Distinguish duplicate repository filters

[aidxun]

What changed

• Added repository root paths to the repository option payload.
• Shows root paths in the sidebar repository filter only when multiple repositories share the same name.
• Includes root path and repo id in command search values so duplicate-name repos remain selectable.
• Added a patch changeset and frontend coverage for duplicate-name filtering.

Why it changed

Users can add repositories with the same display name from different directories. The sidebar filter previously showed identical labels, making it unclear which repository would be selected.

Follow-up / test notes

• Ran bun x vitest run src/features/navigation/index.test.tsx.
• Pre-commit hook passed after staging the sidecar vendor artifact locally with cd sidecar && bun run build so Rust clippy could resolve the expected resource path.

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