ontoref/CHANGELOG.md

# Changelog

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

---

## [Unreleased]

### 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.*