docs(agents): add submit --wait, --check-only, and --json flags

Update mainline workflow docs with latest mq features:
submit dry-run, wait mode, allow-newer-head, repo root
trust, and --json for machine-readable output.

Co-authored-by: Andrew <andrewxhill@gmail.com>

Author: 4ndr3wxh1ll

AGENTS.md

@@ -28,17 +28,31 @@ wtnew my-feature
 pnpm install
 # ... edit, test, commit ...
 
-# Submit from the feature worktree
-mq submit
+# Validate before submitting (dry run)
+mq submit --check-only
+
+# Submit and wait for integration to complete
+mq submit --wait --timeout 15m
 
-# Integrate and publish from the main worktree
+# Or submit and integrate/publish manually from the main worktree
+mq submit
 mq run-once
 mq publish
 
 # Clean up
 wtdrop <worktree-path>
 ```
 
+### Submit options
+
+- `mq submit` — queue the branch for integration
+- `mq submit --check-only` — dry-run validation (no side effects)
+- `mq submit --wait` — submit and block until integration finishes
+- `mq submit --wait --timeout 15m` — with timeout
+- `mq submit --allow-newer-head` — allow if branch advanced since last
+  submit
+- Add `--json` to any command for machine-readable output
+
 ### Handling failures
 
 - If `mq run-once` fails (conflict, test failure), the protected branch
@@ -52,6 +66,7 @@ wtdrop <worktree-path>
 - `mq status` — current queue state
 - `mq doctor` — health check (branch, locks, queue)
 - `mq repo show` — config and worktree info
+- `mq repo root` — canonical root trust status
 - `mq logs --follow` — integration history
 - `mq watch` — live queue updates
 - `mq events --follow` — raw audit trail