Fix apply-diff test and add ntc apply-diff test

[dcbartlett]

Description

Fixes the Apply-Diff e2e test. Adds new tests for native tooling for apply-diff
Adds debug launch configuration for e2e tests.

Test Procedure

Run e2e test suite using pnpm test:run in the e2e app or with the debug launch profile.

Pre-Submission Checklist

• [-] Issue Linked: This PR is linked to an approved GitHub Issue (see "Related GitHub Issue" above).
• Scope: My changes are focused on the linked issue (one major feature/fix per PR).
• Self-Review: I have performed a thorough self-review of my code.
• Testing: New and/or updated tests have been added to cover my changes (if applicable).
• [-] Documentation Impact: I have considered if my changes require documentation updates (see "Documentation Updates" section below).
• Contribution Guidelines: I have read and agree to the Contributor Guidelines.

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Important

Fixes apply-diff e2e test, adds native tool calling tests, and introduces debug configuration in vscode-e2e app.

• Behavior:
  • Fixes apply-diff e2e test and adds new tests for native tool calling in apply-diff-native.test.ts.
  • Introduces debug launch configuration for e2e tests.
• Tests:
  • Adds apply-diff-native.test.ts, execute-command-native.test.ts, list-files-native.test.ts, read-file-native.test.ts, search-files-native.test.ts, use-mcp-tool-native.test.ts, and write-to-file-native.test.ts for native tool calling.
  • Removes apply-diff.test.ts, execute-command.test.ts, list-files.test.ts, write-to-file.test.ts, and others, replacing them with native versions.
• Misc:
  • Adds retries: 3 to mochaOptions in index.ts to improve test reliability.

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Closes #10647

[roomote]

Rooviewer   See task on Roo Cloud

Reviewed at a0127d8. All previously flagged issues have been resolved.

• Misleading comments about model/provider (e.g., "Claude Sonnet 4.5" comment with OpenAI model ID)
• Native protocol verification doesn't actually assert hasNativeApiProtocol is true
• Error handling test uses testFile.content instead of testFile.name for target file
• New test files (execute-command-native.test.ts, list-files-native.test.ts, read-file-native.test.ts) missing hasNativeApiProtocol assertion
• Remaining native test files (search-files-native.test.ts, use-mcp-tool-native.test.ts, write-to-file-native.test.ts) missing hasNativeApiProtocol assertion

Previous reviews

• 7055a62: Review #1
• c0160dc: Review #2
• b901846: Review #3
• 58be120: Review #4
• bdd2326: Review #5
• 9f11105: Review #6
• 5d5d80b: Review #7
• ebfd585: Review #8
• ac3ac8e: Review #9
• 60f4a86: Review #10
• 836aa04: Review #11
• 0121f71: Review #12

_{Mention @roomote in a comment to request specific changes to this pull request or fix all unresolved issues.}