fix: dedupe home agent directories

[he-yufeng]

Fixes #27692.

Summary

• deduplicate project-level and user-level agent directories before loading local agents
• keep project/user precedence unchanged when the directories are different
• add a regression test for the home-directory workspace case where both paths resolve to ~/.gemini/agents

To verify

• npm exec -- vitest run packages/core/src/agents/registry.test.ts
• npm run typecheck --workspace @google/gemini-cli-core
• npm exec -- eslint packages/core/src/agents/registry.ts packages/core/src/agents/registry.test.ts --max-warnings 0
• git diff --check HEAD~1..HEAD

[github-actions]

📊 PR Size: size/M

• Lines changed: 55
• Additions: +53
• Deletions: -2
• Files changed: 2

[gemini-code-assist]

Warning

Gemini encountered an error creating the summary. You can try again by commenting /gemini summary.

[gemini-cli]

Hi there! Thank you for your interest in contributing to Gemini CLI.

To ensure we maintain high code quality and focus on our prioritized roadmap, we only guarantee review and consideration of pull requests for issues that are explicitly labeled as 'help wanted'.

This PR will be closed in 7 days if it remains without that designation. We encourage you to find and contribute to existing 'help wanted' issues in our backlog! Thank you for your understanding.

[he-yufeng]

Closing this myself to stay within the repository's open-PR limit. The newer web-search timeout fix is tied to a P1 issue and looks higher priority than this home-directory dedupe change right now. This branch stays in my fork if maintainers want to revisit it later.