Installer should no-op in already-integrated repos and preserve Git hooks config #401

Graphify's installer can damage a repository that already vendors its Graphify integration. We hit this in LucentiveLabs/intuitive-agent-system after adding tracked Graphify integration files and repo-local launchd scripts.

Observed failure modes:

• graphify install unset core.hooksPath when .husky/_ was not present yet, which disabled Husky pre-commit / pre-push hooks.
• It wrote Graphify hooks into .git/hooks/post-commit and .git/hooks/post-checkout, even though the repo uses Husky through core.hooksPath.
• It created files such as .claude/settings.json, .codex/hooks.json, and .cursor/rules/graphify.mdc that were already tracked in the repo, leaving duplicate untracked files that blocked the next git pull with a "would be overwritten by merge" error.
• In at least one affected checkout, core.bare=true was set on a non-bare working tree. The exact path to this state is unclear, but the installer should never leave a working checkout with core.bare=true.

Requested behavior:

• Detect an already-integrated repo, for example by checking for scripts/graphify/ plus tracked .claude/settings.json / .codex/hooks.json, and no-op or print repo-specific guidance.
• Do not unset core.hooksPath just because the target hook directory is missing; regenerate it or warn instead.
• Do not write duplicate Graphify hooks to .git/hooks when core.hooksPath points elsewhere.
• Never set core.bare=true on a working tree.

This is not a request for Lucentive-specific behavior; the general ask is for the installer to be idempotent and conservative in repos that already ship Graphify integration.