ontoref/README.md

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  <img src="assets/ontoref-logo.svg" alt="ontoref" width="320" />
</p>

<br>

**ontoref** is a protocol specification and tooling layer for structured self-knowledge in
software projects. It provides schemas, Nushell automation, and Rust crates so that projects
can describe what they are, record architectural decisions, track operational state, and
execute formalized procedures — all as typed, queryable artifacts.

---

## Axioms

| Axiom | Meaning |
| --- | --- |
| **Protocol, Not Runtime** | Never a runtime dependency. Projects adopt the protocol; ontoref provides the schemas and modules to do so. |
| **Self-Describing** | Consumes its own protocol: `.ontology/`, `adrs/`, `reflection/` in this repo ARE ontoref running against itself. |
| **No Enforcement** | ontoref defines contracts. There is no enforcement mechanism. Coherence is voluntary and emerges from justified adoption. |
| **DAG-Formalized Knowledge** | Concepts, tensions, decisions, state — encoded as DAGs. Enables transversal queries and impact analysis. |

## Layers

```text
ontology/          Protocol specification — Nickel schemas for nodes, edges, ADRs, state, gates
adrs/              Architecture Decision Records — typed NCL with constraints and ontology checks
reflection/        Operational tooling — Nushell modules, DAG modes, forms, and schemas
crates/            Rust implementation — typed struct loaders and mode executors
.ontology/         Self-description — ontoref's own ontology, state, gate, and manifest
```

## Crates

| Crate | Purpose |
| --- | --- |
| `ontoref-ontology` | `.ontology/` NCL → typed Rust structs: Node, Edge, Dimension, Gate, Membrane. `Node` carries `artifact_paths` and `adrs` (`Vec<String>`, both `serde(default)`). Graph traversal, invariant queries. Zero deps. |
| `ontoref-reflection` | NCL DAG contract executor with guards (pre-flight Block/Warn checks) and convergence loops (RetryFailed/RetryAll). ADR lifecycle, step dep resolution, config seal. `stratum-graph` + `stratum-state` required. |
| `ontoref-daemon` | HTTP UI (11 pages), actor registry, notification barrier, MCP (34 tools), search engine, search bookmarks, SurrealDB, NCL export cache, per-file ontology versioning, annotated API catalog, Agent Task Composer. |
| `ontoref-derive` | Proc-macro crate. `#[onto_api(...)]` annotates HTTP handlers — `description` is optional when a `///` doc comment exists (first line used as fallback). `#[onto_mcp_tool(name, description, input_schema)]` registers MCP tool unit-structs in the catalog at link time via `inventory::submit!(McpToolEntry{...})`; the annotated item is emitted unchanged and `ToolBase`/`AsyncTool` impls remain on the struct. `#[derive(OntologyNode)]` + `#[onto(id, name, paths, description, adrs)]` auto-registers nodes via `inventory::submit!` at link time, merged into `Core` by `merge_contributors()`. `#[derive(ConfigFields)]` + `#[config_section(id, ncl_file)]` registers config struct fields. All four aggregate via `inventory::collect!`. |

`ontoref-daemon` caches `nickel export` results (keyed by path + mtime), reducing full sync
scans from ~2m42s to <30s. The daemon is always optional — every module falls back to direct
subprocess when unavailable.

### Daemon Capabilities

**Unified Auth Model** — all surfaces (CLI, UI, MCP) exchange a key for a UUID v4 session token
via `POST /sessions`. Token lifetime: 30 days, O(1) lookup. Project keys carry `role`
(admin|viewer) and `label` for audit trail. Daemon-level admin via `ONTOREF_ADMIN_TOKEN_FILE`.
`GET /sessions` and `DELETE /sessions/{id}` for session visibility and revocation. Key rotation
invalidates all sessions for the rotated project. CLI injects `ONTOREF_TOKEN` as Bearer
automatically.

**Q&A Knowledge Store** — accumulated Q&A entries persist to `reflection/qa.ncl` (typed NCL,
git-versioned). Not localStorage. Any actor — developer, agent, CI — reads the same store.

**MCP Server** — 34 tools over stdio and streamable-HTTP, all registered at link time via
`#[onto_mcp_tool]` (no manual catalog wiring). Categories: discovery, retrieval, project
state, ontology, backlog, validation, Q&A, bookmarks, API surface. Representative subset:

| Tool | What it does |
| --- | --- |
| `ontoref_guides` | Full project context on cold start: axioms, practices, gate, actor policy |
| `ontoref_api_catalog` | Annotated HTTP surface — all routes with auth, actors, params, tags |
| `ontoref_file_versions` | Per-file reload counters — detect which ontology files changed |
| `ontoref_validate_adrs` | Run typed ADR constraint checks; returns pass/fail per constraint |
| `ontoref_validate` | Full project validation: ADRs, content assets, connections, gate consistency, manifest coverage |
| `ontoref_impact` | BFS impact graph from a node, optionally across project connections |
| `ontoref_qa_list` | List Q&A entries with optional filter |
| `ontoref_qa_add` | Append a new Q&A entry to `reflection/qa.ncl` |
| `ontoref_action_list` | List quick actions from `.ontoref/config.ncl` |
| `ontoref_action_add` | Create a reflection mode + register as a quick action |

**Search Bookmarks** — search results persist to `reflection/search_bookmarks.ncl` (typed NCL,
`BookmarkEntry` schema). Same atomic-write pattern as Q&A. IDs are sequential `sb-NNN`.
Concurrency-safe via `NclWriteLock`. Add and remove from the daemon search UI.

**Personal Ontology Schemas** — `ontology/schemas/career.ncl`, `personal.ncl`, `project-card.ncl`
provide typed contract layers for career and content artifacts (Skills, WorkExperience, Talks,
Content lifecycle, Opportunities, PublicationCards). All types carry `linked_nodes` referencing
core ontology node IDs — bridging career artifacts into the DAG. Five content/career reflection
modes (`draft-application`, `draft-email`, `generate-article`, `update-cv`, `write-cfp`) query
these schemas to ground output in declared project artifacts rather than free-form prose.

**API Catalog** — every HTTP handler carries `#[onto_api(method, path, auth, actors, params, tags)]`.
`description` is sourced from the first `///` doc line above the handler — no duplication with doc comments.
At link time `inventory::submit!` registers each route. `GET /api/catalog` returns the full annotated
surface as JSON. The `/ui/{slug}/api` page renders it with client-side filtering (method, auth, path).
`describe api [--actor] [--tag] [--fmt]` renders the catalog in the CLI. `ontoref_api_catalog` exposes
it to MCP agents.

**Semantic Diff** — `describe diff [--file <ncl>] [--fmt json|text]` computes a node- and edge-level
diff of `.ontology/` files against the last git commit. Reports added/removed/changed nodes by id and
edges by `from→to[kind]` key — not a text diff.

**Per-File Versioning** — each ontology file tracked in `ProjectContext.file_versions: DashMap<PathBuf, u64>`.
Counter increments on every watcher-triggered reload. `GET /projects/{slug}/ontology/versions` and
`ontoref_file_versions` MCP tool expose the map. Dashboard surfaces the counters.

**ADR–Node Linkage** — nodes declare which ADRs validate them via `adrs: Array String`.
`describe` surfaces a **Validated by** section per node (CLI and `--fmt md`). The graph UI
renders each ADR as a clickable link that opens the full ADR content via `GET /api/adr/{id}`.

**Browser-Style Panel Navigation** — graph, search, and api_catalog UI pages carry a
back/forward history stack (cursor-into-array model). Clicking nodes, ADRs, or search results
pushes to history; clicking artifacts opens the source file in the configured repository or
docs. `card.repo` in `card.ncl` resolves to `{repo}/src/branch/main/{path}` (Gitea format).
For `.rs` files, `card.docs` redirects to the cargo docs URL instead. `insert_brand_ctx`
injects both as `card_repo`/`card_docs` into every Tera template.

**Passive Drift Observation** — background file watcher that detects divergence between Yang
code artifacts and Yin ontology. Watches `crates/`, `.ontology/`, `adrs/`, `reflection/modes/`.
After a 15s debounce runs `sync scan + sync diff`; emits an `ontology_drift` notification when
MISSING/STALE/DRIFT/BROKEN items are found. Never applies changes — `apply` is always deliberate.

**Quick Actions** — runnable shortcuts over reflection modes, configured as `quick_actions` in
`.ontoref/config.ncl`. Accessible from HTTP (`/actions`), CLI (`ontoref`), and MCP
(`ontoref_action_list/add`).

**Config Surface** — per-project config introspection, coherence verification, and documented
mutation. Rust structs annotated with `#[derive(ConfigFields)]` + `#[config_section(id, ncl_file)]`
register their field names at link time via `inventory::submit!(ConfigFieldsEntry{...})`. The daemon
queries `inventory::iter::<ConfigFieldsEntry>()` at startup to build a zero-maintenance registry of
which Rust fields each struct reads from each NCL section. Multi-consumer coherence
(`GET /projects/{slug}/config/coherence`) compares the inventory registry against NCL export keys,
Nu script accessor patterns, and CI fields declared in `manifest.ncl` — any NCL field claimed by no
consumer is flagged unclaimed. `GET /projects/{slug}/config/quickref` generates living documentation
(rationales, override history, coherence status) on demand.

Config mutation never modifies source NCL files. `PUT /projects/{slug}/config/{section}` writes a
`{section}.overrides.ncl` file with only the changed fields plus a `_overrides_meta` audit record
(actor, reason, timestamp, previous value), then appends a single idempotent import line to the
entry-point NCL using the `&` merge operator. `nickel export` validates the merged result against the
section's declared contract before committing; contract violations revert the override file and return
the nickel error verbatim. NCL contracts (`std.contract.from_validator`) are the single validation
gate — Rust structs are contract-trusted readers with `#[serde(default)]`.

Ontoref demonstrates the pattern on itself: `.ontoref/contracts.ncl` applies `LogConfig` and
`DaemonConfig` contracts to `.ontoref/config.ncl`. ([ADR-008](adrs/adr-008-ncl-first-config-validation-and-override-layer.ncl))

**Protocol Migration System** — protocol upgrades for consumer projects expressed as ordered NCL files
in `reflection/migrations/NNN-slug.ncl`. Each migration declares a typed check (`FileExists | Grep |
NuCmd`) whose result IS the applied state — no state file, fully idempotent. `migrate list` shows all
migrations with applied/pending status; `migrate pending` lists only what is missing; `migrate show <id>`
renders runtime-interpolated instructions (project_root and project_name auto-detected). NuCmd checks are
valid Nushell (no bash `&&`, `$env.VAR` not `$VAR`). Grep checks targeting ADR files scope to
`adr-[0-9][0-9][0-9]-*.ncl` to exclude schema/template infrastructure files. 12 migrations shipped;
`0012-rust-doc-authoring-pattern` adds the `/// → //! → node description` three-layer doc convention
and optional pre-commit hooks (`docs-links`, `docs-drift`) to consumer `CLAUDE.md`. ([ADR-010](adrs/adr-010-protocol-migration-system.ncl))

**Manifest Self-Interrogation** — `manifest_type` gains three typed arrays that answer self-knowledge
queries agents and operators need on cold start: `capabilities[]` (what the project does, why it was
built, how it works — with explicit `nodes[]` and `adrs[]` cross-references into the DAG),
`requirements[]` (prerequisites classified by environment: `'Production | 'Development | 'Both` and
kind: `'Tool | 'Service | 'EnvVar | 'Infrastructure`), `critical_deps[]` (external dependencies with
required `failure_impact` and optional `mitigation`). `describe requirements` surfaces these; `describe
guides` and `ontoref_guides` include all three arrays in their output. ([ADR-009](adrs/adr-009-manifest-self-interrogation-layer-three-semantic-axes.ncl))

**Domain Extension System** — CLI commands conditional on `repo_kind`. The ontoref bash wrapper
resolves the first argument against `$ONTOREF_ROOT/domains/{id}/repo_kinds.txt` before delegating to
the Nu dispatcher; if the project's `repo_kind` matches, the domain's `commands.nu` is dispatched
directly. Each domain ships `domain.ncl` (typed contract: commands, pages, short_alias, repo_kinds),
`commands.nu` (Nu entry point), and `repo_kinds.txt` (grep-readable, sub-1ms dispatch). Two domains
shipped: `personal` (PersonalOntology — cfp, career, content, opportunities) and `provisioning`
(DevWorkspace/Mixed — state, connections, gates, card, backlog). Short aliases (`personal`, `prov`)
work as both `ore prov <cmd>` and standalone `prov <cmd>`. `ore help` and `describe capabilities`
surface the active domain automatically. New domains require only three files — no changes to the Nu
dispatcher. ([ADR-012](adrs/adr-012-domain-extension-system.ncl))

**Mode Hierarchy Validation** — `validate modes [--check]` reads `reflection/defaults/workflow.ncl::level_hierarchy`
and checks every `.ncl` mode file for: level declared, strategy declared, delegate chain coherent,
compose `extends` references valid. `mode resolve <id>` prints which hierarchy level handles the
given mode and why. `validate modes --self-test` generates synthetic fixtures in a temp dir for
fast CI smoke-testing of the validator itself. ([ADR-018](adrs/adr-018-workflow-layer-model.ncl))

**Project Picker — vault and registry badges** — each project card surfaces OCI state inline:
registry participant badge (`⟳ <participant>`) when `registry_provides` is declared; vault badge
(`⛁ <vault_id> · N`) coloured green (declarative) or amber (legacy) when `sops.enabled` is true.
Expanded project panel shows a collapsible **Registry** section with namespace, endpoint, and
push/pull capability. The manage page adds **Runtime Services** toggles — MCP and GraphQL can be
switched without a daemon restart via HTMX `POST /ui/manage/services/{service}/toggle`.

**VCS Abstraction Layer** — `reflection/modules/vcs.nu` exposes a uniform API over jj and git:
`detect`, `show-committed`, `restore-file`, `remote-url`, `current-branch`, `uncommitted-files`,
`commit-count`. All ontoref modules consume `vcs.nu` — never hardcoded `^git`. Detection is
filesystem-based (`.jj/` vs `.git/`), no config required. jj is opt-in: all operations degrade to
git when `.jj/` is absent. `reflection/bin/jjw.nu` wraps jj workspaces, ontoref runs, and optional
Radicle patch submission into a single `jjw agent create|step|publish|merge|discard` lifecycle for
agent-driven development. `jjw-ncl-merge.nu` is a jj merge tool for `.ontology/` NCL conflicts,
registered manually in `~/.config/jj/config.toml`. jj and Radicle are not protocol requirements —
consumer projects use plain git without any configuration change.

## Install

```sh
just install-daemon        # build + install binary, bootstrapper, CLI, UI assets, config skeleton
ontoref config-edit        # browser form → ~/.config/ontoref/config.ncl
ontoref-daemon-boot        # NCL pipe bootstrap: nickel export config.ncl | daemon --config-stdin
ontoref-daemon-boot --dry-run   # preview composed JSON without starting
```

Installed layout (`~/.local/bin/`):

| Binary | Role |
| --- | --- |
| `ontoref` | Global CLI dispatcher — all reflection modes, ADR lifecycle, daemon control |
| `ontoref-daemon` | Bootstrapper (public entrypoint) — validates config via Nickel, pipes JSON to binary |
| `ontoref-daemon.bin` | Compiled Rust binary — never called directly |

Global config at `~/.config/ontoref/config.ncl` (type-checked Nickel). Global NATS stream topology at
`~/.config/ontoref/streams.json`. Project-local topology override via `nats/streams.json` +
`nats_events.streams_config` in `.ontoref/config.ncl`.

## Onboarding a project

```sh
cd /path/to/my-project
ontoref setup                          # idempotent; kind: Service by default
ontoref setup --kind Library           # Library | Service | DevWorkspace | PublishedCrate | AgentResource | Mixed | PersonalOntology
ontoref setup --parent /path/to/fw     # implementation child: adds framework layer + browse mode
ontoref setup --gen-keys ["admin:dev" "viewer:ci"]   # bootstrap auth keys (no-op if keys already exist)
```

`ontoref setup` creates `.ontoref/project.ncl`, `.ontoref/config.ncl` (with logo auto-detection),
`.ontology/` scaffold, `adrs/`, `reflection/modes/`, `backlog.ncl`, `qa.ncl`, git hooks, and
registers the project in `~/.config/ontoref/projects.ncl`.

For existing projects that predate `setup`, or to bring an already-adopted project up to the
current protocol version (adds `manifest.ncl` and `connections.ncl`):

```sh
ontoref --actor developer adopt_ontoref    # first-time adoption
ontoref run update_ontoref                 # bring existing project to protocol v2
```

The `update_ontoref` mode detects missing v2 files, adds them idempotently, validates both with
`nickel export`, scans ADRs for deprecated `check_hint` fields, and prints a protocol update
report. The reusable `reflection/templates/update-ontology-prompt.md` guides an agent through
full ontology enrichment in 8 phases.

`ONTOREF_PROJECT_ROOT` is set by the consumer wrapper — one ontoref checkout serves multiple projects.

## Credential vault and registry federation

ontoref ships a credential model for projects publishing or consuming OCI artifacts
(domain contracts and integration modes) on a self-hosted registry like ZOT.
The model is layered, declarative, and avoids ambient docker config:

- **Layer 0** — master age private key (`.kage`) per actor, declared in
  `~/.config/ontoref/config.ncl::vault.master_key_path` (override per-project
  in `<project>/.ontoref/project.ncl::sops.master_key_path`)
- **Layer 1** — `access.sops.yaml` per project, multi-recipient encrypted; carries
  `zot_username`, `zot_password`, `vault_key`, `cosign_password`
- **Layer 2** — operation credentials (RO/RW per registry entry) under
  `src-vault/registry/`, referenced by `manifest.ncl::registry_provides[].credential_sops*`

Tenant isolation within a single vault uses sops `creation_rules` driven by
`sops.recipient_groups` + `sops.recipient_rules` in `project.ncl` — different
clients/agents get disjoint recipient sets per file, all in one vault. Multi-vault
is explicitly out of scope ([ADR-019](adrs/adr-019-per-file-recipient-routing-tenant-isolation.ncl)).

**Adoption** — copy a template from `install/resources/templates/sops/`:

| Template | When to use |
|---|---|
| `single-team/` | One team, no tenant separation |
| `multi-tenant/` | Multiple clients with isolated credentials |
| `agent-first/` | AI agents (MCP) read a single read-only credential |

For integration artifacts (publishing domain contracts or consuming someone's mode),
templates in `install/resources/templates/integration/`: `domain-producer/`,
`mode-producer/`, `mode-consumer/`.

**Day-to-day**:

```sh
ore secrets bootstrap         # create vault for a new project (admin only)
ore secrets sync              # pull latest src-vault from ZOT
ore secrets open              # acquire OCI lock + edit access.sops.yaml
ore secrets close             # impact report → push → release lock
ore secrets describe          # full inventory: groups, rules, scopes, ops
ore secrets audit             # 6 ADR-017 + ADR-019 constraint checks
```

See FAQ entries in `reflection/qa.ncl` for diagrams, troubleshooting, and the
15 named errors. ADRs: [017](adrs/adr-017-registry-credential-vault-model.ncl)
(vault model) and [019](adrs/adr-019-per-file-recipient-routing-tenant-isolation.ncl)
(per-file recipient routing).

## Prerequisites

- [Nushell](https://www.nushell.sh/) >= 0.110.0
- [Nickel](https://nickel-lang.org/) (for schema evaluation)
- Rust toolchain (for building crates)
- [Just](https://just.systems/) (for CI recipes)
- [age](https://github.com/FiloSottile/age) + [sops](https://github.com/getsops/sops) (credential vault, ADR-017/019)
- [oras](https://oras.land/) + [cosign](https://github.com/sigstore/cosign) ≥ 2 (OCI artifact federation)
- [restic](https://restic.net/) or [kopia](https://kopia.io/) (vault snapshots)

To build `ontoref-daemon` and `ontoref-reflection` with NATS/SurrealDB support, the
stratumiops repo must be checked out at `../../../stratumiops`. Without it, build without
default features:

```sh
cargo build -p ontoref-daemon --no-default-features
cargo build -p ontoref-ontology   # always standalone
```

## Development

```sh
cargo check-all                              # check all targets + features
cargo test-all                               # run full test suite
just ci-lint                                 # clippy + TOML + Nickel + Markdown
just ci-docs                                 # rustdoc broken intra-doc link check
just ci-full                                 # all CI checks
nu --ide-check 50 reflection/modules/<file>.nu  # validate a Nushell module
./ontoref --actor developer <mode>           # run a reflection mode
./ontoref sync diff --docs                   # crate //! drift against ontology nodes
./ontoref describe workspace                 # per-crate doc coverage + drift status
```

### Doc authoring convention

Three canonical layers — no duplication across them:

| Layer | Where | Read by |
|-------|-------|---------|
| `///` first line | handlers, structs, types | `#[onto_api]`, `#[derive(OntologyNode)]`, MCP |
| `//!` first sentence | `lib.rs` | `describe features`, mdBook crates chapter, drift check |
| node `description` | `.ontology/core.ncl` | UI graph, `describe project`, CLI |

`sync diff --docs --fail-on-drift` (used by pre-commit `docs-drift` hook) enforces that `//!` first
sentence stays aligned with the practice node description (Jaccard ≥ 0.20 threshold).

## License

MIT OR Apache-2.0