fix(config): add notebook permission schema

[markijbema]

Summary

• Add notebook_read, notebook_edit, and notebook_execute to Kilo's published CLI permission schema.
• Extend the upstream schema overlay to merge Kilo permission definitions without dropping existing permission keys.
• Add regression coverage for the nested PermissionConfig merge.

Verification

• N/A — schema-only change with no manual user flow.

Visual Changes

N/A

Reviewer Notes

Follow-up for Kilo-Org/kilocode#11644 discussion_r3473007520.

[kilo-code-bot]

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (3 files)

• apps/web/src/app/config.json/extras.ts
• apps/web/src/app/config.json/route.ts
• apps/web/src/tests/cli-config-schema.test.ts

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_{Review guidance: REVIEW.md from base branch main}