fix(utils): save config

[LuciNyan]

Description

When saveConfig is called, the project doc is incorrectly saved into user instructions. This change ensures that only user instructions are saved to instructions.md during saveConfig, preventing data corruption.

close: #576

[github-actions]

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[LuciNyan]

I have read the CLA Document and I hereby sign the CLA

[LuciNyan]

recheck

[tibo-openai]

Nice one, thank you for contributing this fix. It looks like there are CI failures for formatting

> @openai/codex@0.1.2504221401 format /home/runner/work/codex/codex/codex-cli
> prettier --check src tests

Checking formatting...
[warn] src/utils/config.ts
[warn] Code style issues found in the above file. Forgot to run Prettier?
 ELIFECYCLE  Command failed with exit code 1.

could you take a look and once resolved then I will merge.

[LuciNyan]

Hi @tibo-openai 👋 Thank you for the feedback! I’ve resolved the Prettier formatting issues.

However, I noticed that the current lint-staged configuration on the main branch has an issue that is blocking most commits. Could you please take a look at the details here: #617?

[tibo-openai]

Merged #617, thank you!

[tibo-openai]

Simplified the code a bit. Thank you for the contribution!