oikos/.agents/dev/CONTRIBUTING.md

# Agent developer guide

Instructions for AI agents working on the Oikos codebase. Read this after
[AGENTS.md](../../AGENTS.md) and [OIKOS.md](../OIKOS.md). Human developers:
see [CONTRIBUTING.md](../../CONTRIBUTING.md) for a human-friendly version.

## Codebase map

```
cmd/oikos/main.go          Entry point. Subcommands: api, scheduler, notifier, migrate,
                             seed, export, secret, all
cmd/nomos/main.go          Nomos MCP client gateway (standalone binary, formerly Hermes)
cmd/webhook/main.go        Gitea deploy-webhook receiver (push-to-deploy on mac-mini)
internal/httpapi/           REST + MCP server. Chi router. OpenAPI-generated types from
                             internal/httpapi/gen/api.gen.go. Strict server in impl.go.
internal/mcp/               MCP tool implementations (get_entity, search_knowledge, etc.)
internal/adapters/postgres/  Connection pool (pool.go), seed ingestion (seed.go), DB→YAML
                             export (export.go), type hierarchy (typetree.go)
internal/adapters/postgres/queries/  SQL query files → sqlc generates sqlcgen/ (same dir)
internal/scheduler/         Observe loop: probes, signals, check_defs
internal/actuator/          SSH execution with circuit breaker + retry
internal/learning/          Pattern extraction, anomaly detection
internal/notifier/          Matrix notification + approval token generation
internal/policy/            Risk classifier (read policy.yaml → classify action)
internal/secrets/           Backend abstraction: Infisical (primary) + SOPS (fallback)
internal/domain/            Core types: entities, approvals, executions, signals, patterns
internal/ontology/          Type hierarchy validation, relationship checks
internal/knowledge/         Knowledge YAML seed ingestion
internal/config/            Config loading from env vars
api/openapi.yaml            REST API contract. Source of truth for endpoints.
api/codegen.yaml            oapi-codegen config → generates internal/httpapi/gen/
migrations/                 Forward-only SQL. Format: NNN_name.up.sql. No down migrations.
seeds/                      Bootstrap YAML. ontology.yaml, inventory.yaml, policy.yaml,
                             knowledge.yaml. Regenerated from DB via oikos export.
compose/                    Dockerfiles. oikos/ (2-stage, Go only — SPA is built/deployed
                             separately), nomos/ (distroless).
                             Caddy config at compose/caddy/Caddyfile.oikos.
scripts/                     Deploy, rollback, watchdog, verification, cutover checklist.
checks/                      Host health-check scripts run over SSH by the scheduler.
tools/                       Client auto-setup scripts (checks).
nomos/                       Nomos config.yaml, SOUL.md, skills.
.agents/                     Agent instruction files, domains, shared conventions, skills.
plans/                       Design documents. active/ + done/.
docs/adr/                    Architecture decision records. Numbered, prefix-sorted.
```

## Development loop

```bash
# Start dependencies
make dev

# Generate code after API/SQL changes
make generate

# Build
make build

# Run tests
make test           # all unit tests
make test-db        # integration tests (needs compose Postgres)

# Lint
make lint

# CI drift guard (run before commit)
make generate-check
```

## Adding a feature or phase

Oikos features follow a phase model (read [OIKOS.md](../OIKOS.md) for the
current phase status). To add a new capability:

1. **ADR first.** Write an architecture decision record in `docs/adr/` with
   the next sequence number. Document the decision, context, alternatives
   considered, and consequences.
2. **Plan.** If the change is non-trivial, create a plan in `plans/` following
   the template in [page-templates.md](../shared/page-templates.md).
3. **Schema.** If the feature needs new DB tables, write a forward-only
   migration in `migrations/`. Use `IF NOT EXISTS` for idempotency.
4. **API.** If the feature exposes endpoints, define them in
   `api/openapi.yaml` first, then run `make generate`, then implement.
5. **Domain.** Add types to `internal/domain/` before adding logic.
6. **Tests.** Write tests alongside implementation. Integration tests go in
   `*_test.go` in the relevant package, using the compose Postgres.
7. **Policy.** If the feature introduces new mutation types, update
   `seeds/policy.yaml` and the classifier in `internal/policy/`.
8. **Run `make generate-check`** before commit to ensure generated code is
   current.

## SQL conventions

- Queries live in `internal/adapters/postgres/queries/*.sql` with `-- name: FuncName :exec`
  annotations for sqlc. Generated code in `internal/adapters/postgres/sqlcgen/` — never
  hand-edit. Call via `sqlcgen.New(pool).QueryName(ctx, params)`.
- **sqlc is the default** for all DB access. Raw `pool.Query/Exec` with inline
  SQL is a documented carve-out for cases sqlc can't express: `LISTEN`/`NOTIFY`,
  dynamic WHERE-clause builders, `blast_radius()` (opaque return type), and
  `COPY`. All other DB access should go through sqlc queries.
- Use `pgx/v5` driver. UUIDs use `pgtype.UUID`, timestamps use `time.Time`
- CTEs for graph traversals (blast radius, dependency chains)
- CAGGs and retention policies for TimescaleDB hypertables
- FTS via `tsvector` + `tsquery` for knowledge search (migration 011)

## OpenAPI codegen

- Config: `api/codegen.yaml`. Uses `oapi-codegen/v2` with Chi server template
- Generated output: `internal/httpapi/gen/api.gen.go` — never hand-edit
- Strict server interface: `api.gen.go` generates the `StrictServerInterface`;
  implement it in `internal/httpapi/impl.go`
- Problem+JSON errors via `internal/httpapi/problem.go` — RFC 9457 format
- Cursor pagination, If-Match/ETag, idempotency keys, SSE streaming
- **Non-OpenAPI routes carve-out:** ~10 routes are registered manually on
  the chi router in `internal/httpapi/server.go` rather than generated from
  `openapi.yaml`. These fall into three categories:
  1. **Auth/infra** (`/healthz`, `/api/v1/auth/oidc-*`, `/oidc-callback`) —
     must bypass the auth middleware or aren't JSON API endpoints.
  2. **SSE override** (`/api/v1/events/stream`) — in the spec but
     re-registered manually because the strict handler can't `Flush()` per
     event.
  3. **Ad-hoc aggregations** (`/api/v1/knowledge/recent`,
     `/api/v1/knowledge/content/{id}`, `/api/v1/activity/recent`,
     `/api/v1/activity/session/{id}`, `/api/v1/learning/timeline`,
     `/api/v1/learning/trend`) — return derived/aggregate shapes that don't
     map cleanly to a schema type. If one of these stabilizes, promote it
     to `openapi.yaml` with a proper schema and migrate the `serve*`
     function to a strict handler.
  The full list with reasons is in the "Non-OpenAPI routes" comment block
  at the top of `NewHandler` in `server.go`.

## Testing philosophy

- **Race detector always on.** `make test` runs `go test -race -cover ./...`
- **Integration tests** use the compose Postgres. Run with `make test-db`.
  Each test creates + tears down its own schema namespace.
- **Coverage gates** in CI: policy + learning ≥ 80%, others ≥ 60%
- Tests use `testing.T` directly, no assertion library
- Table-driven tests for validation and classification logic

## Migration rules

- Forward-only. No down migrations (ADR 0008)
- Idempotent: use `IF NOT EXISTS`, `DO $$ BEGIN ... END $$` blocks
- Sequence numbers are sequential integers (001, 002, ...)
- Each migration file is `NNN_name.up.sql`
- Migrations are embedded in the binary via `migrations/embed.go`

## Seed files

- `seeds/ontology.yaml` — entity types, relationship types, lifecycles
  (validated against schema in `internal/ontology/`)
- `seeds/inventory.yaml` — hosts, services, entities (the topology)
- `seeds/policy.yaml` — risk classes, approval rules, autonomy settings
- `seeds/knowledge.yaml` — documents, investigations, runbooks (DB is source
  of truth; this file is the DR export)
- After DB changes via the API, run `make export` to regenerate seeds

## Secrets handling

- No secrets in code, config, or commits
- Dev secrets in `.env` (gitignored)
- Primary: Infisical (`internal/secrets/infisical.go`)
- Fallback: SOPS + age (`internal/secrets/sops.go`)
- Backend interface: `internal/secrets/backend.go`
- Machine identities via Infisical UniversalAuth
- In-memory cache with TTL for performance

## Staging and deployment

- CI pipeline: `.gitea/workflows/ci.yml` — lint, vet, vulncheck, test, docker build
- Deploy: `scripts/deploy.sh` — git pull → docker build → compose up → health check
- Watchdog: `scripts/watchdog.sh` — 2-minute cron, Matrix alert on failure
- Rollback: `scripts/rollback.sh` — checkout SHA + pg_restore
- Cutover checklist: `scripts/cutover-checklist.md`

## Writing conventions

Apply [writing-style.md](../shared/writing-style.md) for all committed prose.
Terse, reference-style, no marketing vocabulary. Code comments explain intent
and trade-offs, not mechanics.

Apply [caveman.md](../shared/caveman.md) for agent communication. The caveman
standard applies to agent *chat responses*, not committed documentation.

## Skills

Agent skills live under `.agents/skills/<name>/SKILL.md`. Each skill has a
frontmatter description that tools match against tasks. To add a skill:

1. Create `.agents/skills/<name>/SKILL.md`
2. Include frontmatter with description field
3. Document the procedure following the runbook template
4. Reference relevant files, commands, and policy classes

Skills that require code (e.g. linting) may include companion scripts in the
same directory.

## When in doubt

- Query MCP tools first (search_knowledge, get_entity)
- Read the relevant ADR in `docs/adr/`
- Grep the codebase: `rg <symbol> internal/`
- Check `plans/` for in-progress work that may conflict
- Classify any new mutation against `seeds/policy.yaml` before suggesting it