feat(cache): migrate canonical cache directory

[bntvllnt]

Summary

• Rename runtime cache/index writes from .code-visualizer/ to .codebase-intelligence/ with safe legacy-only migration.
• Add canonical + legacy cache ignore handling, init --gitignore, MCP clean/status help updates, and repo .gitignore.
• Add unit/E2E chains for cache states, CLI migration/status/clean, and gitignore idempotence.
• Update roadmap/docs/LLM docs for 2.5.0 canary P0 status and deterministic test runner.

Validation

• pnpm lint
• pnpm typecheck
• pnpm build
• pnpm test -> 28 files, 429 tests
• pnpm verify:cli-real -> pass=56 fail=0
• Dogfood: node dist/cli.js overview . --json migrated repo cache to .codebase-intelligence/.

Review

• Code-review pass ran with codebase-intelligence gates.
• Fix loop removed new persistence dead exports.
• Verdict: warnings-only; remaining roadmap item is JSON migration metadata for a later P0 slice.

Release

• Canary-mode only. No stable release, tag, or npm publish in this PR.