feat: SCIP import, git hooks manager, version tracking, CLI enhancements

[MO2k4]

Summary

• SCIP import (src/scip/index.ts): ScipImporter class with two-pass SCIP JSON processing (definitions first, then references), content-hash fingerprinting for idempotent imports, and findSCIPFiles() auto-detection
• Git hooks (src/sync/git-hooks.ts): GitHooksManager class for installing/removing post-commit hooks with worktree support, marker-based hook identification, and safe append/remove operations
• Version tracking (src/version.ts): getRuntimeVersion() returning package version + git rev with caching
• CLI enhancements (src/bin/codegraph.ts): hooks install/hooks remove/hooks status commands, displayIndexStats in status output, version display
• Public API (src/index.ts): New methods on CodeGraph class — importSCIP(), getVersion(), installGitHooks(), removeGitHooks(), isGitRepository(), isGitHookInstalled(), getMetadata()

Details

SCIP Import

The ScipImporter processes SCIP (Source Code Intelligence Protocol) JSON files in two passes:

1. Pass 1 — Build symbol definitions map from SCIP occurrences with SymbolRole.Definition
2. Pass 2 — Resolve references by matching SCIP symbols to indexed CodeGraph nodes using line-proximity matching

Content-hash fingerprinting (SHA-256 of the SCIP file) enables idempotent imports — re-importing the same file is a no-op.

Git Hooks Manager

The GitHooksManager handles post-commit hook installation for automatic codegraph sync:

• Resolves .git directory correctly for worktrees
• Uses CODEGRAPH_MARKER comments to identify managed hook sections
• Safely appends to existing hooks without overwriting user content
• Returns structured HookInstallResult/HookRemoveResult with status details

Dead code verification

Every new export has at least one caller within this PR:

• ScipImporter → called by importSCIP() in src/index.ts
• GitHooksManager → used in CodeGraph constructor + CLI commands
• createGitHooksManager → called in CodeGraph constructor
• getRuntimeVersion() → called by CLI status + CodeGraph.getVersion()
• HookInstallResult/HookRemoveResult → used in method signatures

Test plan

• npm run build compiles without errors
• npm test passes with same baseline (28 pre-existing failures, 326 passing)
• 6 files changed/created: src/scip/index.ts (new), src/sync/git-hooks.ts (new), src/version.ts (new), src/sync/index.ts, src/index.ts, src/bin/codegraph.ts
• All new exports verified to have callers (see dead code verification above)
• Sentry preserved — 17 references in CLI (initSentry, captureException, error handlers)
• All existing exports from src/index.ts preserved
• No upstream features removed