Fix doc gaps: remove qualify --workspace, add plugin options/schema annotations/programmatic API docs

docs/cli.md

@@ -221,7 +221,7 @@ apophis replay --artifact reports/apophis/failure-*.json
 
 - `--changed` requires a git repository
 - `migrate` defaults to `--dry-run` (safe by default)
-- `--workspace` is only supported by `verify` and `doctor` commands
+- `--workspace` is fully implemented by `verify` and `doctor`. `observe` and `qualify` accept the flag but run in the current package only.
 - Seeds ensure deterministic generation; handler nondeterminism (e.g., `Date.now()`) can still cause replay divergence
 
 ## Exit Codes

docs/getting-started.md

@@ -130,6 +130,102 @@ app.get('/users', {
 })
 ```
 
+## Plugin Options
+
+When registering the APOPHIS plugin, you can pass these options:
+
+```javascript
+await fastify.register(apophis, {
+  // Swagger config passthrough (if @fastify/swagger is not already registered)
+  swagger: { openapi: { info: { title: 'API', version: '1.0.0' } } },
+
+  // Runtime contract validation hooks: 'off', 'warn', or 'error'
+  // Only active in non-production environments
+  runtime: 'warn',
+
+  // Automatically clean up tracked resources after tests
+  cleanup: true,
+
+  // Global timeout in milliseconds for all requests
+  timeout: 5000,
+
+  // Tenant isolation scopes
+  scopes: {
+    tenant1: { headers: { 'x-tenant-id': '1' } },
+    tenant2: { headers: { 'x-tenant-id': '2' } },
+  },
+
+  // Auth and protocol extensions
+  extensions: [jwtAuth, apiKeyAuth],
+
+  // Plugin hook-phase contracts
+  pluginContracts: {
+    'rate-limit': { appliesTo: 'POST /users', ensures: ['status != 429'] },
+  },
+
+  // Outbound dependency contracts
+  outboundContracts: {
+    'payment-api': {
+      target: 'https://payments.example.com',
+      method: 'POST',
+      response: { 200: { type: 'object', properties: { id: { type: 'string' } } } }
+    }
+  }
+})
+```
+
+## Schema Annotations
+
+APOPHIS reads these OpenAPI schema extensions:
+
+| Annotation | Location | Description |
+|---|---|---|
+| `x-category` | Top-level | Route classification: `constructor`, `mutator`, `observer`, `destructor`, `utility` |
+| `x-ensures` | Top-level or `response[statusCode]` | Post-condition contracts (APOSTL formulas) |
+| `x-requires` | Top-level or `response[statusCode]` | Pre-condition contracts (APOSTL formulas) |
+| `x-variants` | Top-level | Request variants for content-type negotiation or feature flags |
+| `x-timeout` | Top-level or `response[statusCode]` | Per-route timeout in milliseconds |
+| `x-outbound` | Top-level | Outbound dependency contracts for this route |
+| `x-streaming` | Top-level | Mark route as streaming (populates `chunks` and `streamDurationMs` in eval context) |
+| `x-validate-runtime` | Top-level or `response[statusCode]` | Toggle runtime validation for this route (default: true) |
+| `x-extension-config` | Top-level | Per-route config for extensions (e.g., `{ jwt: { verify: false } }`) |
+
+Annotations can be placed on the top-level schema or nested inside `response[statusCode]`. Nested annotations take precedence for that status code.
+
+## Programmatic API
+
+After registration, `fastify.apophis` provides:
+
+```javascript
+// Run contract tests for all routes
+const suite = await fastify.apophis.contract({ runs: 50, seed: 42 })
+
+// Run stateful tests
+const stateful = await fastify.apophis.stateful({ runs: 50, seed: 42 })
+
+// Run a single scenario
+const scenario = await fastify.apophis.scenario({
+  name: 'oauth-basic',
+  steps: [...]
+})
+
+// Check a single route
+const result = await fastify.apophis.check('GET', '/users/:id')
+
+// Get enriched OpenAPI spec with contract metadata
+const spec = fastify.apophis.spec()
+
+// Clean up tracked resources
+await fastify.apophis.cleanup()
+
+// Test-only utilities (NODE_ENV=test only)
+fastify.apophis.test.registerPluginContracts('name', spec)
+fastify.apophis.test.registerOutboundContracts({ ... })
+fastify.apophis.test.enableOutboundMocks({ mode: 'example' })
+fastify.apophis.test.disableOutboundMocks()
+const calls = fastify.apophis.test.getOutboundCalls('payment-api')
+```
+
 ## Config Reference
 
 For the full configuration reference, see [CLI Reference](cli.md).

docs/qualify.md

@@ -250,14 +250,6 @@ Human output shows per-gate execution counts (scenario, stateful, chaos, adversi
 
 Qualify exits with code 1 if zero checks executed. This prevents silent passes when all routes are filtered out or gates are disabled.
 
-## `--workspace` Flag
-
-Run qualify across all packages in a monorepo workspace:
-
-```bash
-apophis qualify --workspace --profile oauth-nightly
-```
-
 ## Test Budget
 
 The `runs` field in your preset controls how many property-based tests execute per route. Default is 50. Lower for faster CI feedback, higher for deeper exploration: