graphify indexes its own installed skill files as project content

[Mpasha17]

Hey! I noticed this while adding Grok Build support (#4047), but it's not Grok-specific; it happens on plain v8 too.

After graphify claude install and graphify install --project --platform claude, running graphify update . picks up graphify's own files as if they were part of the project: .claude/skills/graphify/SKILL.md, everything under references/, .claude/CLAUDE.md, CLAUDE.md and AGENTS.md.

To reproduce on 0.9.75, take a fresh repo with one small auth.py (two functions), run the installs above, then run graphify update .. I got 69 nodes, and only 3 of them came from auth.py. The rest were graphify's own skill docs. In a small repo that drowns out the real code in queries and the report.

I'm happy to send a PR. The skill folders and hook files seem easy to skip in detect.py, but AGENTS.md and CLAUDE.md are trickier since they're the user's files and graphify only adds a section. Would you rather skip just the ## graphify section, or leave those files as they are? @safishamsi

[github-actions]

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[Mpasha17]

I've opened #4062 for this. It skips graphify's own installed skill folders and the single files graphify writes whole (.kiro/steering/graphify.md, .windsurf/rules/graphify.md, the opencode/kilo plugins, etc.). They're matched on their exact install paths, so the user's own files are still indexed. With every platform installed, the repro graph goes from 1050 nodes to 11.

I left AGENTS.md, CLAUDE.md and GEMINI.md alone for now, since graphify only adds a section to them. If you'd like those handled too (for example, skipping just the ## graphify section), or you'd prefer a different approach overall, let me know and I'll update the PR.