docs: final cleanup and accuracy pass before public push

- Fix const inference bug: wrap inferred contracts with status-code guards
- Add integration test for status-guarded contract inference
- Tighten and deduplicate docs across verify, qualify, getting-started, cli
- Fix broken cross-references and TypeScript→JavaScript conversions
- Fix factual errors: license, Date.now(), sampling defaults, cache env
- Add missing features: --workspace, --generation-profile, json-summary formats
- Move stale extension docs (AUTH-RATE-LIMIT-REVISED, HTTP-EXTENSIONS) to attic
- Update PLUGIN_CONTRACTS_SPEC status to Implemented
- Build: clean | Tests: 849 pass, 0 fail

docs/qualify.md

@@ -58,7 +58,11 @@ Stateful tests generate sequences of operations and track resources:
 3. **Observer**: Read resources (GET)
 4. **Destructor**: Remove resources (DELETE)
 
-APOPHIS automatically tracks created resources and cleans them up after testing.
+APOPHIS tracks created resources and runs cleanup after test completion.
+
+## Route Transparency
+
+Artifacts include `executedRoutes` and `skippedRoutes` arrays. `skippedRoutes` contains reasons such as mode mismatch, environment policy, or route filter exclusion.
 
 ## Chaos and Adversity
 
@@ -67,7 +71,9 @@ Chaos testing injects controlled failures:
 - **Delay**: Slow responses
 - **Error**: Return error status codes
 - **Dropout**: Connection failures
-- **Corruption**: Malformed response bodies
+- **Truncate**: Truncated response bodies
+- **Malformed**: Invalid JSON or content-type
+- **Field-corrupt**: Random field mutation in response objects
 
 Configure chaos in your preset:
 
@@ -84,36 +90,6 @@ presets: {
 }
 ```
 
-## Profile Examples
-
-### oauth-nightly
-
-```javascript
-profiles: {
-  'oauth-nightly': {
-    name: 'oauth-nightly',
-    mode: 'qualify',
-    preset: 'protocol-lab',
-    routes: [],
-    seed: 42
-  }
-}
-```
-
-### lifecycle-deep
-
-```javascript
-profiles: {
-  'lifecycle-deep': {
-    name: 'lifecycle-deep',
-    mode: 'qualify',
-    preset: 'protocol-lab',
-    routes: [],
-    seed: 42
-  }
-}
-```
-
 ## Non-Prod Boundaries
 
 Qualify mode is gated away from production by default:
@@ -122,7 +98,7 @@ Qualify mode is gated away from production by default:
 |---|---|---|---|
 | local | enabled | enabled | enabled |
 | test/CI | enabled | enabled | enabled |
-| staging | enabled with allowlist | synthetic-only | canary-only |
+| staging | enabled with allowlist | enabled | blocked on protected routes |
 | production | disabled by default | disabled by default | disabled by default |
 
 ## Machine Output for CI
@@ -224,3 +200,27 @@ export default {
   }
 };
 ```
+
+## Gate Execution Counts
+
+Human output shows per-gate execution counts (scenario, stateful, chaos, adversity) so you can verify which gates actually ran.
+
+## Zero-Execution Guardrail
+
+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
+```
+
+## `--generation-profile` Flag
+
+Control test data generation depth independently from the qualification profile:
+
+```bash
+apophis qualify --profile oauth-nightly --generation-profile quick
+```