feat:Add ~/.gemini/system.md fallback for GEMINI_SYSTEM_MD=1|true

[facelezzzz]

Summary

This PR allows setting GEMINI_SYSTEM_MD=1 or true so that when .gemini/system.md does not exist in the project root, the system will fall back to $HOME/.gemini/system.md.

Details

Although GEMINI_SYSTEM_MD can be used to specify an explicit path, once a path is set, .gemini/system.md inside certain repositories will no longer take effect, which is inconvenient for our team.

What we want instead is:
- Use .gemini/system.md if it exists in the project
- Otherwise, fall back to $HOME/.gemini/system.md
-
This allows our team to keep a consistent global setup while still easily enabling repository-specific .gemini/system.md files when needed.
The behavior is intuitive and provides good flexibility.

Related Issues

#15549

How to Validate

Run test at packages/core/src/core/prompts.test.ts

Use .gemini/system.md in the project directory.

(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % echo 'YOU ANSWER "I am just a robot" NO MATTER WHAT USER ASK.' >> .gemini/system.md
(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % GEMINI_SYSTEM_MD=1 npm start

Use ~/.gemini/system.md

(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % rm .gemini/system.md                                                               
(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % echo 'YOU ANSWER "I am just a human" NO MATTER WHAT USER ASK.' >> ~/.gemini/system.md
(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % GEMINI_SYSTEM_MD=1 npm start

Prefer .gemini/system.md in the project directory even when ~/.gemini/system.md exists.

(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % echo 'YOU ANSWER "I am just a human" NO MATTER WHAT USER ASK.' >> ~/.gemini/system.md
(base) wangboxue@wangboxuedeMacBook-Air gemini-cli % echo 'YOU ANSWER "I am just a robot" NO MATTER WHAT USER ASK.' >> .gemini/system.md 

Pre-Merge Checklist

• Updated relevant documentation and README (if needed)
• Added/updated tests (if needed)
• [ ] Noted breaking changes (if any)
• Validated on required platforms/methods:
  • MacOS
    • npm run
    • npx
    • Docker
    • Podman
    • Seatbelt
  • Windows
    • npm run
    • npx
    • Docker
  • Linux
    • npm run
    • npx
    • Docker

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[gemini-code-assist]

Summary of Changes

Hello @facelezzzz, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request introduces a significant improvement to how the GEMINI_SYSTEM_MD environment variable is handled, providing a more robust and flexible system prompt resolution mechanism. It enables a fallback to a user's global system prompt configuration (~/.gemini/system.md) if a project-specific one (.gemini/system.md) is not present, streamlining workflow for teams and individual developers.

Highlights

• Enhanced GEMINI_SYSTEM_MD Behavior: When GEMINI_SYSTEM_MD is set to 1 or true, the system now first checks for .gemini/system.md in the project root.
• Global System Prompt Fallback: If the project-specific .gemini/system.md is not found, the system will automatically fall back to using ~/.gemini/system.md in the user's home directory.
• Improved Flexibility: This change allows teams to maintain a consistent global system prompt setup while still providing the flexibility for individual repositories to define their own specific system prompts when needed.
• Documentation Updates: Relevant documentation files (docs/cli/configuration.md, docs/cli/system-prompt.md, docs/get-started/configuration.md) have been updated to reflect this new fallback behavior.
• New Test Case: A new test has been added in packages/core/src/core/prompts.test.ts to ensure the fallback mechanism works as expected.

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[gemini-code-assist]

Code Review

This pull request introduces a fallback mechanism to use a global system prompt from ~/.gemini/system.md when the project-specific one is not found. The implementation is logically correct and includes corresponding documentation updates and tests. However, the core logic relies on fs.existsSync() before reading the file, which introduces a Time-of-Check to Time-of-Use (TOCTOU) race condition. This could lead to an unhandled exception if the file is removed between the check and the read operation. I've provided a high-severity comment with a recommendation to refactor the logic to avoid this anti-pattern by attempting to read the files directly and handling any 'file not found' errors.