docs: mention index-only analyze mode in quick start

[YuanHanzhong]

Summary

• Document npx gitnexus analyze --index-only in both quick start sections.
• Clarify that this mode refreshes the index without touching existing agent files and skills.

Testing

• git diff --check HEAD~1 HEAD
• rg "analyze --index-only|leave existing agent files" README.md gitnexus/README.md

Notes

• Related to analyze re-emits npx gitnexus in SKILL templates + AGENTS.md/CLAUDE.md every run; clobbers projects that standardized on bare gitnexus #1663

[vercel]

@YuanHanzhong is attempting to deploy a commit to the NexusCore Team on Vercel.

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