Fix plugin Filter exclusion accounting - #351

Problem

Active plugin default Filters can remove workspace files before analysis, but the Filters control only counted Nodes removed later in the Graph View. The control could therefore report zero while plugin Filters visibly reduced graph membership.

Fix

• Core records one required discovery accounting value: Filter-excluded workspace files and Git-ignored paths are separate fields in the same snapshot.
• Workspace metadata version 2 persists that snapshot. Cached replay reads the persisted value instead of trying to infer exclusions from analyzed cache files. Metadata without current accounting requires a re-index and never reports a fabricated zero.
• The existing graph-controls snapshot carries accounting through full analysis, scoped refresh, plugin broadcast, and webview bootstrap. The separate Filter-accounting message and optional getter fallback were removed.
• The Filters panel reports two explicit metrics with different units: workspace files excluded before analysis and Nodes excluded in the Graph View. It does not add, maximize, or reconcile them, so overlap cannot create a false total.
• Plugin-owned defaults and .gitignore stay conceptually separate. This change does not alter any plugin default Filter.

Verification

• 51 focused Core tests: discovery accounting, Git-ignore separation, analysis wiring, metadata persistence, invalid metadata, and concurrent metadata updates.
• 70 focused extension Node tests: mixed TypeScript/Godot/Unity defaults, restart/cache replay, re-index persistence, scoped refresh modes, graph-controls delivery, and bootstrap settings paths.
• 25 focused webview tests: rendered accounting, unavailable accounting, simultaneous discovery-time and Graph View exclusions, and overlap without reconciliation.
• pnpm --filter @codegraphy-dev/extension typecheck
• Focused ESLint on all changed TypeScript and TSX files.
• Extension Development Host Playwright scenario that indexes a real workspace, enables the TypeScript plugin, re-indexes, and verifies the rendered graph/count change.

Visual proof

Before plugin activation: 19 Nodes, no active Filters, and 0 workspace files excluded before analysis.

After enabling the TypeScript plugin defaults and re-indexing: 18 Nodes and 1 workspace file excluded before analysis. Graph View exclusions remain a separate 0-Node metric.

Trello

Trello #242