docs: document agent index tooling

[BenSheridanEdwards]

Why

The template already treats Graphify as generated agentic infrastructure, but it did not name GitNexus or ignore its local index. That made the north-star architecture incomplete for repos that use both indexes.

What Changed

• Document GitNexus beside Graphify in the external agentic-tooling setup.
• Ignore .gitnexus/ as generated local index output.
• Update the install-agentic-infrastructure skill so downstream repos ignore graphify-out/ and .gitnexus/ in VCS and formatter/linter tools.

Proof

• pnpm setup:agents
• pnpm verify
• pnpm e2e
• Visual proof attached or linked, or N/A with reason: N/A, docs/setup/ignore change only.
• StyleProof reviewed, or N/A with reason: N/A, no rendered UI or CSS change.
• Other proof: gitnexus analyze --index-only --skip-agents-md --skip-skills . produced an up-to-date local index on f161d8e with 133 nodes / 143 edges; graphify update . --no-cluster produced an ignored local graph with 1,007 nodes / 2,065 edges.

CI Status

• Latest-sha GitHub Actions are green.
• Pending checks are named below.
• Failing checks are named below with the fix plan.

Pending at PR open: CI, CodeQL, Lighthouse, StyleProof workflow/status.

Risk And Rollback

Low risk. This is docs/setup/ignore ownership only; rollback is reverting this PR.

Definition Of Done

• Behaviour is covered by the E2E map when user-visible behaviour changed. N/A, no user-visible behaviour changed.
• Logic is unit-tested where logic changed. N/A, no application logic changed.
• Accessibility was considered and verified for interactive/UI changes. N/A, no interactive/UI change.
• The diff follows .agents/project/ARCHITECTURE.md and CONVENTIONS.md.
• Any new architectural decision is recorded as an ADR. N/A, documents existing external generated-index ownership.
• No gates were bypassed or weakened.

[github-actions]

Fallow audit report

Found 1 finding.

Details

Severity	Rule	Location	Description
minor	fallow/unused-dev-dependency	package.json:44	Package '@lhci/cli' is in devDependencies but never imported

Generated by fallow.

[github-actions]

Fallow audit report

0 inline findings selected for GitHub review.

[github-actions]

🗺️ StyleProof report

✓ No visual changes detected.