-6 —
+shipped capture-only; the rank-time demotion was dropped after measurement
+showed no crowding), `akm mv` (SPEC-7), and bounded native body indexing
+(SPEC-8) — see the closed bullets below. What remains genuinely open:
+vocabulary governance, scheduled consolidation (argued down in the spec — the
+improve pipeline already injects the amended conventions), and the typed
+provenance channel.
+
+- **A thin HARD floor.** `akm lint` runs a deterministic `missing-ref` check
+  over body text and `refs:` frontmatter for non-wiki markdown assets; the gap
+  was precisely the `xrefs:`/`supersededBy:`/`contradictedBy:` frontmatter
+  channels the conventions mandate — closed by SPEC-1 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md) (implemented:
+  the same check now scans those keys too). Orphan and uncited-source checks for
+  non-wiki assets are argued down (orphanhood is the sanctioned normal state
+  under discretionary linking; uncited-source is undecidable without knowing
+  whether an asset is derived).
+- **Kill the tag footgun in code.** Closed by SPEC-2 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md)
+  (implemented: directory tokens from the canonical ref subpath now always
+  merge into `tags`; filename tokens still derive only when `tags` is empty).
+  Takes effect on reindex; operators with collapse-detector canary sets should
+  re-mint baselines via `akm improve canary --refresh`.
+- **Vocabulary governance.** How an agent proposes a `fact:conventions/domains`
+  addition mid-task without blocking on human review (interim: flat type-root
+  fallback + a proposal note).
+- **Scheduled consolidation.** A curate/consolidate trigger to dedup near-duplicate
+  atoms, promote recurring memories into domain knowledge, and fix danglers —
+  since no reorg pass happens organically and utility ranking is cold-start-biased
+  toward incumbents.
+- **Naming collision.** The convention's "scope" wording vs the existing
+  `entry.scope` (user/agent/run/channel) / `scopeKey` concepts in code — the
+  convention facts deliberately say "project/client slug" and "partition axis" to
+  avoid cross-wiring; keep it that way.
+- **Ref-prefix filter in code.** Closed by SPEC-4 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md)
+  (implemented: `parseRefPrefixQuery` detects `<type>:<prefix>/` — and bare
+  `<type>:` — queries on the untyped search path and translates them to a
+  typed index enumeration with name-prefix narrowing; hits carry the fixed
+  browse score 1, an explicit `--type` wins over the parsed type, and the
+  in-memory prefix filter leaves an `entry_key LIKE` SQL push-down as a later
+  optimization). Whether the skeleton convention facts should re-adopt the
+  idiom over `akm search "<slug>" --type <type>` stays deferred one release so
+  older CLI versions aren't taught a query shape they don't support.
+- **A tooled rename.** Closed by SPEC-7, then **re-opened in 0.9.0 and answered
+  "not as a contract"**: `akm mv` ships Experimental and a rename is delete plus
+  create. The recommended forced-rename procedure is the manual one this
+  document originally prescribed — move the file (a memory's `.derived.md` twin
+  moves with it), grep and fix inbound refs in the same pass, then `akm index`
+  and `akm lint`. The no-rename default is again the primary defence, which
+  strengthens it. See
+  [0.9.0-decisions.md D3](0.9.0-decisions.md#d3--renames-are-delete--create-akm-mv-ships-experimental).
+- **Index self-situating body text.** Closed by SPEC-8 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md)
+  (implemented: the native adapter normalizes bounded Markdown prose into the
+  lowest-weight `content` field; secrets, env files, raw sessions, and session
+  checkpoints are excluded at the adapter boundary). The
+  `description:`/`when_to_use:` orientation routing the conventions teach
+  remains primary.
+- **Typed provenance channel.** Evaluate `sources:` for all types, indexed
+  outside `hints` — it would separate provenance from associative links and
+  resolve the xref-cap tension mechanically. Rejected for the shipped
+  convention because non-wiki `sources:` earns no retrieval benefit today and
+  provenance-in-xrefs powers the "what did we build on this?" query.
+- **Convention facts crowd domain-term queries.** Their name/description/
+  when_to_use tokens (bodies are unindexed) match via prefix expansion and carry
+  the fact type boost (0.22); consider excluding `category: convention` facts
+  from default untyped search (their delivery channel is prompt injection,
+  parallel to the `session` default exclusion) or demoting the category at rank
+  time. *Amendment (2026-07-12): closed by SPEC-6 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md), shipped
+  capture-only. The `category:` key is now captured into the index as
+  `entry.category` (takes effect on reindex), making a category-keyed policy
+  implementable — but the spec's prescribed measurement (full skeleton
+  convention facts plus a real `knowledge/auth` asset, untyped `auth` query,
+  semantic off) showed NO crowding: FTS is exact-first, so prefix expansion
+  onto the facts' tokens fires only when nothing matches the query exactly,
+  and a real domain asset always outranks the facts. The rank-time demotion
+  contributor was therefore dropped;
+  `tests/integration/search-convention-fact-demotion.test.ts` pins the no-crowding
+  invariant and is the regression guard if demotion is ever revisited.*
+- **Automate correction demotion.** Closed by SPEC-5 in
+  [stash-conventions-code-spec.md](stash-conventions-code-spec.md)
+  (implemented as the deterministic CLI form: `--supersedes <old ref>` on
+  `akm remember`/`akm import` writes the correction with the xref, sets
+  `beliefState: superseded` + `supersededBy: [<new ref>]` on the old asset,
+  and reindexes it; demoting belief states now also cap the final search
+  score so the stale incumbent cannot outrank its correction). An LLM-side
+  `curate`/`improve` pass that detects citing corrections automatically
+  remains open.