Remove Graphify coupling and use repository-configured code intelligence

[bpstr]

Removes vendor-specific code-intelligence coupling and makes retrieval fully host/repository configured.

Behavior

Applicable repository/ancestor instructions (AGENTS.md, CLAUDE.md, and equivalent host guidance) define which installed code-intelligence tools are available. Native investigations may use any configured symbol, semantic-search, structural, or code-graph tool to narrow retrieval. When none is configured, available, or sufficient, the workflow falls back to bounded source/file search.

External tool output is retrieval context only. It never becomes persisted evidence and never establishes runtime behavior; accepted claims still require exact current-source evidence.

Completed removal

• deleted the vendor-specific importer from canonical source and bundled skill
• removed the vendor-specific CLI flag, planner context, manifest status, metadata exports, handoff files, automatic knowledge gap, package keyword, ignore entry, tests, and reference document
• removed vendor-specific assumptions from README, installation, architecture, acceptance, workflow, skill, changelog, and repository guidance
• kept the deterministic engine independent of external code-intelligence clients
• added an explicit offline regression proving bootstrap has no vendor integration requirement
• kept canonical source and bundled engine copies synchronized

Validation

GitHub Actions Offline validation passes on Python 3.10, 3.12, and 3.13, including source contracts, distribution consistency, plugin archive builds, wheel installation, and packaged-entrypoint fixture exercises.

This PR is feature complete and ready to merge.