# Changelog

All notable changes to ontoref are documented here.
ADRs referenced below live in `adrs/` as typed Nickel records.

---

## [Unreleased]

### Protocol Migration System — progressive NCL checks for consumer project upgrades (ADR-010)

Replaces the template-prompt approach with an ordered, idempotent migration system. Applied state
determined by check result alone — no state file. 6 migrations shipped; runtime ships
`migrate list/pending/show` with interactive group dispatch.

#### `reflection/migrations/` — 6 ordered migrations

- `0001-ontology-infrastructure` — `.ontology/manifest.ncl` and `connections.ncl` present.
- `0002-adr-typed-checks` — no `check_hint` in ADR instance files (`adr-[0-9][0-9][0-9]-*.ncl`);
  check narrowed from `adrs/` broad scan to exclude schema/template infrastructure files.
- `0003-manifest-self-interrogation` — `capabilities[]` and `requirements[]` non-empty in manifest.ncl.
- `0004-just-convention` — justfile validates against canonical module convention (pending in this repo — documented gap).
- `0005-mode-step-schema` — all reflection mode steps declare `actor`, `on_error`, `depends_on`.
- `0006-claude-agent-entrypoint` — `Agent Entry-Point Protocol` section present in `.claude/CLAUDE.md`.

All NuCmd checks rewritten from bash to valid Nushell: `&&` removed, `$env.VAR` replacing `$VAR`,
no bash-style redirects. Grep checks on ADR files use `adr-[0-9][0-9][0-9]-*.ncl` glob.

#### `reflection/modules/migrate.nu` — new module

- `migrate list [--fmt] [--actor]` — all migrations with applied/pending status; JSON for agents.
- `migrate pending [--fmt] [--actor]` — pending only.
- `migrate show <id> [--fmt]` — runtime-interpolated instructions; accepts short ids (`002` → `0002`).
- Applied state: `run-migration-check` dispatches over `FileExists | Grep | NuCmd`.
- No state file — idempotent by construction.

#### `reflection/nulib/interactive.nu` + `help.nu` — `migrate` group wired

- `group-command-info` — `migrate` case added (list, pending, show).
- `run-group-command` — `migrate` dispatch added.
- `help-group` — `migrate` help section added; fallback "Available groups" updated.

#### `reflection/bin/ontoref.nu` — shims + aliases

- `main migrate`, `main migrate list/pending/show` added.
- Short aliases: `mg`, `mg l`, `mg p`.

#### `reflection/schemas/justfile-convention.ncl` — export fix

- Removed `Module` and `ModuleSystem` from the exported record (open contract fields with no default
  value caused `nickel export` to fail). Both remain as `let` bindings for internal NCL use.

#### on+re update

| Artifact | Change |
|----------|--------|
| `adrs/adr-010-...ncl` | Created — protocol migration system, progressive NCL checks |
| `.ontology/core.ncl` | `protocol-migration-system` node added; `adopt-ontoref-tooling` artifacts updated; `adr-lifecycle` updated with ADR-010; 4 new edges |
| `.ontology/state.ncl` | `protocol-maturity` catalyst updated (10 consumers, all features complete); blocker narrowed to `ontoref.dev not yet published` |

---

### Manifest Self-Interrogation Layer — capabilities, requirements, critical deps (ADR-009)

Three new typed arrays in `manifest_type` answering operational self-knowledge queries distinct from
ontology Practice nodes. `describe requirements` new subcommand; `describe guides` extended.

#### `ontology/schemas/manifest.ncl` — three new types

- `capability_type` — `id`, `name`, `summary`, `rationale`, `how`, `artifacts[]`, `adrs[]`, `nodes[]`.
  `nodes[]` cross-references ontology node IDs; `adrs[]` cross-references ADR IDs.
- `env_target_type` — `'Production | 'Development | 'Both` classification axis for requirements.
- `requirement_kind_type` — `'Tool | 'Service | 'EnvVar | 'Infrastructure`.
- `requirement_type` — `id`, `name`, `env`, `kind`, `version`, `required`, `impact`, `provision`.
- `critical_dep_type` — `id`, `name`, `ref`, `used_for`, `failure_impact` (required), `mitigation`.
- `manifest_type` gains `description | String | default = ""` (bug fix — `collect-identity` was reading
  a field that didn't exist), `capabilities[]`, `requirements[]`, `critical_deps[]` (all `default = []`).
- New exports: `EnvTarget`, `RequirementKind`, `Capability`, `Requirement`, `CriticalDep`.

#### `ontology/defaults/manifest.ncl` — three new builders

- `make_capability`, `make_requirement`, `make_critical_dep` added alongside existing builders.
- New type re-exports: `EnvTarget`, `RequirementKind`, `Capability`, `Requirement`, `CriticalDep`.

#### `reflection/modules/describe.nu` — new subcommand + extended outputs

- `describe requirements` — renders requirements grouped by env (Production / Development / Both) and
  critical deps table (name, ref, used_for, failure_impact, mitigation). `--environment` flag filters.
- `describe capabilities` extended — loads `manifest.capabilities?` and renders a `PROJECT CAPABILITIES
  (manifest)` section with name, summary, artifacts per entry.
- `describe guides` output gains `capabilities`, `requirements`, `critical_deps` keys — agents on cold
  start via `ontoref_guides` MCP tool receive full self-interrogation context without extra tool calls.
- Bug fix: `collect-identity` was reading `manifest.kind?` (field absent from schema, always returned
  `""`) — changed to `manifest.repo_kind?`. Same fix for `manifest.description?` (now exists).

#### `.ontology/manifest.ncl` — ontoref self-described

- `description` field populated.
- 3 capabilities: `protocol-spec`, `daemon-api`, `reflection-modes` — each with rationale, how,
  artifacts, adrs, nodes cross-references.
- 5 requirements: `nushell` (both), `nickel` (both), `rust-nightly` (dev), `surrealdb` (prod optional),
  `stratumiops` (dev optional) — each with impact and provision.
- 3 critical deps: `nickel-lang`, `inventory`, `axum` — each with failure_impact and mitigation.

#### on+re update

| Artifact | Change |
|----------|--------|
| `adrs/adr-009-...ncl` | Created — manifest self-interrogation layer, three semantic axes |
| `.ontology/core.ncl` | `manifest-self-description` node added (29 nodes, 59 edges); `adr-lifecycle` updated with ADR-009 |
| `.ontology/state.ncl` | `protocol-maturity` blocker + `self-description-coverage` catalyst updated |

---

### Config Surface — typed config, NCL contracts, override-layer mutation

Per-project config introspection, coherence verification, and audited mutation. NCL contracts are the single
validation gate; config mutation never modifies source NCL files.

#### `crates/ontoref-daemon/src/config.rs` — typed `DaemonNclConfig` (parse-at-boundary)

- `DaemonNclConfig` — top-level deserialize target for `nickel export .ontoref/config.ncl | daemon --config-stdin`;
  fields: `nickel_import_paths`, `ui: UiConfig`, `log: LogConfig`, `mode_run: ModeRunConfig`,
  `nats_events: NatsEventsConfig`, `actor_init: Vec<ActorInit>`, `quick_actions: Vec<QuickAction>`,
  `daemon: DaemonRuntimeConfig`. `#[cfg(feature = "db")] db: DbConfig`. All `#[serde(default)]`.
- Each section struct derives `#[derive(Deserialize, ConfigFields)]` + `#[config_section(id, ncl_file)]`
  — emits `inventory::submit!(ConfigFieldsEntry{...})` at link time.
- `DaemonRuntimeConfig` — optional port, timeouts, sweep intervals, `notification_ack_required: Vec<String>`.

#### `crates/ontoref-daemon/src/main.rs` — 3-tuple bootstrap block

- Bootstrap block changed to `(nickel_import_path, loaded_ncl_config, stdin_raw)` — `loaded_ncl_config: Option<DaemonNclConfig>`
  replaces raw `Option<serde_json::Value>`. `stdin_raw: Option<serde_json::Value>` retained only
  for service-mode `projects` extraction.
- `apply_stdin_config` now deserializes JSON to `DaemonNclConfig` before applying CLI overrides;
  `apply_ui_config` signature changed from `&serde_json::Value` to `&UiConfig`.
- `load_config_overrides` returns `(Option<String>, Option<DaemonNclConfig>)` — all `.get("daemon").and_then(...)` chains
  replaced with typed field access (`ncl.daemon.port`, etc.).
- NATS call site updated to `loaded_ncl_config.as_ref().map(|c| &c.nats_events)`.
- `resolve_asset_dir` gated with `#[cfg(feature = "ui")]`; `#[allow(unused_variables)]` on bootstrap tuple for `--no-default-features`.

#### `crates/ontoref-derive/src/lib.rs` — `#[derive(ConfigFields)]` macro

- New `proc_macro_derive` `ConfigFields` with helper attribute `config_section(id, ncl_file)`.
  Extracts serde-renamed field names; emits `inventory::submit!(ConfigFieldsEntry{section_id, ncl_file, struct_name, fields})`.
- Extracted `serde_rename_of(field)` helper to fix `clippy::excessive_nesting` (depth was 6).
  Field names collected via `.iter().map(|f| serde_rename_of(f).unwrap_or_else(|| f.ident...)).filter(|s| !s.is_empty())`.

#### `crates/ontoref-daemon/src/config_coherence.rs` — clippy fixes

- `and_then(|_| full_export.as_ref())` → `.and(full_export.as_ref())` (unnecessary lazy evaluation).
- Extracted `merge_meta_into_section` helper to reduce nesting depth for `_meta_*` record merging.

#### `crates/ontoref-daemon/src/api.rs` — `index_section_fields` helper

- Extracted `index_section_fields` to fix `clippy::excessive_nesting` at the cross-project field indexing loop.
  Skips `_meta_*` and `_overrides_meta` keys; indexes `(section_id, field) → Vec<(slug, value)>`.

#### `.ontoref/contracts.ncl` — new file

NCL contracts for ontoref's own config sections using `std.contract.from_validator` (not the deprecated `fun label value =>` pattern):

- `LogLevel` — enum validator: `error | warn | info | debug | trace`
- `LogRotation` — enum validator: `daily | hourly | never`
- `PositiveInt` — `value > 0 && is_number`
- `Port` — `value >= 1 && value <= 65535`
- `LogConfig` — applies per-field contracts + defaults (`level = "info"`, `rotation = "daily"`, `max_files = 7`)
- `DaemonConfig` — all fields optional (override-only); port, timeouts, intervals, `notification_ack_required`

#### `.ontoref/config.ncl` — contracts applied

- `let C = import "contracts.ncl"` added at top.
- `log | C.LogConfig = { ... }` — contract enforced before JSON reaches Rust.

#### `.ontology/manifest.ncl` — config surface enriched

- `contracts_path = ".ontoref"` added to `config_surface`.
- `log` section: `contract = "contracts.ncl → LogConfig"` added.
- New `daemon` section: `contract = "contracts.ncl → DaemonConfig"`, consumer `daemon-config` pointing to
  `crates/ontoref-daemon/src/config.rs → DaemonRuntimeConfig` with 7 declared fields.

### Protocol

- ADR-007 extended: `#[derive(ConfigFields)]` is a second application of the `inventory::submit!` / `inventory::collect!`
  linker registration pattern first established by `#[onto_api]`. Both are now referenced from the `config-surface` node.
- ADR-008 accepted: NCL-first config validation and override-layer mutation. NCL contracts are the single validation gate;
  Rust structs are contract-trusted with `#[serde(default)]`. Config mutation writes `{section}.overrides.ncl` with
  `_overrides_meta` audit record; original NCL source files are never modified. nickel export validates the merged
  result before commit; contract violations revert the override file.
  ([adr-008](adrs/adr-008-ncl-first-config-validation-and-override-layer.ncl))

### Self-Description — on+re Update

`.ontology/core.ncl` — new Practice node, updated nodes, 6 new edges:

| Change | Detail |
| --- | --- |
| New node `config-surface` | Yang — typed DaemonNclConfig, ConfigFields inventory registry, override-layer mutation API, NCL contracts, multi-consumer manifest schema; `adrs = ["adr-007", "adr-008"]` |
| Updated `adr-lifecycle` | ADR-007 + ADR-008 added to `artifact_paths` and `adrs` list (now 8 ADRs) |

New edges: `config-surface → ontoref-daemon` (ManifestsIn/High),
`config-surface → ontoref-ontology-crate` (DependsOn/High — ConfigFieldsEntry lives in zero-dep crate),
`config-surface → api-catalog-surface` (Complements/High — shared inventory pattern),
`config-surface → dag-formalized` (ManifestsIn/High),
`config-surface → self-describing` (Complements/High — ontoref validates its own config with its own contracts),
`config-surface → adopt-ontoref-tooling` (Complements/Medium).

`.ontology/state.ncl` — `protocol-maturity` blocker updated to record config surface completion.
`self-description-coverage` catalyst updated with session 2026-03-26 additions.

Previous: 4 axioms, 2 tensions, 27 practices. Current: 4 axioms, 2 tensions, 28 practices.

---

### API Catalog Surface — `#[onto_api]` proc-macro

Annotated HTTP surface discoverable at compile time via `inventory`.

- `crates/ontoref-derive/src/lib.rs` — `#[proc_macro_attribute] onto_api(method, path, description, auth, actors,
  params, tags)` emits `inventory::submit!(ApiRouteEntry{...})` for each handler; auth validated at compile time
  (`none | viewer | admin`); param entries parsed as `name:type:constraint:description` semicolon-delimited
- `crates/ontoref-daemon/src/api_catalog.rs` — `ApiRouteEntry` + `ApiParam` structs (`&'static str` fields for
  process lifetime); `inventory::collect!(ApiRouteEntry)`; `catalog()` returns sorted `Vec<&'static ApiRouteEntry>`
- `GET /api/catalog` — annotated with `#[onto_api]`; returns all registered routes as JSON sorted by path+method;
  no auth required
- `GET /projects/{slug}/ontology/versions` — per-file reload counters as `BTreeMap<filename, u64>`;
  counter bumped on every watcher-triggered NCL cache invalidation
- `describe api [--actor] [--tag] [--auth] [--fmt json|text]` — queries `/api/catalog`, groups by first tag,
  renders auth badges, param detail per route; available as `onref da` alias
- `describe diff [--file <ncl>] [--fmt json|text]` — semantic diff of `.ontology/` files vs HEAD via
  `git show HEAD:<rel> | mktemp | nickel export`; diffs nodes by id, edges by `from→to[kind]` key;
  available as `onref df` alias
- `ontoref_api_catalog` MCP tool — calls `api_catalog::catalog()` directly; filters by actor/tag/auth; returns `{ routes, total }`
- `ontoref_file_versions` MCP tool — reads `ProjectContext.file_versions` DashMap; returns per-filename counters
- Web UI: `/{slug}/api` page — table with client-side filtering (path, auth, method) + expandable detail panel; linked from nav and dashboard
- Dashboard: "Ontology File Versions" section showing per-file counters; "API Catalog" card
- `insert_mcp_ctx` in `handlers.rs` updated: 15 → 28 tools (previously stale for qa, bookmark, action, ontology extensions, validate, impact, guides)
- `HelpTool` JSON updated: 8 entries added (validate_adrs, validate, impact, guides, bookmark_list, bookmark_add, api_catalog, file_versions)
- `MCP ServerHandler::get_info()` instructions updated to mention `ontoref_guides`, `ontoref_api_catalog`, `ontoref_file_versions`, `ontoref_validate`

### Protocol Update Mode

- `reflection/modes/update_ontoref.ncl` — new mode bringing existing ontoref-adopted projects to protocol v2;
  9-step DAG: 5 parallel detect steps (manifest, connections, ADR check_hint scan, ADRs missing check, daemon
  /api/catalog probe), 2 parallel update steps (add-manifest, add-connections — both idempotent via
  `test -f || sed`), 2 validate steps (nickel export with explicit import paths), 1 aggregate report step
- `templates/ontology/manifest.ncl` — consumer-project stub; imports `ontology/defaults/manifest.ncl` via import-path-relative resolution
- `templates/ontology/connections.ncl` — consumer-project stub; imports `connections` schema; empty upstream/downstream/peers with format docs
- `reflection/modes/adopt_ontoref.ncl` — updated: adds `copy_ontology_manifest` and `copy_ontology_connections`
  steps (parallel, `'Continue`, idempotent); `validate_ontology` depends on both with `'Always`
- `reflection/templates/update-ontology-prompt.md` — 8-phase reusable prompt for full ontology enrichment:
  infrastructure update, audit, core.ncl nodes/edges, state.ncl dimensions, manifest.ncl assets,
  connections.ncl cross-project, ADR migration, final validation

### CLI — `describe` group extensions and aliases

- `main describe diff` and `main describe api` wrappers in `reflection/bin/ontoref.nu`
- `main d diff`, `main d api` — short aliases within `d` group
- `main df`, `main da` — toplevel aliases (consistent with `d`, `ad`, `bkl` pattern)
- QUICK REFERENCE: `describe diff`, `describe api`, `run update_ontoref` entries added
- `help describe` description updated to include `diff, api surface`

### Self-Description — on+re Update

`.ontology/core.ncl` — 1 new Practice node, 3 updated nodes, 3 new edges:

| Change | Detail |
| --- | --- |
| New node `api-catalog-surface` | Yang — #[onto_api] proc-macro + inventory catalog; GET /api/catalog; describe api; ApiCatalogTool; /ui/{slug}/api page |
| Updated `describe-query-layer` | Description extended: describe diff (semantic vs HEAD) and describe api (annotated surface) |
| Updated `adopt-ontoref-tooling` | Description extended: update_ontoref mode, manifest/connections templates, enrichment prompt; artifact_paths updated |
| Updated `ontoref-daemon` | 11 pages, 29 MCP tools, per-file versioning, API catalog endpoint; artifact_paths: api_catalog.rs, api_catalog.html, crates/ontoref-derive/ |
| New edge `api-catalog-surface → ontoref-daemon` | ManifestsIn/High |
| New edge `api-catalog-surface → describe-query-layer` | Complements/High |
| New edge `api-catalog-surface → protocol-not-runtime` | Complements/Medium — catalog is link-time, no runtime |

`.ontology/state.ncl` — `self-description-coverage` catalyst updated (session 2026-03-23).
`protocol-maturity` blocker updated to reflect protocol v2 completeness.

Previous: 4 axioms, 2 tensions, 20 practices. Current: 4 axioms, 2 tensions, 21 practices.

---

### Personal Ontology Schemas & Content Modes

Three new typed NCL schema families added to `ontology/schemas/` and `ontology/defaults/`:

| Schema | Types exported |
| --- | --- |
| `career.ncl` | `Skill`, `WorkExperience`, `Talk`, `Positioning`, `CompanyTarget`, `PublicationCard`, `CareerConfig` |
| `personal.ncl` | `Content` (BlogPost / ConferenceProposal / CV / Application / Email / Thread), `Opportunity` (Job / Conference / Grant / Collaboration / Podcast), `PersonalConfig` |
| `project-card.ncl` | `ProjectCard` — canonical display metadata (name, tagline, status, tags, tools, features, sort_order) for portfolio and cv_repo publication |

All types carry `linked_nodes | Array String` referencing `.ontology/core.ncl` node IDs.
`PublicationCard` is a career overlay referencing a canonical `project_node` from the portfolio repo.

Five NCL DAG reflection modes added to `reflection/modes/`:

| Mode | Purpose |
| --- | --- |
| `draft-application` | Job/grant/collaboration application anchored in personal ontology — gate alignment check, node selection, career trajectory render, status update |
| `draft-email` | Context-grounded email composition using ontology nodes as evidence |
| `generate-article` | Blog post / thread generation from project nodes and tensions |
| `update-cv` | CV refresh loop querying current career.ncl and core.ncl state |
| `write-cfp` | Conference proposal from Practice/Project nodes with gate alignment check |

### Search Bookmarks

Bookmark persistence for search results over the ontology graph. Mirrors Q&A NCL pattern (ADR-003).

- `reflection/schemas/search_bookmarks.ncl` — `BookmarkEntry` (id, node_id, kind, title, level, term, actor, created_at, tags) and `BookmarkStore` contracts
- `reflection/search_bookmarks.ncl` — typed store file; conforms to `BookmarkStore` contract
- `crates/ontoref-daemon/src/ui/search_bookmarks_ncl.rs` — `add_entry` / `remove_entry` via
  line-level NCL surgery; auto-incremented `sb-NNN` ids; concurrency-safe via `NclWriteLock`

Tests: `next_id_empty`, `next_id_increments`, `insert_into_empty_store`, `delete_first_entry`,
`delete_second_entry`, `delete_missing_id_errors`, `escape_quotes_and_backslashes`,
`concurrent_add_produces_unique_ids` (tokio, 6 concurrent tasks, asserts unique ids).

### Protocol

- ADR-006 accepted: Nushell 0.111 string interpolation compatibility fix. Four print statements in
  `reflection/bin/ontoref.nu` used `(identifier: expr)` patterns inside `$"..."` — parsed as
  command calls by Nu 0.111 parser. Fix: bare `identifier: (expr)` for label-value pairs; plain
  strings (no `$`) for zero-interpolation prints. Hard constraint: no `(label: expr)` inside
  `$"..."` in any `.nu` file. Soft constraint: zero-interpolation strings must not use `$"..."`.
  ([adr-006](adrs/adr-006-nushell-0111-string-interpolation-compat.ncl))

### Self-Description — on+re Update

`.ontology/core.ncl` — 3 new Practice nodes, updated `adr-lifecycle` and `ontoref-daemon` nodes:

| Change | Detail |
| --- | --- |
| New node `personal-ontology-schemas` | Yin — career/personal/project-card typed NCL schemas with linked_nodes DAG bridges |
| New node `content-modes` | Yang — 5 NCL DAG modes for personal content and career operations |
| New node `search-bookmarks` | Yin — bookmark persistence layer; NCL surgery via search_bookmarks_ncl.rs |
| `adr-lifecycle` | ADR-006 added to `artifact_paths` and `adrs` list |
| `ontoref-daemon` | `search_bookmarks_ncl.rs` added to `artifact_paths` |

New edges: `personal-ontology-schemas → dag-formalized` (ManifestsIn/High),
`personal-ontology-schemas → self-describing` (Complements/Medium),
`content-modes → reflection-modes` (ManifestsIn/High),
`content-modes → personal-ontology-schemas` (DependsOn/High),
`search-bookmarks → qa-knowledge-store` (Complements/High),
`search-bookmarks → ontoref-daemon` (ManifestsIn/High),
`ontoref-daemon → search-bookmarks` (Contains/High).

`.ontology/state.ncl` — `self-description-coverage` catalyst updated to include 2026-03-15 session
additions. `protocol-maturity` blocker updated to reflect Nu 0.111 fix and personal schema layer
completion.

Previous: 4 axioms, 2 tensions, 17 practices. Current: 4 axioms, 2 tensions, 20 practices.

---

### ADR–Node Declared Linkage

- `Node` schema extended with `adrs | Array String | default = []` (Nickel `ontology/schemas/core.ncl`
  and inline `CoreConfig` type).
- Rust `Node` struct gains `artifact_paths: Vec<String>` and `adrs: Vec<String>`, both
  `#[serde(default)]` — zero migration cost for existing nodes that omit the fields.
- `describe.nu` `build-howto` populates `adrs` from the node record; `render-howto` (ANSI),
  `render-howto-md`, and `howto-to-md-string` (clipboard) all emit a **Validated by** section
  when `adrs` is non-empty.
- New `GET /api/adr/{id}?slug=<slug>` endpoint — reads `adrs/<stem>.ncl`, exports via NCL
  cache, returns JSON. No auth required (read-only, loopback boundary).
- Graph UI (`graph.html`): `adrs` field passed into Cytoscape node data. Detail panel renders
  "Validated by" section with clickable `◆ <adr-id>` buttons that open a DaisyUI modal
  fetching full ADR content via the new endpoint.
- Fixed glob pattern error in `describe.nu:build-howto`: `glob $"($full)/*.rs"` replaced with
  `glob ($full | path join "*.rs")` — eliminates `//` in pattern when path has trailing separator.

### Self-Description — on+re Update

`.ontology/core.ncl` — new node, updated nodes, new edges:

| Change | Detail |
| --- | --- |
| New node `adr-node-linkage` | Practice: declares `adrs` field pattern, lists all 5 modified artifacts |
| `adr-lifecycle` | Description updated; `adrs = ["adr-001"…"adr-005"]` declared |
| `describe-query-layer` | Description updated to mention Validated by rendering |
| `ontoref-ontology-crate` | Description updated to mention `artifact_paths` + `adrs` fields; `adrs = ["adr-001"]` |
| New edge `adr-node-linkage → adr-lifecycle` | ManifestsIn/High |
| New edge `adr-node-linkage → describe-query-layer` | Complements/High |

Previous: 4 axioms, 2 tensions, 16 practices. Current: 4 axioms, 2 tensions, 17 practices.

### Ontology Three-File Split

- New Practice node `ontology-three-file-split` in `.ontology/core.ncl`: documents the
  `core.ncl` (what IS) / `state.ncl` (where we ARE vs want to BE) / `gate.ncl` (when READY
  to cross a boundary) separation and the role of `reflection/` in answering self-knowledge
  queries without reading code.
- `assets/presentation/slides.md` speaker note updated to English with reflection mention.
- `assets/web/src/index.html` "Scattered Project Knowledge" solution bullets updated (bilingual)
  to express the three-file split and `reflection/` self-knowledge layer.

### Auth & Session Model (ADR-005)

Unified key-to-session token exchange across all surfaces. All work gated on `#[cfg(feature = "ui")]`.

- `KeyEntry` gains `label: String` (`#[serde(default)]`) — audit trail for key-based sessions.
  NCL schema `install/resources/schemas/ontoref-project.ncl` updated accordingly.
- `verify_keys_list` returns `Option<KeyMatch { role, label }>` instead of `Option<Role>`.
- `SessionEntry` gains `id: String` — stable public identifier distinct from the bearer token,
  safe to expose in list responses. Prevents session enumeration by admins.
- `SessionStore` gains secondary `id_index: DashMap<id, token>` for O(1) `revoke_by_id`.
- New `SessionStore` methods: `list_for_slug`, `list_all`, `revoke_all_for_slug`,
  `revoke_by_id(id, acting_slug, acting_role) -> RevokeResult`.
- `POST /sessions` — key → UUID v4 token exchange. Accepts project keys or daemon admin password
  (`project: "_daemon"`). Rate-limited. No authentication required (it is the credential exchange endpoint).
- `GET /sessions?project=slug` — list active sessions for a project (viewer+). Without `?project=`
  param requires daemon admin and returns all sessions.
- `DELETE /sessions/{id}` — revoke by public id. Project admin: own project only. Daemon admin: any.
- `require_session()` helper: validates UUID v4 Bearer → `SessionEntry`, error boxed (`Box<Response>`)
  to satisfy `clippy::result_large_err`.
- `check_primary_auth` fast-path: UUID v4 bearer → session lookup (O(1)) before argon2 fallback (~100ms).
- `project_update_keys` (`PUT /projects/{slug}/keys`) now calls `sessions.revoke_all_for_slug` in
  addition to actor deregistration. All in-flight UI sessions for the rotated project are immediately
  invalidated.
- Daemon admin: `ONTOREF_ADMIN_TOKEN_FILE` (preferred — hash not visible in `ps aux`) or
  `ONTOREF_ADMIN_TOKEN`. Sessions use virtual slug `"_daemon"`.
- `manage_login_page` / `manage_login_submit` / `manage_logout` handlers for `/ui/manage/login`
  and `/ui/manage/logout`.
- `AdminGuard` redirects to `/ui/manage/login` when `daemon_admin_hash` is set.

### CLI Bearer Token

- `bearer-args` exported from `reflection/modules/store.nu`: returns `["-H" "Authorization: Bearer $token"]`
  when `ONTOREF_TOKEN` is set, `[]` otherwise.
- `http-get`, `http-post-json`, `http-delete` (new) in `store.nu` use `...$auth` — Bearer injected
  transparently, no behavior change when `ONTOREF_TOKEN` is unset.
- `notify-daemon-project-add` and `notify-daemon-project-remove` in `reflection/bin/ontoref.nu`
  use `bearer-args`.

### Project Setup & Onboarding

- `ontoref setup` is now the primary onboarding command (replaces manual `cp templates/` pattern).
- `--kind <K>` flag: `Service` (default) | `Library` | `DevWorkspace` | `PublishedCrate` |
  `AgentResource` | `Mixed`.
- `--parent <path>` flag: generates manifest with `implementation` layer + `<slug>-framework` layer
  and `<slug>-browse` op mode for implementation children.
- Logo auto-detection: `setup` scans `assets/` for `<slug>-logo.svg`, `<slug>.svg`, `logo.svg`
  (and `.png` variants); inserts `ui.logo` into generated `config.ncl` when found.
- `--gen-keys ["admin:label" "viewer:label"]` flag: idempotent bootstrap — skips if `role =` already
  present in `project.ncl`. Hashes via `ontoref-daemon.bin --hash-password`; prints passwords once
  to stdout.
- All `mkdir` calls in setup guarded by `if not (path | path exists)`.

### Self-Description — on+re Update

`.ontology/core.ncl` — 3 new Practice nodes, updated `ontoref-daemon` description and `artifact_paths`:

| Node | Pole | Description |
| --- | --- | --- |
| `unified-auth-model` | Yang | Key→session token exchange; session.id ≠ bearer; revoke on key rotation |
| `project-onboarding` | Yang | `ontoref setup` — idempotent scaffold, `--kind`, `--parent`, `--gen-keys` |

`ontoref-daemon` node updated: auth/session management added to description and `artifact_paths`
(`session.rs`, `auth.rs`, `login.rs`).

New edges: `unified-auth-model → ontoref-daemon`, `unified-auth-model → no-enforcement`
(Contradicts/Low — auth is opt-in), `ontoref-daemon → unified-auth-model` (Contains),
`project-onboarding → unified-auth-model` (DependsOn),
`project-onboarding → adopt-ontoref-tooling` (Complements),
`project-onboarding → daemon-config-management` (DependsOn).

`.ontology/state.ncl` — `self-description-coverage` transitions to `current_state = "fully-self-described"`.
Blocker resolved: `reflection/backlog.ncl` created, ADR-005 recorded.

`reflection/backlog.ncl` — created with 6 items: bl-001 (ontoref.dev), bl-002 (first external project),
bl-003 (`ontoref keys` CLI), bl-004 (session UI views), bl-005 (Syntaxis migration),
bl-006 (ADR-001 acceptance).

Previous state: 4 axioms, 2 tensions, 13 practices. Current: 4 axioms, 2 tensions, 15 practices.

### Protocol

- ADR-004 accepted: NCL pipe bootstrap pattern —
  `nickel export config.ncl | ontoref-daemon.bin --config-stdin`.
  Stages: Nickel evaluation → optional SOPS/Vault merge → binary via stdin.
  ([adr-004](adrs/adr-004-ncl-pipe-bootstrap-pattern.ncl))
- ADR-005 accepted: unified key-to-session auth model across CLI, UI, and MCP. Opaque UUID v4 tokens,
  `session.id ≠ bearer`, revocation on key rotation, daemon admin via `_daemon` slug.
  ([adr-005](adrs/adr-005-unified-auth-session-model.ncl))

---

### Install Infrastructure

- `install/` directory reorganized: binaries, bootstrapper, global CLI, resources, and validation
  scripts co-located.
- Binary installed as `ontoref-daemon.bin`; public entrypoint bootstrapper installed as `ontoref-daemon`.
  Users never call `.bin` directly.
- `install/ontoref-daemon-boot` (renamed from `ontoref-daemon-start`) — NCL pipe bootstrapper
  implementing ADR-004. Stages: `nickel export config.ncl` → optional SOPS/Vault secret merge →
  `ontoref-daemon.bin --config-stdin`. Supports `--dry-run`, `--sops`, `--vault`.
- `install/ontoref-daemon-boot` sets `NICKEL_IMPORT_PATH` (config dir + platform data dir schemas)
  and `NATS_STREAMS_CONFIG` (default `~/.config/ontoref/streams.json`) before launching the binary.
- `install/install.nu` — installs binary, bootstrapper, global `ontoref` CLI (ONTOREF_ROOT baked in
  at install time), UI assets, config skeleton, and global NATS topology.
  Hash-checked — unchanged files are not overwritten.
- `install/config-setup.nu` — standalone validation script: `nickel typecheck` + `nickel export`,
  path existence checks, DB and NATS liveness probes (`nc -z -w2`).
- `install/check-config-sync.nu` — CI guard asserting that every `nickel_path`-bearing field in
  `reflection/forms/config.ncl` has a matching `{{ name }}` reference in `reflection/forms/config.ncl.j2`,
  and vice versa. Wired into `just ci-lint` and `just ci-full`.

### Config Management

- `install/resources/config.ncl` — default global config skeleton with full Nickel contracts
  (`Port`, `LogLevel`, `Rotation`, `Actor`, `Severity`). Covers: daemon, db, nats_events, log,
  cache, ui, mode_run, actor_init, quick_actions, nickel_import_paths.
- `install/resources/streams.json` — global default NATS JetStream topology: ECOSYSTEM stream
  (`ecosystem.>`, 30-day retention), no project-specific consumers.
  Installed to `~/.config/ontoref/streams.json`.
- `nats/streams.json` — ontoref project-local topology with `daemon-ontoref` and `cli-notifications`
  consumers on ECOSYSTEM stream.
- `reflection/forms/config.ncl` + `reflection/forms/config.ncl.j2` — typedialog roundtrip for
  browser-based config editing (`ontoref config-edit`). Form populates fields from existing config
  via `nickel_path`; Tera template reconstructs full NCL with all contracts on save.
- `reflection/nulib/bootstrap.nu` — Nu bootstrapper helper updated: `nats-streams-config` function
  resolves `NATS_STREAMS_CONFIG` default; env var passed to daemon process via `with-env`.
- Daemon `nats.rs`: empty `streams_config` string → `None`, activating `TopologyConfig::load` fallback
  to `NATS_STREAMS_CONFIG` env var. Projects with a local `nats/streams.json` set `streams_config`
  explicitly in their config.

### Daemon Fixes

- `--config-stdin` now exclusively skips `.ontoref/config.ncl` — project config is never loaded when
  stdin config is active. Previously both paths could run.
- DB connection (`stratum-db`) only established when `db.enabled = true` in config. Previously
  connected regardless of `enabled` flag.
- NATS connection (`platform-nats`) only established when `nats_events.enabled = true`.
  "Connecting to NATS..." log moved after the enabled check.
- `NatsPublisher::connect` signature changed from `config_path: &PathBuf` (re-read file) to
  `config: Option<&serde_json::Value>` (already-loaded JSON). Eliminates double file read and ensures
  NATS uses the same config source as the rest of the daemon.
- `load_config_overrides` returns `(Option<String>, Option<serde_json::Value>)` — nickel import path
  and parsed config JSON returned together. `apply_stdin_config` returns `serde_json::Value` directly.

### Self-Description — on+re Update

`.ontology/core.ncl` — 1 new Practice node, updated `ontoref-daemon` description and artifact_paths:

| Node | Pole | Description |
| --- | --- | --- |
| `daemon-config-management` | Yang | Install + config form/template roundtrip, CI guard, global NATS topology, config-setup validation |

New edges: `daemon-config-management → ontoref-daemon` (DependsOn),
`daemon-config-management → adopt-ontoref-tooling` (Complements).

`.ontology/state.ncl` — `operational-mode` dimension description updated to reference ADR-004 bootstrap
and `NATS_STREAMS_CONFIG` mechanism. `protocol-maturity` blocker updated to reflect install pipeline
completion.

`.ontology/manifest.ncl` — `tooling` layer paths updated to include `install/` and `nats/`.

Previous state: 4 axioms, 2 tensions, 12 practices. Current: 4 axioms, 2 tensions, 13 practices.

### Protocol

- ADR-001 accepted: ontoref extracted as a standalone protocol project, independent of
  stratumiops versioning and release cycle. Consumer projects adopt via `scripts/ontoref`
  wrapper + `.ontoref/config.ncl`.
  ([adr-001](adrs/adr-001-protocol-as-standalone-project.ncl))
- ADR-002 accepted: `ontoref-daemon` introduced as optional persistent daemon for NCL export
  caching (keyed by path+mtime), actor registry (developer/agent/CI), and notification barrier
  (pre-commit hook, fail-open). Supersedes stratumiops ADR-007.
  ([adr-002](adrs/adr-002-daemon-for-caching-and-notification-barrier.ncl))
- ADR-003 accepted: Q&A and accumulated operational knowledge persist to `reflection/qa.ncl`
  — typed NCL, git-versioned, accessible via MCP tools and HTTP endpoints. localStorage
  eliminated. Q&A entries survive session boundaries and are queryable by any actor.
  ([adr-003](adrs/adr-003-qa-and-knowledge-persistence-as-ncl.ncl))

### Crates

- `ontoref-ontology`: Rust crate for loading `.ontology/*.ncl` as typed structs (`Core`, `Gate`,
  `State`). Zero stratumiops dependencies.
- `ontoref-reflection`: Rust crate for loading, validating, and executing Reflection modes as NCL
  DAG contracts. Optional `nats` feature (path dep: `platform-nats`).
- `ontoref-daemon`: Rust crate providing HTTP API (axum), DashMap-backed NCL export cache,
  notify-based file watcher, and actor registry. Optional `db` feature (path dep: `stratum-db`)
  and `nats` feature (path dep: `platform-nats`).

### Daemon — Q&A NCL Persistence (`crates/ontoref-daemon/src/ui/qa_ncl.rs`)

Line-level NCL surgery for `reflection/qa.ncl` — same pattern as `backlog_ncl.rs`. No AST parsing,
no nickel-lang-core dependency.

- `add_entry` — appends a typed `QaEntry` block before `],` array close; generates sequential `qa-NNN` ids
- `update_entry` — in-place field mutation via bidirectional scan (question + answer fields)
- `remove_entry` — removes the full block by id using backward scan for `{` and forward scan for `},`

HTTP endpoints (all under `#[cfg(feature = "ui")]` except read-only GET):

- `GET /qa-json` — export all Q&A entries as JSON (read-only, always enabled)
- `POST /qa/add` — append new entry; returns generated id
- `POST /qa/delete` — remove entry by id; invalidates NCL cache
- `POST /qa/update` — mutate question + answer fields by id; invalidates NCL cache
- `GET /actions/run` / `POST /actions/run` — execute a quick action by id; spawns `./ontoref <mode>`

Server-side hydration: `qa.html` receives `entries` as Tera context variable, embeds
`SERVER_ENTRIES` JSON literal in the page `<script>` — no fetch round-trip on load.

### Daemon — MCP Tools (`crates/ontoref-daemon/src/mcp/mod.rs`)

Four new MCP tools exposed to AI agents:

| Tool | Description |
| --- | --- |
| `ontoref_qa_list` | List Q&A entries with optional `filter` substring match. Never triggers ontology sync. |
| `ontoref_qa_add` | Append a new Q&A entry to `reflection/qa.ncl`; invalidates NCL cache. |
| `ontoref_action_list` | List all quick actions from `.ontoref/config.ncl` export. |
| `ontoref_action_add` | Create a new reflection mode at `reflection/modes/<id>.ncl` and register it as a quick action. |

Constraint: `ontoref_qa_list` and `ontoref_qa_add` never trigger `apply` steps or modify `.ontology/`
files (enforced by ADR-003).

### Daemon — Passive Drift Observation (`crates/ontoref-daemon/src/ui/drift_watcher.rs`)

Background observer bridging Yang code artifacts with Yin ontology declarations:

- Watches `crates/`, `.ontology/`, `adrs/`, `reflection/modes/` via `notify` file watcher
- 15-second debounce window before triggering scan
- Spawns `./ontoref sync scan && ./ontoref sync diff` as read-only subprocesses
- Parses stdout for MISSING / STALE / DRIFT / BROKEN markers
- Emits `ontology_drift` notification via `push_custom` when any drift is found
- Never applies changes automatically — `apply` remains a deliberate human or agent act

Started from `main.rs` under `#[cfg(feature = "ui")]`; failure to start is non-fatal (logged as warning).

### Tooling

- `reflection/modules/`: 16 Nushell operational modules (`adr.nu`, `backlog.nu`, `coder.nu`,
  `describe.nu`, `sync.nu`, etc.)
- `reflection/modes/`: 10 NCL DAG operational modes including `adopt_ontoref`, `sync-ontology`,
  `coder-workflow`, `create-pr`
- `reflection/forms/`: 7 interactive NCL forms for ADR lifecycle, backlog, and adoption
- `templates/`: Consumer-facing adoption templates (`ontoref-config.ncl`, `ontology/`, `scripts-ontoref`)
- `./ontoref`: Bash entry point with actor auto-detection, advisory file locking, and Nushell version
  guard (>= 0.110.0)

### Self-Description — on+re Update

`.ontology/core.ncl` updated with 3 new Practice nodes and 9 new edges:

| Node | Pole | Description |
| --- | --- | --- |
| `qa-knowledge-store` | Yin | Q&A entries as typed NCL — accumulated knowledge queryable by any actor |
| `quick-actions` | Yang | Runnable shortcuts over reflection modes; configured in `.ontoref/config.ncl` |
| `drift-observation` | Spiral | Passive bridge between Yang code artifacts and Yin ontology declarations |

New edges: `qa-knowledge-store → dag-formalized`, `qa-knowledge-store → coder-process-memory`,
`ontoref-daemon → qa-knowledge-store`, `quick-actions → reflection-modes`,
`quick-actions → ontoref-daemon`, `describe-query-layer → quick-actions`,
`drift-observation → ontoref-daemon`, `drift-observation → ontology-vs-reflection`,
`drift-observation → reflection-modes`.

Previous state: 4 axioms, 2 tensions, 9 practices. Current: 4 axioms, 2 tensions, 12 practices.

`reflection/schemas/qa.ncl` — `QaStore` and `QaEntry` types (id, question, answer, actor, created_at,
tags, related, verified).
`reflection/qa.ncl` — typed store file, conforms to `QaStore` contract, Nickel typecheck must pass.

---

*ontoref uses its own ADR system to track decisions. Architectural rationale lives in `adrs/`, not in this file.*
