diff --git a/.changeset/calm-filters-count.md b/.changeset/calm-filters-count.md
new file mode 100644
index 0000000000..cff4326505
--- /dev/null
+++ b/.changeset/calm-filters-count.md
@@ -0,0 +1,6 @@
+---
+"@codegraphy-dev/core": patch
+"@codegraphy-dev/extension": patch
+---
+
+Persist discovery-time Filter and Git-ignore accounting, restore it from the Graph Cache, and report Filter-excluded workspace files separately from Nodes excluded in the Graph View.
diff --git a/packages/core/src/analysis/workspaceAnalyze.ts b/packages/core/src/analysis/workspaceAnalyze.ts
index 977c2a6792..a248b66b5c 100644
--- a/packages/core/src/analysis/workspaceAnalyze.ts
+++ b/packages/core/src/analysis/workspaceAnalyze.ts
@@ -1,5 +1,5 @@
 import type { IFileAnalysisResult, IPluginNodeType } from '@codegraphy-dev/plugin-api';
-import type { IDiscoveredFile } from '../discovery/contracts';
+import type { IDiscoveredFile, WorkspaceFilterAccounting } from '../discovery/contracts';
 import type { IGraphData } from '../graph/contracts';
 import { throwIfWorkspaceAnalysisAborted } from './abort';
 import type { IWorkspaceFileAnalysisResult } from './fileAnalysis';
@@ -41,6 +41,7 @@ export interface WorkspacePipelineAnalysisSource {
   _completeGraphData?: IGraphData;
   _lastDiscoveredDirectories: string[];
   _lastDiscoveredFiles: IDiscoveredFile[];
+  _filterAccounting: WorkspaceFilterAccounting;
   _lastFileAnalysis: Map<string, IFileAnalysisResult>;
   _lastFileConnections: Map<string, IProjectedConnection[]>;
   _lastGitIgnoredPaths?: string[];
@@ -164,6 +165,7 @@ export async function analyzeWorkspaceWithAnalyzer(
   source._lastFileConnections = analysisResult.fileConnections;
   source._lastDiscoveredDirectories = discoveryResult.directories ?? [];
   source._lastDiscoveredFiles = discoveryResult.files;
+  source._filterAccounting = discoveryResult.filterAccounting;
   source._lastGitIgnoredPaths = discoveryResult.gitIgnoredPaths ?? [];
   source._lastWorkspaceRoot = workspaceRoot;
 
diff --git a/packages/core/src/analysis/workspaceDiscovery.ts b/packages/core/src/analysis/workspaceDiscovery.ts
index 45fa7b578c..4a7b934b3a 100644
--- a/packages/core/src/analysis/workspaceDiscovery.ts
+++ b/packages/core/src/analysis/workspaceDiscovery.ts
@@ -1,3 +1,4 @@
+import type { WorkspaceFilterAccounting } from '../discovery/contracts';
 import { DEFAULT_EXCLUDE } from '../discovery/pathMatching';
 
 export interface WorkspacePipelineDiscoveryConfig {
@@ -10,6 +11,7 @@ export interface WorkspacePipelineDiscoveryResult<TFile> {
   directories?: string[];
   durationMs: number;
   files: TFile[];
+  filterAccounting: Extract<WorkspaceFilterAccounting, { kind: 'current' }>;
   gitIgnoredPaths?: string[];
   limitReached: boolean;
   totalFound: number;
diff --git a/packages/core/src/discovery/contracts.ts b/packages/core/src/discovery/contracts.ts
index 93da533cd0..f2b79d79b4 100644
--- a/packages/core/src/discovery/contracts.ts
+++ b/packages/core/src/discovery/contracts.ts
@@ -43,12 +43,22 @@ export interface IDiscoveredFile {
   gitIgnored?: boolean;
 }
 
+export type WorkspaceFilterAccounting =
+  | {
+      kind: 'current';
+      excludedFileCount: number;
+      gitIgnoredPathCount: number;
+    }
+  | { kind: 'unavailable' };
+
 /**
  * Result of a discovery operation.
  */
 export interface IDiscoveryResult {
   /** Eligible discovered files, capped by maxFiles */
   files: IDiscoveredFile[];
+  /** Filter and Git ignored state accounting captured by this discovery. */
+  filterAccounting: Extract<WorkspaceFilterAccounting, { kind: 'current' }>;
   /** Discovered directory paths relative to the workspace root */
   directories: string[];
   /** Discovered file and directory paths reported by Git as ignored */
diff --git a/packages/core/src/discovery/file/service.ts b/packages/core/src/discovery/file/service.ts
index cbfe8ef3e3..00f735eac9 100644
--- a/packages/core/src/discovery/file/service.ts
+++ b/packages/core/src/discovery/file/service.ts
@@ -305,6 +305,12 @@ export class FileDiscovery {
           directories,
         )
         : new Set<string>();
+    const filterExcludedFileCount = candidateFiles
+      .filter(file => (
+        !gitIgnoredPaths.has(file.relativePath)
+        && matchesAnyPattern(file.relativePath, filterPatterns)
+      ))
+      .length;
     const eligibleFiles = candidateFiles.filter(file => (
       !matchesAnyPattern(file.relativePath, filterPatterns)
       && !gitIgnoredPaths.has(file.relativePath)
@@ -339,6 +345,11 @@ export class FileDiscovery {
       cacheFilePaths,
       cachePathPrefixes: gitWorkspacePaths?.ignoredPathPrefixes ?? [],
       directories: eligibleDirectories,
+      filterAccounting: {
+        kind: 'current',
+        excludedFileCount: filterExcludedFileCount,
+        gitIgnoredPathCount: gitIgnoredPaths.size + (gitWorkspacePaths?.ignoredPathPrefixes.length ?? 0),
+      },
       gitIgnoredPaths: [
         ...gitIgnoredPaths,
         ...(gitWorkspacePaths?.ignoredPathPrefixes ?? []),
diff --git a/packages/core/src/index.ts b/packages/core/src/index.ts
index 41ab7558c9..07bf427a4f 100644
--- a/packages/core/src/index.ts
+++ b/packages/core/src/index.ts
@@ -111,6 +111,7 @@ export type {
   IDiscoveredFile,
   IDiscoveryOptions,
   IDiscoveryResult,
+  WorkspaceFilterAccounting,
 } from './discovery/contracts';
 export { createAbortError, throwIfAborted } from './discovery/abort';
 export { FileDiscovery } from './discovery/file/service';
diff --git a/packages/core/src/indexing/engineGraph.ts b/packages/core/src/indexing/engineGraph.ts
index 3ee4584fa2..d323ec91d8 100644
--- a/packages/core/src/indexing/engineGraph.ts
+++ b/packages/core/src/indexing/engineGraph.ts
@@ -77,6 +77,7 @@ async function persistMetadata(runtime: WorkspaceEngineRuntime): Promise<void> {
       registry: state.registry,
     });
   await persistWorkspaceIndexMetadata({
+    filterAccounting: state.filterAccounting,
     pluginBuildSignature: createWorkspaceIndexPluginBuildSignature(state.loadedPackagePlugins),
     pluginSignature,
     failedPluginIds: state.failedPluginIds,
diff --git a/packages/core/src/indexing/engineSetup.ts b/packages/core/src/indexing/engineSetup.ts
index f0187935a9..98a268457b 100644
--- a/packages/core/src/indexing/engineSetup.ts
+++ b/packages/core/src/indexing/engineSetup.ts
@@ -80,6 +80,7 @@ export async function discoverWorkspaceEngineFiles(
   });
   state.discoveredDirectories = state.discoveryResult.directories ?? [];
   state.discoveredFiles = state.discoveryResult.files;
+  state.filterAccounting = state.discoveryResult.filterAccounting;
 }
 
 export function createWorkspaceEngineDisabledPlugins(runtime: WorkspaceEngineRuntime): Set<string> {
diff --git a/packages/core/src/indexing/metadata.ts b/packages/core/src/indexing/metadata.ts
index 55fb016472..b8930004dd 100644
--- a/packages/core/src/indexing/metadata.ts
+++ b/packages/core/src/indexing/metadata.ts
@@ -9,6 +9,7 @@ import {
   createCodeGraphyWorkspaceSettingsSignature,
 } from '../workspace/signatures';
 import type { CodeGraphyWorkspaceSettings } from '../workspace/settings';
+import type { WorkspaceFilterAccounting } from '../discovery/contracts';
 import type { IndexCodeGraphyWorkspacePlugin } from './contracts';
 
 function runtimeSignaturePlugins(registry: CorePluginRegistry): IPlugin[] {
@@ -70,6 +71,7 @@ export function createWorkspaceIndexPluginBuildSignature(
 }
 
 export async function persistWorkspaceIndexMetadata(input: {
+  filterAccounting: WorkspaceFilterAccounting;
   pluginSignature: string | null;
   pluginBuildSignature: string | null;
   failedPluginIds: ReadonlySet<string>;
@@ -79,6 +81,7 @@ export async function persistWorkspaceIndexMetadata(input: {
   workspaceRoot: string;
 }): Promise<void> {
   await persistCodeGraphyWorkspaceIndexMetadata(input.workspaceRoot, {
+    filterAccounting: input.filterAccounting,
     pluginSignature: input.pluginSignature,
     pluginBuildSignature: input.pluginBuildSignature,
     failedPluginIds: [...input.failedPluginIds].sort((left, right) => left.localeCompare(right)),
diff --git a/packages/core/src/indexing/state.ts b/packages/core/src/indexing/state.ts
index f49dd477a6..93b0539bb5 100644
--- a/packages/core/src/indexing/state.ts
+++ b/packages/core/src/indexing/state.ts
@@ -1,13 +1,14 @@
 import { createEmptyWorkspaceAnalysisCache, type IWorkspaceAnalysisCache } from '../analysis/cache';
 import type { IProjectedConnection } from '../analysis/projectedConnection';
 import type { IFileAnalysisResult } from '@codegraphy-dev/plugin-api';
-import type { IDiscoveredFile } from '../discovery/contracts';
+import type { IDiscoveredFile, WorkspaceFilterAccounting } from '../discovery/contracts';
 import type { IGraphData } from '../graph/contracts';
 
 export interface WorkspaceIndexEngineState {
   cache: IWorkspaceAnalysisCache;
   discoveredDirectories: string[];
   discoveredFiles: IDiscoveredFile[];
+  filterAccounting: WorkspaceFilterAccounting;
   gitIgnoredPaths: string[];
   fileAnalysis: Map<string, IFileAnalysisResult>;
   fileConnections: Map<string, IProjectedConnection[]>;
@@ -22,6 +23,7 @@ export function createWorkspaceIndexEngineState(
     cache,
     discoveredDirectories: [],
     discoveredFiles: [],
+    filterAccounting: { kind: 'unavailable' },
     gitIgnoredPaths: [],
     fileAnalysis: new Map(),
     fileConnections: new Map(),
diff --git a/packages/core/src/indexing/workspace.ts b/packages/core/src/indexing/workspace.ts
index a4815ea514..c9774954e1 100644
--- a/packages/core/src/indexing/workspace.ts
+++ b/packages/core/src/indexing/workspace.ts
@@ -383,6 +383,7 @@ export async function indexCodeGraphyWorkspace(
         }, recovery);
       }
       await persistWorkspaceIndexMetadata({
+        filterAccounting: discoveryResult.filterAccounting,
         pluginBuildSignature,
         pluginSignature,
         failedPluginIds,
diff --git a/packages/core/src/workspace/meta.ts b/packages/core/src/workspace/meta.ts
index c5bce63409..fba401e871 100644
--- a/packages/core/src/workspace/meta.ts
+++ b/packages/core/src/workspace/meta.ts
@@ -3,6 +3,7 @@ import * as path from 'node:path';
 import { randomUUID } from 'node:crypto';
 import { z } from 'zod';
 import { WORKSPACE_ANALYSIS_CACHE_VERSION } from '../analysis/cache';
+import type { WorkspaceFilterAccounting } from '../discovery/contracts';
 import { looseStringArraySchema } from '../values';
 import { getWorkspaceMetaPath } from './paths';
 import { getWorkspaceAnalysisDatabasePath } from '../graphCache/database/storage';
@@ -13,7 +14,7 @@ import {
 } from '../graphCache/database/writeCoordination/model';
 
 export interface CodeGraphyWorkspaceMeta {
-  version: 1;
+  version: 2;
   lastIndexedAt: string | null;
   lastIndexedCommit?: string | null;
   pluginSignature: string | null;
@@ -22,11 +23,21 @@ export interface CodeGraphyWorkspaceMeta {
   analysisVersion: string | null;
   pendingChangedFiles: string[];
   failedPluginIds: string[];
+  filterAccounting: WorkspaceFilterAccounting;
 }
 
 const optionalNullableStringSchema = z.union([z.string(), z.null()]).optional().catch(undefined);
+const filterAccountingSchema = z.discriminatedUnion('kind', [
+  z.object({
+    kind: z.literal('current'),
+    excludedFileCount: z.number().int().nonnegative(),
+    gitIgnoredPathCount: z.number().int().nonnegative(),
+  }),
+  z.object({ kind: z.literal('unavailable') }),
+]);
 
 const codeGraphyWorkspaceMetaSchema = z.looseObject({
+  version: z.literal(2),
   analysisVersion: optionalNullableStringSchema,
   lastIndexedAt: optionalNullableStringSchema,
   lastIndexedCommit: optionalNullableStringSchema,
@@ -35,6 +46,7 @@ const codeGraphyWorkspaceMetaSchema = z.looseObject({
   pluginSignature: optionalNullableStringSchema,
   pluginBuildSignature: optionalNullableStringSchema,
   settingsSignature: optionalNullableStringSchema,
+  filterAccounting: filterAccountingSchema,
 }).transform((meta): CodeGraphyWorkspaceMeta => ({
   ...createDefaultCodeGraphyWorkspaceMeta(),
   ...(meta.analysisVersion !== undefined ? { analysisVersion: meta.analysisVersion } : {}),
@@ -45,12 +57,13 @@ const codeGraphyWorkspaceMetaSchema = z.looseObject({
   ...(meta.settingsSignature !== undefined ? { settingsSignature: meta.settingsSignature } : {}),
   pendingChangedFiles: meta.pendingChangedFiles,
   failedPluginIds: meta.failedPluginIds,
-  version: 1,
+  filterAccounting: meta.filterAccounting,
+  version: 2,
 }));
 
 export function createDefaultCodeGraphyWorkspaceMeta(): CodeGraphyWorkspaceMeta {
   return {
-    version: 1,
+    version: 2,
     lastIndexedAt: null,
     lastIndexedCommit: null,
     pluginSignature: null,
@@ -59,6 +72,7 @@ export function createDefaultCodeGraphyWorkspaceMeta(): CodeGraphyWorkspaceMeta
     analysisVersion: WORKSPACE_ANALYSIS_CACHE_VERSION,
     pendingChangedFiles: [],
     failedPluginIds: [],
+    filterAccounting: { kind: 'unavailable' },
   };
 }
 
@@ -148,6 +162,7 @@ export async function persistCodeGraphyWorkspaceIndexMetadata(
     pluginBuildSignature?: string | null;
     settingsSignature: string;
     failedPluginIds?: readonly string[];
+    filterAccounting: WorkspaceFilterAccounting;
     resolvedChangedFilePaths?: readonly string[];
   },
 ): Promise<void> {
@@ -171,5 +186,6 @@ export async function persistCodeGraphyWorkspaceIndexMetadata(
     failedPluginIds: metadata.failedPluginIds === undefined
       ? previous.failedPluginIds
       : [...metadata.failedPluginIds],
+    filterAccounting: metadata.filterAccounting,
   }));
 }
diff --git a/packages/core/tests/analysis/workspaceAnalyze.test.ts b/packages/core/tests/analysis/workspaceAnalyze.test.ts
index 360efb3f3e..5aaf662659 100644
--- a/packages/core/tests/analysis/workspaceAnalyze.test.ts
+++ b/packages/core/tests/analysis/workspaceAnalyze.test.ts
@@ -36,6 +36,7 @@ function createSource() {
     _completeGraphData: undefined as IGraphData | undefined,
     _lastDiscoveredDirectories: [] as string[],
     _lastDiscoveredFiles: [] as IDiscoveredFile[],
+    _filterAccounting: { kind: 'unavailable' as const },
     _lastFileAnalysis: new Map(),
     _lastFileConnections: new Map<string, IProjectedConnection[]>(),
     _lastGitIgnoredPaths: [] as string[],
@@ -51,6 +52,7 @@ function createDependencies() {
       directories: [] as string[],
       durationMs: 3,
       files: [] as IDiscoveredFile[],
+      filterAccounting: { kind: 'current' as const, excludedFileCount: 0, gitIgnoredPathCount: 0 },
       gitIgnoredPaths: [] as string[],
       limitReached: false,
       totalFound: 0,
@@ -134,6 +136,7 @@ describe('pipeline/analysis/analyze', () => {
       directories: ['src/new-folder'],
       durationMs: 4,
       files,
+      filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 1 },
       gitIgnoredPaths: ['src/index.ts'],
       limitReached: false,
       totalFound: 1,
@@ -185,6 +188,11 @@ describe('pipeline/analysis/analyze', () => {
       new Set<string>(['plugin.python']),
     );
     expect(source._lastDiscoveredFiles).toEqual(files);
+    expect(source._filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 1,
+      gitIgnoredPathCount: 1,
+    });
     expect(source._lastDiscoveredDirectories).toEqual(['src/new-folder']);
     expect(source._lastGitIgnoredPaths).toEqual(['src/index.ts']);
     expect(source._lastFileAnalysis).toBe(fileAnalysis);
@@ -254,6 +262,7 @@ describe('pipeline/analysis/analyze', () => {
       directories: [],
       durationMs: 5,
       files: [] as IDiscoveredFile[],
+      filterAccounting: { kind: 'current', excludedFileCount: 0, gitIgnoredPathCount: 0 },
       limitReached: true,
       totalFound: 27,
     });
@@ -276,6 +285,7 @@ describe('pipeline/analysis/analyze', () => {
       directories: [],
       durationMs: 4,
       files,
+      filterAccounting: { kind: 'current', excludedFileCount: 0, gitIgnoredPathCount: 0 },
       limitReached: false,
       totalFound: 1,
     });
@@ -330,6 +340,7 @@ describe('pipeline/analysis/analyze', () => {
         directories: [],
         durationMs: 4,
         files: [] as IDiscoveredFile[],
+        filterAccounting: { kind: 'current' as const, excludedFileCount: 0, gitIgnoredPathCount: 0 },
         limitReached: false,
         totalFound: 0,
       };
@@ -358,6 +369,7 @@ describe('pipeline/analysis/analyze', () => {
       directories: [],
       durationMs: 2,
       files: [] as IDiscoveredFile[],
+      filterAccounting: { kind: 'current', excludedFileCount: 0, gitIgnoredPathCount: 0 },
       limitReached: false,
       totalFound: 0,
     });
diff --git a/packages/core/tests/analysis/workspaceDiscovery.test.ts b/packages/core/tests/analysis/workspaceDiscovery.test.ts
index d946107ff7..fff4db6035 100644
--- a/packages/core/tests/analysis/workspaceDiscovery.test.ts
+++ b/packages/core/tests/analysis/workspaceDiscovery.test.ts
@@ -10,6 +10,7 @@ describe('pipeline/discovery', () => {
     const discover = vi.fn(async () => ({
       durationMs: 2,
       files: ['src/index.ts'],
+      filterAccounting: { kind: 'current' as const, excludedFileCount: 0, gitIgnoredPathCount: 0 },
       limitReached: false,
       totalFound: 1,
     }));
diff --git a/packages/core/tests/discovery/file/discovery.discover.test.ts b/packages/core/tests/discovery/file/discovery.discover.test.ts
index 72e5597236..c2374735c0 100644
--- a/packages/core/tests/discovery/file/discovery.discover.test.ts
+++ b/packages/core/tests/discovery/file/discovery.discover.test.ts
@@ -83,9 +83,45 @@ describe('FileDiscovery discover', () => {
     });
 
     expect(result.files.map(file => file.relativePath)).toEqual([path.join('src', 'app.ts')]);
+    expect(result.filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 1,
+      gitIgnoredPathCount: 27,
+    });
     expect(onProgress.mock.calls.map(([progress]) => progress.current)).toEqual([1]);
   });
 
+  it('accounts for mixed TypeScript, Godot, and Unity plugin Filters separately from Git ignored state', async () => {
+    initGitRepo();
+    createFile('.gitignore', 'ignored/**\n');
+    createFile('src/app.ts');
+    createFile('dist/app.js');
+    createFile('.godot/editor/project_metadata.cfg');
+    createFile('Assets/Player.prefab');
+    createFile('Assets/Player.prefab.meta');
+    createFile('ProjectSettings/ProjectSettings.asset');
+    createFile('ignored/generated.ts');
+
+    const result = await discovery.discover({
+      rootPath: tempDir,
+      filter: [
+        '**/dist/**',
+        '**/.godot/**',
+        '**/*.meta',
+        '**/[Pp]roject[Ss]ettings/**',
+      ],
+    });
+
+    expect(result.filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 3,
+      gitIgnoredPathCount: 2,
+    });
+    expect(result.files.map(file => file.relativePath)).toContain('src/app.ts');
+    expect(result.files.map(file => file.relativePath)).toContain('Assets/Player.prefab');
+    expect(result.gitIgnoredPaths).toContain('ignored');
+  });
+
   it('uses Git paths without recursively reading ignored or filtered workspace trees', async () => {
     initGitRepo();
     createFile('.gitignore', 'ignored/**\n');
diff --git a/packages/core/tests/indexing/analysis.test.ts b/packages/core/tests/indexing/analysis.test.ts
index 0d8d2ab1eb..3d6e4b5fbb 100644
--- a/packages/core/tests/indexing/analysis.test.ts
+++ b/packages/core/tests/indexing/analysis.test.ts
@@ -51,6 +51,7 @@ describe('indexing/analysis', () => {
       discoveryResult: {
         durationMs: 1,
         files,
+        filterAccounting: { kind: 'current', excludedFileCount: 0, gitIgnoredPathCount: 0 },
         directories: [],
         gitIgnoredPaths: [],
         limitReached: false,
diff --git a/packages/core/tests/workspace/meta.concurrent.test.ts b/packages/core/tests/workspace/meta.concurrent.test.ts
index d1d1ccf185..debc2134d6 100644
--- a/packages/core/tests/workspace/meta.concurrent.test.ts
+++ b/packages/core/tests/workspace/meta.concurrent.test.ts
@@ -88,6 +88,7 @@ describe('workspace metadata concurrency', () => {
       reportOwnership?.();
       await ownedCommitGate;
       await persistCodeGraphyWorkspaceIndexMetadata(workspaceRoot, {
+        filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
         pluginSignature: 'plugins-sha',
         settingsSignature: 'settings-sha',
         resolvedChangedFilePaths: ['src/resolved.ts'],
diff --git a/packages/core/tests/workspace/meta.test.ts b/packages/core/tests/workspace/meta.test.ts
index 4a9f7f050f..f4ccb2cbd5 100644
--- a/packages/core/tests/workspace/meta.test.ts
+++ b/packages/core/tests/workspace/meta.test.ts
@@ -42,7 +42,7 @@ describe('workspace/meta', () => {
   it('writes and reads workspace metadata', () => {
     const workspaceRoot = createTempWorkspace();
     const meta = {
-      version: 1 as const,
+      version: 2 as const,
       lastIndexedAt: '2026-04-08T19:00:00.000Z',
       lastIndexedCommit: 'abc123',
       pluginSignature: 'codegraphy.markdown@1.0.0',
@@ -51,6 +51,7 @@ describe('workspace/meta', () => {
       analysisVersion: null,
       pendingChangedFiles: ['src/index.ts'],
       failedPluginIds: ['acme.failed'],
+      filterAccounting: { kind: 'current' as const, excludedFileCount: 3, gitIgnoredPathCount: 2 },
     };
 
     writeWorkspaceMetaFixture(workspaceRoot, meta);
@@ -110,6 +111,7 @@ describe('workspace/meta', () => {
     });
 
     await persistCodeGraphyWorkspaceIndexMetadata(workspaceRoot, {
+      filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
       pluginSignature: 'plugins-sha',
       settingsSignature: 'settings-sha',
       resolvedChangedFilePaths: ['src/resolved.ts'],
@@ -122,7 +124,7 @@ describe('workspace/meta', () => {
     });
   });
 
-  it('filters invalid persisted metadata fields through the workspace meta schema', () => {
+  it('requires re-indexing when persisted metadata cannot provide current accounting', () => {
     const workspaceRoot = createTempWorkspace();
     const metaPath = getWorkspaceMetaPath(workspaceRoot);
 
@@ -141,14 +143,7 @@ describe('workspace/meta', () => {
       'utf8',
     );
 
-    expect(readCodeGraphyWorkspaceMeta(workspaceRoot)).toEqual({
-      ...createDefaultCodeGraphyWorkspaceMeta(),
-      analysisVersion: null,
-      pluginSignature: 'plugins-sha',
-      pendingChangedFiles: ['src/app.ts', 'src/index.ts'],
-      failedPluginIds: ['acme.failed'],
-      version: 1,
-    });
+    expect(readCodeGraphyWorkspaceMeta(workspaceRoot)).toEqual(createDefaultCodeGraphyWorkspaceMeta());
   });
 
   it('falls back to defaults when metadata JSON is invalid', () => {
diff --git a/packages/extension/src/extension/graphView/analysis/execution.ts b/packages/extension/src/extension/graphView/analysis/execution.ts
index 2a3010d660..3538d30d76 100644
--- a/packages/extension/src/extension/graphView/analysis/execution.ts
+++ b/packages/extension/src/extension/graphView/analysis/execution.ts
@@ -1,5 +1,9 @@
 import type { IGraphData } from '../../../shared/graph/contracts';
-import type { AnalysisCacheTier, DiagnosticEventInput } from '@codegraphy-dev/core';
+import type {
+  AnalysisCacheTier,
+  DiagnosticEventInput,
+  WorkspaceFilterAccounting,
+} from '@codegraphy-dev/core';
 import { publishAnalysisFailure } from './execution/publish';
 import { prepareGraphViewAnalysis } from './execution/prepare';
 import { runGraphViewAnalysis } from './execution/run';
@@ -12,6 +16,7 @@ interface GraphViewAnalyzerLike {
   initialize(): Promise<void>;
   syncWorkspacePlugins(): Promise<void>;
   hasIndex(): boolean;
+  getFilterAccounting(): WorkspaceFilterAccounting;
   getIndexStatus?(): {
     freshness: CodeGraphyIndexFreshness;
     detail: string;
diff --git a/packages/extension/src/extension/graphView/controls/send.ts b/packages/extension/src/extension/graphView/controls/send.ts
index bfd011084d..cfe7fe81c8 100644
--- a/packages/extension/src/extension/graphView/controls/send.ts
+++ b/packages/extension/src/extension/graphView/controls/send.ts
@@ -55,6 +55,9 @@ export function sendGraphControlsUpdated(
   disabledPlugins: ReadonlySet<string> = new Set(),
 ): void {
   const registry = analyzer?.registry;
+  const filterAccounting = analyzer
+    ? analyzer.getFilterAccounting()
+    : { kind: 'unavailable' as const };
   const controlsGraphData = filterDisabledPluginEdgesForControls(graphData, disabledPlugins);
   const filePaths = controlsGraphData.nodes
     .filter(isFileNode)
@@ -67,6 +70,7 @@ export function sendGraphControlsUpdated(
         controlsGraphData,
         readNodeTypes(registry, disabledPlugins),
         readEdgeTypes(registry, disabledPlugins),
+        filterAccounting,
         readGraphScopeCapabilities(registry, filePaths, disabledPlugins),
       ),
     ),
diff --git a/packages/extension/src/extension/graphView/controls/send/definitions/contracts.ts b/packages/extension/src/extension/graphView/controls/send/definitions/contracts.ts
index 80b3136b0a..ecd2bcd719 100644
--- a/packages/extension/src/extension/graphView/controls/send/definitions/contracts.ts
+++ b/packages/extension/src/extension/graphView/controls/send/definitions/contracts.ts
@@ -1,4 +1,5 @@
 import type { GraphEdgeKind } from '../../../../../shared/graph/contracts';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 
 export interface GraphNodeTypeLike {
   id: string;
@@ -29,6 +30,7 @@ export interface GraphTypeDescriptionLike {
 
 export interface GraphControlsAnalyzerLike {
   registry?: unknown;
+  getFilterAccounting(): WorkspaceFilterAccounting;
 }
 
 export interface GraphControlsConfigurationLike {
diff --git a/packages/extension/src/extension/graphView/controls/send/definitions/snapshot.ts b/packages/extension/src/extension/graphView/controls/send/definitions/snapshot.ts
index de29a0878c..122a40fd00 100644
--- a/packages/extension/src/extension/graphView/controls/send/definitions/snapshot.ts
+++ b/packages/extension/src/extension/graphView/controls/send/definitions/snapshot.ts
@@ -1,5 +1,6 @@
 import type { IGraphData } from '../../../../../shared/graph/contracts';
 import type { IGraphControlsSnapshot } from '../../../../../shared/graphControls/contracts';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import { mergeEdgeTypes, mergeNodeTypes } from './merge';
 import {
   resolveNodeColors,
@@ -17,6 +18,7 @@ export function captureGraphControlsSnapshot(
   graphData: IGraphData,
   pluginNodeTypes: GraphNodeTypeLike[],
   pluginEdgeTypes: GraphEdgeTypeLike[],
+  filterAccounting: WorkspaceFilterAccounting,
   graphScopeCapabilities: GraphScopeCapabilitiesLike = { nodeTypes: [], edgeTypes: [] },
 ): IGraphControlsSnapshot {
   const configuredNodeColors = config.get<Record<string, string>>('nodeColors', {}) ?? {};
@@ -31,6 +33,7 @@ export function captureGraphControlsSnapshot(
   const edgeTypes = mergeEdgeTypes(graphData, pluginEdgeTypes, graphScopeCapabilities.edgeTypes);
 
   return {
+    filterAccounting,
     nodeTypes,
     edgeTypes,
     nodeColors: resolveNodeColors(nodeTypes, configuredNodeColors),
diff --git a/packages/extension/src/extension/graphView/provider/analysis/methods.ts b/packages/extension/src/extension/graphView/provider/analysis/methods.ts
index 82e1955763..effdbceae6 100644
--- a/packages/extension/src/extension/graphView/provider/analysis/methods.ts
+++ b/packages/extension/src/extension/graphView/provider/analysis/methods.ts
@@ -1,4 +1,5 @@
 import type { IGraphData } from '../../../../shared/graph/contracts';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import type { ExtensionToWebviewMessage } from '../../../../shared/protocol/extensionToWebview';
 import type { GraphViewIndexingProgress } from '../../analysis/execution';
 import type { GraphViewProviderAnalysisState } from '../../analysis/lifecycle';
@@ -31,6 +32,7 @@ export interface GraphViewProviderWorkspaceReadyRegistryLike {
 
 interface GraphViewProviderAnalysisAnalyzerLike {
   registry?: GraphViewProviderWorkspaceReadyRegistryLike;
+  getFilterAccounting(): WorkspaceFilterAccounting;
 }
 
 export interface GraphViewProviderAnalysisMethodsSource {
diff --git a/packages/extension/src/extension/graphView/provider/plugin/methods.ts b/packages/extension/src/extension/graphView/provider/plugin/methods.ts
index 94e5585ace..fb643b4f15 100644
--- a/packages/extension/src/extension/graphView/provider/plugin/methods.ts
+++ b/packages/extension/src/extension/graphView/provider/plugin/methods.ts
@@ -4,6 +4,7 @@ import type { ViewRegistry } from '../../../../core/views/registry';
 import type { IGraphData } from '../../../../shared/graph/contracts';
 import type { ExtensionToWebviewMessage } from '../../../../shared/protocol/extensionToWebview';
 import type { IGroup } from '../../../../shared/settings/groups';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import { sendGraphViewPluginWebviewInjections } from '../../webview/plugins/contributionDispatch';
 import {
   sendGraphViewDecorations,
@@ -19,7 +20,8 @@ const DEFAULT_DEPTH_LIMIT = 1;
 
 type GraphViewPluginAnalyzerLike =
   NonNullable<Parameters<typeof sendGraphViewPluginWebviewInjections>[0]>
-  & NonNullable<Parameters<typeof sendGraphViewPluginStatuses>[0]>;
+  & NonNullable<Parameters<typeof sendGraphViewPluginStatuses>[0]>
+  & { getFilterAccounting(): WorkspaceFilterAccounting };
 
 type GraphViewDecorationManagerLike =
   Parameters<typeof sendGraphViewDecorations>[0];
diff --git a/packages/extension/src/extension/graphView/provider/settingsState.ts b/packages/extension/src/extension/graphView/provider/settingsState.ts
index 05fce6810b..920886d55e 100644
--- a/packages/extension/src/extension/graphView/provider/settingsState.ts
+++ b/packages/extension/src/extension/graphView/provider/settingsState.ts
@@ -13,9 +13,11 @@ import { captureGraphViewSettingsSnapshot } from '../settings/snapshot';
 import { sendGraphViewProviderAllSettings, sendGraphViewProviderSettings } from '../settings/lifecycle';
 import { sendGraphControlsUpdated } from '../controls/send';
 import type { IPluginFilterPatternGroup } from '../../../shared/protocol/extensionToWebview';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import { resolveCssSnippetStylesheets } from '../cssSnippets/resolve';
 
 interface GraphViewProviderSettingsAnalyzerLike {
+  getFilterAccounting(): WorkspaceFilterAccounting;
   getPluginFilterPatterns(): string[];
   getPluginFilterGroups?(disabledPlugins?: ReadonlySet<string>): IPluginFilterPatternGroup[];
   registry?: unknown;
diff --git a/packages/extension/src/extension/pipeline/analysis/run.ts b/packages/extension/src/extension/pipeline/analysis/run.ts
index 833a9b2064..edd7de08ba 100644
--- a/packages/extension/src/extension/pipeline/analysis/run.ts
+++ b/packages/extension/src/extension/pipeline/analysis/run.ts
@@ -35,6 +35,7 @@ export function runWorkspacePipelineAnalysis(
           directories: result.directories,
           durationMs: result.durationMs,
           files: result.files,
+          filterAccounting: result.filterAccounting,
           gitIgnoredPaths: result.gitIgnoredPaths,
           limitReached: result.limitReached,
           totalFound: result.totalFound ?? result.files.length,
diff --git a/packages/extension/src/extension/pipeline/analysisSource.ts b/packages/extension/src/extension/pipeline/analysisSource.ts
index 54a386d164..b58b98a3ff 100644
--- a/packages/extension/src/extension/pipeline/analysisSource.ts
+++ b/packages/extension/src/extension/pipeline/analysisSource.ts
@@ -2,7 +2,7 @@ import type {
   IProjectedConnection,
   IFileAnalysisResult,
 } from '../../core/plugins/types/contracts';
-import type { IDiscoveredFile } from '@codegraphy-dev/core';
+import type { IDiscoveredFile, WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import type { EventBus } from '../events/bus';
 import type { PluginRegistry } from '../../core/plugins/registry/manager';
 import type { FileDiscovery } from '@codegraphy-dev/core';
@@ -46,6 +46,7 @@ export interface WorkspacePipelineSourceOwner {
   _completeGraphData: IGraphData;
   _lastDiscoveredDirectories: string[];
   _lastDiscoveredFiles: IDiscoveredFile[];
+  _filterAccounting: WorkspaceFilterAccounting;
   _lastFileAnalysis: Map<string, IFileAnalysisResult>;
   _lastFileConnections: Map<string, IProjectedConnection[]>;
   _lastGitIgnoredPaths: string[];
@@ -135,6 +136,12 @@ export function createWorkspacePipelineAnalysisSource(
         owner._lastDiscoveredDirectories = directories;
       },
     },
+    _filterAccounting: {
+      get: () => owner._filterAccounting,
+      set: (accounting: WorkspaceFilterAccounting) => {
+        owner._filterAccounting = accounting;
+      },
+    },
     _lastFileConnections: {
       get: () => owner._lastFileConnections,
       set: (fileConnections: Map<string, IProjectedConnection[]>) => {
diff --git a/packages/extension/src/extension/pipeline/indexingState/model.ts b/packages/extension/src/extension/pipeline/indexingState/model.ts
index abf0d72bb4..db02ce43cc 100644
--- a/packages/extension/src/extension/pipeline/indexingState/model.ts
+++ b/packages/extension/src/extension/pipeline/indexingState/model.ts
@@ -3,6 +3,7 @@ import {
   createWorkspaceIndexEngineState,
   FileDiscovery,
   type IDiscoveredFile,
+  type WorkspaceFilterAccounting,
   type WorkspaceIndexEngineState,
 } from '@codegraphy-dev/core';
 import type { IFileAnalysisResult, IProjectedConnection } from '../../../core/plugins/types/contracts';
@@ -58,6 +59,12 @@ export abstract class WorkspacePipelineEngineStateBase {
   protected set _lastDiscoveredFiles(value: IDiscoveredFile[]) {
     this._engineState.discoveredFiles = value;
   }
+  protected get _filterAccounting(): WorkspaceFilterAccounting {
+    return this._engineState.filterAccounting;
+  }
+  protected set _filterAccounting(value: WorkspaceFilterAccounting) {
+    this._engineState.filterAccounting = value;
+  }
   protected get _lastGitIgnoredPaths(): string[] { return this._engineState.gitIgnoredPaths; }
   protected set _lastGitIgnoredPaths(value: string[]) { this._engineState.gitIgnoredPaths = value; }
   protected get _lastWorkspaceRoot(): string { return this._engineState.workspaceRoot; }
diff --git a/packages/extension/src/extension/pipeline/service/base/internal.ts b/packages/extension/src/extension/pipeline/service/base/internal.ts
index f33ac49e1a..6b373a2030 100644
--- a/packages/extension/src/extension/pipeline/service/base/internal.ts
+++ b/packages/extension/src/extension/pipeline/service/base/internal.ts
@@ -247,6 +247,7 @@ export abstract class WorkspacePipelineInternalBase extends WorkspacePipelineSta
   ): Promise<void> {
     const workspaceRoot = this._getWorkspaceRoot();
     const dependencies = {
+      getFilterAccounting: () => this._filterAccounting,
       getCurrentCommitSha: () =>
         workspaceRoot ? this._getCurrentCommitShaSync(workspaceRoot) : null,
       getPluginSignature: () => this._getPluginSignature(),
diff --git a/packages/extension/src/extension/pipeline/service/cache/index.ts b/packages/extension/src/extension/pipeline/service/cache/index.ts
index 494fa3bbd3..ab5708e410 100644
--- a/packages/extension/src/extension/pipeline/service/cache/index.ts
+++ b/packages/extension/src/extension/pipeline/service/cache/index.ts
@@ -11,6 +11,7 @@ interface WorkspacePipelineSignatureDependencies {
 
 interface WorkspacePipelinePersistIndexDependencies
   extends WorkspacePipelineSignatureDependencies {
+  getFilterAccounting(): Parameters<typeof persistCodeGraphyWorkspaceIndexMetadata>[1]['filterAccounting'];
   getCurrentCommitSha?: () => Promise<string | null> | string | null;
   persistIndexMetadata?: (
     workspaceRoot: string,
@@ -48,6 +49,7 @@ export async function persistWorkspacePipelineIndexMetadata(
   try {
     const currentCommitSha = await dependencies.getCurrentCommitSha?.();
     await (dependencies.persistIndexMetadata ?? persistCodeGraphyWorkspaceIndexMetadata)(workspaceRoot, {
+      filterAccounting: dependencies.getFilterAccounting(),
       ...(dependencies.getCurrentCommitSha
         ? { lastIndexedCommit: currentCommitSha ?? null }
         : {}),
diff --git a/packages/extension/src/extension/pipeline/service/cache/invalidation.ts b/packages/extension/src/extension/pipeline/service/cache/invalidation.ts
index 2b4f59591a..90a0bcbe82 100644
--- a/packages/extension/src/extension/pipeline/service/cache/invalidation.ts
+++ b/packages/extension/src/extension/pipeline/service/cache/invalidation.ts
@@ -20,6 +20,7 @@ export function invalidateWorkspacePipelineFiles(
       cache: state.cache,
       discoveredDirectories: [],
       discoveredFiles: [],
+      filterAccounting: { kind: 'unavailable' },
       gitIgnoredPaths: [],
       fileAnalysis: state.lastFileAnalysis,
       fileConnections: state.lastFileConnections,
diff --git a/packages/extension/src/extension/pipeline/service/cachedGraph.ts b/packages/extension/src/extension/pipeline/service/cachedGraph.ts
index 195625355e..266dcc09f1 100644
--- a/packages/extension/src/extension/pipeline/service/cachedGraph.ts
+++ b/packages/extension/src/extension/pipeline/service/cachedGraph.ts
@@ -9,6 +9,7 @@ import {
   projectFileAnalysisConnections,
   throwIfWorkspaceAnalysisAborted,
 } from '@codegraphy-dev/core';
+import { readCodeGraphyWorkspaceMeta } from '@codegraphy-dev/core';
 import type { IGraphData } from '../../../shared/graph/contracts';
 import {
   collectCachedDirectoryPaths,
@@ -55,11 +56,12 @@ export abstract class WorkspacePipelineCachedGraphFacade extends WorkspacePipeli
       cachedFilePaths,
     );
 
+    this._filterAccounting = readCodeGraphyWorkspaceMeta(workspaceRoot).filterAccounting;
+    const gitIgnoredPaths = new Set(cachedDiscovery.gitIgnoredPaths);
     const activeFilterPatterns = [
       ...this._getEffectiveCustomFilterPatterns(filterPatterns),
       ...this._getEffectivePluginFilterPatterns(disabledPlugins),
     ];
-    const gitIgnoredPaths = new Set(cachedDiscovery.gitIgnoredPaths);
     const eligibleFiles = cachedDiscovery.files.filter(file => (
       !gitIgnoredPaths.has(file.relativePath)
       && !matchesAnyPattern(file.relativePath, activeFilterPatterns)
diff --git a/packages/extension/src/extension/pipeline/service/graphDiscovery.ts b/packages/extension/src/extension/pipeline/service/graphDiscovery.ts
index 3cdefcb11f..560965aa8c 100644
--- a/packages/extension/src/extension/pipeline/service/graphDiscovery.ts
+++ b/packages/extension/src/extension/pipeline/service/graphDiscovery.ts
@@ -37,6 +37,7 @@ export abstract class WorkspacePipelineGraphDiscoveryFacade extends WorkspacePip
 
     this._lastDiscoveredDirectories = discoveryResult.directories ?? [];
     this._lastDiscoveredFiles = discoveryResult.files;
+    this._filterAccounting = discoveryResult.filterAccounting;
     this._lastGitIgnoredPaths = discoveryResult.gitIgnoredPaths ?? [];
     this._lastFileAnalysis = new Map();
     this._lastFileConnections = fileConnections;
diff --git a/packages/extension/src/extension/pipeline/service/pluginFacade.ts b/packages/extension/src/extension/pipeline/service/pluginFacade.ts
index d42363477f..8337f9019c 100644
--- a/packages/extension/src/extension/pipeline/service/pluginFacade.ts
+++ b/packages/extension/src/extension/pipeline/service/pluginFacade.ts
@@ -1,4 +1,5 @@
 import type { IPluginFilterPatternGroup } from '../../../shared/protocol/extensionToWebview';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import { hasWorkspacePipelineIndex } from './cache/index';
 import { WorkspacePipelineInternalBase } from './base/internal';
 import { getWorkspacePipelineIndexStatus } from './indexStatus';
@@ -79,6 +80,10 @@ export abstract class WorkspacePipelinePluginFacade extends WorkspacePipelineInt
     return getPipelinePluginFilterGroups(this._registry, disabledPlugins);
   }
 
+  getFilterAccounting(): WorkspaceFilterAccounting {
+    return this._filterAccounting;
+  }
+
   protected _getEffectiveCustomFilterPatterns(filterPatterns: string[]): string[] {
     return getEffectiveCustomFilterPatterns(this._config, filterPatterns);
   }
diff --git a/packages/extension/src/extension/pipeline/service/refresh/context.ts b/packages/extension/src/extension/pipeline/service/refresh/context.ts
index 950fd8af7e..169e0eb8cb 100644
--- a/packages/extension/src/extension/pipeline/service/refresh/context.ts
+++ b/packages/extension/src/extension/pipeline/service/refresh/context.ts
@@ -1,4 +1,8 @@
-import type { AnalysisCacheTier, FileDiscovery } from '@codegraphy-dev/core';
+import type {
+  AnalysisCacheTier,
+  FileDiscovery,
+  WorkspaceFilterAccounting,
+} from '@codegraphy-dev/core';
 import type { Configuration } from '../../../config/reader';
 import type { PluginRegistry } from '../../../../core/plugins/registry/manager';
 import type { IGraphData } from '../../../../shared/graph/contracts';
@@ -27,6 +31,7 @@ export interface RefreshFacadeContext
   _captureRefreshState(): WorkspacePipelineRefreshState;
   _getWorkspaceRoot(): string | undefined;
   _lastGitIgnoredPaths: string[];
+  _filterAccounting: WorkspaceFilterAccounting;
   _persistCache(): void;
   _persistCachePatch(patch: WorkspacePipelineCachePatch): Promise<void>;
   _persistIndexMetadata(resolvedChangedFilePaths?: readonly string[]): Promise<void>;
diff --git a/packages/extension/src/extension/pipeline/service/refresh/modes/analysisScope.ts b/packages/extension/src/extension/pipeline/service/refresh/modes/analysisScope.ts
index ef7f05308c..deff12fba2 100644
--- a/packages/extension/src/extension/pipeline/service/refresh/modes/analysisScope.ts
+++ b/packages/extension/src/extension/pipeline/service/refresh/modes/analysisScope.ts
@@ -34,6 +34,7 @@ export async function refreshAnalysisScopeForFacade(
     signal: input.signal,
     workspaceRoot,
   });
+  facade._filterAccounting = discoveryResult.filterAccounting;
   facade._lastGitIgnoredPaths = discoveryResult.gitIgnoredPaths ?? [];
 
   if (canReuseCurrentAnalysisForScope({
diff --git a/packages/extension/src/extension/pipeline/service/refresh/modes/changedFiles.ts b/packages/extension/src/extension/pipeline/service/refresh/modes/changedFiles.ts
index 05838aba56..6ba69aa765 100644
--- a/packages/extension/src/extension/pipeline/service/refresh/modes/changedFiles.ts
+++ b/packages/extension/src/extension/pipeline/service/refresh/modes/changedFiles.ts
@@ -136,6 +136,7 @@ async function getChangedFileDiscoveryState(
     files: discovered.discoveryResult.files,
     limitReached: discovered.discoveryResult.limitReached,
   };
+  facade._filterAccounting = discovered.discoveryResult.filterAccounting;
   facade._lastGitIgnoredPaths = discovered.discoveryResult.gitIgnoredPaths ?? [];
   return discoveryResult;
 }
diff --git a/packages/extension/src/extension/pipeline/service/refresh/modes/gitignoreMetadata.ts b/packages/extension/src/extension/pipeline/service/refresh/modes/gitignoreMetadata.ts
index 64b991aca5..c85937ca37 100644
--- a/packages/extension/src/extension/pipeline/service/refresh/modes/gitignoreMetadata.ts
+++ b/packages/extension/src/extension/pipeline/service/refresh/modes/gitignoreMetadata.ts
@@ -31,12 +31,11 @@ export async function refreshGitignoreMetadataForFacade(
 
   facade._lastDiscoveredDirectories = discoveryResult.directories ?? [];
   facade._lastDiscoveredFiles = discoveryResult.files;
+  facade._filterAccounting = discoveryResult.filterAccounting;
   facade._lastGitIgnoredPaths = discoveryResult.gitIgnoredPaths ?? [];
   facade._lastWorkspaceRoot = workspaceRoot;
 
-  void facade._persistIndexMetadata().catch(error => {
-    console.warn('[CodeGraphy] Failed to persist gitignore metadata refresh.', error);
-  });
+  await facade._persistIndexMetadata();
 
   const eligibleFilePaths = new Set(
     discoveryResult.files.map(file => file.relativePath),
diff --git a/packages/extension/src/extension/pipeline/service/refresh/modes/pluginFiles.ts b/packages/extension/src/extension/pipeline/service/refresh/modes/pluginFiles.ts
index 4c797515d6..5e357c1ee1 100644
--- a/packages/extension/src/extension/pipeline/service/refresh/modes/pluginFiles.ts
+++ b/packages/extension/src/extension/pipeline/service/refresh/modes/pluginFiles.ts
@@ -31,6 +31,7 @@ export async function refreshPluginFilesForFacade(
     signal: input.signal,
     workspaceRoot,
   });
+  facade._filterAccounting = discoveryResult.filterAccounting;
   facade._lastGitIgnoredPaths = discoveryResult.gitIgnoredPaths ?? [];
 
   return refreshWorkspacePipelinePluginFiles(createWorkspaceIndexRefreshSource(
diff --git a/packages/extension/src/extension/pipeline/service/runtime/discovery.ts b/packages/extension/src/extension/pipeline/service/runtime/discovery.ts
index f2dc975e4f..7f2e3b3c6d 100644
--- a/packages/extension/src/extension/pipeline/service/runtime/discovery.ts
+++ b/packages/extension/src/extension/pipeline/service/runtime/discovery.ts
@@ -18,6 +18,7 @@ export function createWorkspacePipelineDiscoveryDependencies(
         directories: result.directories,
         durationMs: result.durationMs,
         files: result.files,
+        filterAccounting: result.filterAccounting,
         gitIgnoredPaths: result.gitIgnoredPaths,
         limitReached: result.limitReached,
         totalFound: result.totalFound ?? result.files.length,
diff --git a/packages/extension/src/extension/repoSettings/meta.ts b/packages/extension/src/extension/repoSettings/meta.ts
index 7921a8ec6a..623c5c0cb1 100644
--- a/packages/extension/src/extension/repoSettings/meta.ts
+++ b/packages/extension/src/extension/repoSettings/meta.ts
@@ -2,16 +2,18 @@ import * as path from 'node:path';
 import {
   createDefaultCodeGraphyWorkspaceMeta,
   readCodeGraphyWorkspaceMeta,
+  type WorkspaceFilterAccounting,
 } from '@codegraphy-dev/core';
 
 export interface ICodeGraphyRepoMeta {
-  version: 1;
+  version: 2;
   lastIndexedAt: string | null;
   lastIndexedCommit: string | null;
   pluginBuildSignature: string | null;
   pluginSignature: string | null;
   settingsSignature: string | null;
   pendingChangedFiles: string[];
+  filterAccounting: WorkspaceFilterAccounting;
 }
 
 export function createDefaultCodeGraphyRepoMeta(): ICodeGraphyRepoMeta {
@@ -28,12 +30,13 @@ export function readCodeGraphyRepoMeta(workspaceRoot: string): ICodeGraphyRepoMe
 
 function toRepoMeta(meta: ReturnType<typeof readCodeGraphyWorkspaceMeta>): ICodeGraphyRepoMeta {
   return {
-    version: 1,
+    version: 2,
     lastIndexedAt: meta.lastIndexedAt,
     lastIndexedCommit: meta.lastIndexedCommit ?? null,
     pluginBuildSignature: meta.pluginBuildSignature,
     pluginSignature: meta.pluginSignature,
     settingsSignature: meta.settingsSignature,
     pendingChangedFiles: [...meta.pendingChangedFiles],
+    filterAccounting: meta.filterAccounting,
   };
 }
diff --git a/packages/extension/src/shared/graphControls/contracts.ts b/packages/extension/src/shared/graphControls/contracts.ts
index 4c4608c4a4..78710385ab 100644
--- a/packages/extension/src/shared/graphControls/contracts.ts
+++ b/packages/extension/src/shared/graphControls/contracts.ts
@@ -2,6 +2,7 @@ import type {
   GraphEdgeKind,
   NodeType,
 } from '../graph/contracts';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 
 export interface IGraphNodeTypeDefinition {
   id: NodeType;
@@ -38,6 +39,7 @@ export interface IGraphTypeDescription {
 }
 
 export interface IGraphControlsSnapshot {
+  filterAccounting: WorkspaceFilterAccounting;
   nodeTypes: IGraphNodeTypeDefinition[];
   edgeTypes: IGraphEdgeTypeDefinition[];
   nodeColors: Record<string, string>;
diff --git a/packages/extension/src/webview/app/shell/storeSelectors.ts b/packages/extension/src/webview/app/shell/storeSelectors.ts
index 9c98064a7f..bede3542dc 100644
--- a/packages/extension/src/webview/app/shell/storeSelectors.ts
+++ b/packages/extension/src/webview/app/shell/storeSelectors.ts
@@ -15,6 +15,7 @@ export function useAppState() {
   const searchOptions = useGraphStore(s => s.searchOptions);
   const legends = useGraphStore(s => s.legends);
   const filterPatterns = useGraphStore(s => s.filterPatterns);
+  const filterAccounting = useGraphStore(s => s.filterAccounting);
   const pluginFilterPatterns = useGraphStore(s => s.pluginFilterPatterns);
   const pluginFilterGroups = useGraphStore(s => s.pluginFilterGroups);
   const disabledCustomFilterPatterns = useGraphStore(s => s.disabledCustomFilterPatterns);
@@ -40,6 +41,7 @@ export function useAppState() {
     searchOptions,
     legends,
     filterPatterns,
+    filterAccounting,
     pluginFilterPatterns,
     pluginFilterGroups,
     disabledCustomFilterPatterns,
diff --git a/packages/extension/src/webview/app/shell/view.tsx b/packages/extension/src/webview/app/shell/view.tsx
index ac2dc4316b..ca1873965e 100644
--- a/packages/extension/src/webview/app/shell/view.tsx
+++ b/packages/extension/src/webview/app/shell/view.tsx
@@ -44,6 +44,7 @@ export default function App({ graphPhysicsPreparation }: AppShellProps): React.R
     searchOptions,
     legends,
     filterPatterns,
+    filterAccounting,
     pluginFilterPatterns,
     pluginFilterGroups,
     disabledCustomFilterPatterns,
@@ -205,7 +206,8 @@ export default function App({ graphPhysicsPreparation }: AppShellProps): React.R
           customPatterns: filterPatterns,
           disabledCustomPatterns: disabledCustomFilterPatterns,
           disabledPluginPatterns: disabledPluginFilterPatterns,
-          excludedCount,
+          filterAccounting,
+          excludedNodeCount: excludedCount,
           onDisabledCustomPatternsChange: setDisabledCustomFilterPatterns,
           onDisabledPluginPatternsChange: setDisabledPluginFilterPatterns,
           buttonRef: filterButtonRef,
diff --git a/packages/extension/src/webview/components/searchBar/field/model.ts b/packages/extension/src/webview/components/searchBar/field/model.ts
index c93144d7d3..2d1154d373 100644
--- a/packages/extension/src/webview/components/searchBar/field/model.ts
+++ b/packages/extension/src/webview/components/searchBar/field/model.ts
@@ -5,6 +5,7 @@
 
 import type React from 'react';
 import type { IPluginFilterPatternGroup } from '../../../../shared/protocol/extensionToWebview';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 
 export interface SearchOptions {
   matchCase: boolean;
@@ -28,7 +29,8 @@ export interface SearchBarProps {
     disabledCustomPatterns: string[];
     disabledPluginPatterns: string[];
     customPatterns: string[];
-    excludedCount: number;
+    filterAccounting: WorkspaceFilterAccounting;
+    excludedNodeCount: number;
     onDisabledCustomPatternsChange: (patterns: string[]) => void;
     onDisabledPluginPatternsChange: (patterns: string[]) => void;
     onOpenChange: (open: boolean) => void;
diff --git a/packages/extension/src/webview/components/searchBar/filters/countState.ts b/packages/extension/src/webview/components/searchBar/filters/countState.ts
index 506845f41b..afab6c86b6 100644
--- a/packages/extension/src/webview/components/searchBar/filters/countState.ts
+++ b/packages/extension/src/webview/components/searchBar/filters/countState.ts
@@ -1,3 +1,5 @@
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
+
 export interface FilterCountInput {
   excludedCount: number;
   filterVisibleCount: number;
@@ -43,10 +45,23 @@ export function getFilterCountState({
   return { kind: 'idle', label: null };
 }
 
-export function formatExcludedCount(count: number): string {
+export function formatExcludedFileCount(accounting: WorkspaceFilterAccounting): string {
+  if (accounting.kind === 'unavailable') {
+    return 'Before analysis: re-index to calculate excluded workspace files';
+  }
+
+  const count = accounting.excludedFileCount;
+  if (count === 1) {
+    return 'Before analysis: 1 workspace file excluded';
+  }
+
+  return `Before analysis: ${count} workspace files excluded`;
+}
+
+export function formatExcludedNodeCount(count: number): string {
   if (count === 1) {
-    return '1 excluded from graph';
+    return 'In Graph View: 1 Node excluded';
   }
 
-  return `${count} excluded from graph`;
+  return `In Graph View: ${count} Nodes excluded`;
 }
diff --git a/packages/extension/src/webview/components/searchBar/filters/popover.tsx b/packages/extension/src/webview/components/searchBar/filters/popover.tsx
index 1e6de2ca42..fee19dbeda 100644
--- a/packages/extension/src/webview/components/searchBar/filters/popover.tsx
+++ b/packages/extension/src/webview/components/searchBar/filters/popover.tsx
@@ -10,7 +10,7 @@ import {
   getDisabledFilterPatterns,
   getEnabledFilterCount,
 } from './model';
-import { formatExcludedCount } from './countState';
+import { formatExcludedFileCount, formatExcludedNodeCount } from './countState';
 import { handleAddPatterns } from './popover/actions';
 import { CustomFiltersSection } from './popover/customSection';
 import { useFilterDraftState } from './popover/draftState';
@@ -23,7 +23,8 @@ export function FilterPopover({
   disabledCustomPatterns,
   disabledPluginPatterns,
   customPatterns,
-  excludedCount,
+  filterAccounting,
+  excludedNodeCount,
   onDisabledCustomPatternsChange,
   onDisabledPluginPatternsChange,
   onOpenChange,
@@ -106,7 +107,7 @@ export function FilterPopover({
         className="h-7 px-2 text-xs"
         aria-expanded={isOpen}
         aria-label={`Filters, ${enabledCount} enabled`}
-        title={formatExcludedCount(excludedCount)}
+        title={`${formatExcludedFileCount(filterAccounting)}\n${formatExcludedNodeCount(excludedNodeCount)}`}
         onClick={() => setOpen(!isOpen)}
       >
         <MdiIcon path={mdiFilterVariant} size={14} />
@@ -123,7 +124,8 @@ export function FilterPopover({
               <h2 className="text-sm font-medium">Filters</h2>
               <span className="text-xs text-muted-foreground">{enabledCount} enabled</span>
             </div>
-            <p className="text-[11px] text-muted-foreground">{formatExcludedCount(excludedCount)}</p>
+            <p className="text-[11px] text-muted-foreground">{formatExcludedFileCount(filterAccounting)}</p>
+            <p className="text-[11px] text-muted-foreground">{formatExcludedNodeCount(excludedNodeCount)}</p>
           </header>
 
           <div className="max-h-[min(320px,35vh)] space-y-3 overflow-y-auto p-3" data-codegraphy-region="panel-body">
diff --git a/packages/extension/src/webview/components/searchBar/filters/popover/types.ts b/packages/extension/src/webview/components/searchBar/filters/popover/types.ts
index a180ab7cb0..4d318ff39b 100644
--- a/packages/extension/src/webview/components/searchBar/filters/popover/types.ts
+++ b/packages/extension/src/webview/components/searchBar/filters/popover/types.ts
@@ -1,12 +1,14 @@
 import type React from 'react';
 import type { IPluginFilterPatternGroup } from '../../../../../shared/protocol/extensionToWebview';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 
 export interface FilterPopoverProps {
   buttonRef?: React.Ref<HTMLButtonElement>;
   disabledCustomPatterns: string[];
   disabledPluginPatterns: string[];
   customPatterns: string[];
-  excludedCount: number;
+  filterAccounting: WorkspaceFilterAccounting;
+  excludedNodeCount: number;
   onDisabledCustomPatternsChange: (patterns: string[]) => void;
   onDisabledPluginPatternsChange: (patterns: string[]) => void;
   onOpenChange?: (open: boolean) => void;
diff --git a/packages/extension/src/webview/store/initialState.ts b/packages/extension/src/webview/store/initialState.ts
index 232fe4a887..7362933e2a 100644
--- a/packages/extension/src/webview/store/initialState.ts
+++ b/packages/extension/src/webview/store/initialState.ts
@@ -37,6 +37,7 @@ export const INITIAL_STATE: GraphStateFields = {
   optimisticLegendUpdates: {},
   optimisticUserLegends: null,
   filterPatterns: [],
+  filterAccounting: { kind: 'unavailable' as const },
   pluginFilterPatterns: [],
   pluginFilterGroups: [],
   disabledCustomFilterPatterns: [],
diff --git a/packages/extension/src/webview/store/messageHandlers/graphControls.ts b/packages/extension/src/webview/store/messageHandlers/graphControls.ts
index fe02944193..6518b2d7ea 100644
--- a/packages/extension/src/webview/store/messageHandlers/graphControls.ts
+++ b/packages/extension/src/webview/store/messageHandlers/graphControls.ts
@@ -35,6 +35,7 @@ export function handleGraphControlsUpdated(
   if (!state) {
     return {
       graphNodeTypes: message.payload.nodeTypes,
+      filterAccounting: message.payload.filterAccounting,
       graphEdgeTypes: message.payload.edgeTypes,
       nodeColors: message.payload.nodeColors,
       nodeVisibility: message.payload.nodeVisibility,
diff --git a/packages/extension/src/webview/store/messageHandlers/graphControls/patch.ts b/packages/extension/src/webview/store/messageHandlers/graphControls/patch.ts
index ad58f76774..6b10843b2f 100644
--- a/packages/extension/src/webview/store/messageHandlers/graphControls/patch.ts
+++ b/packages/extension/src/webview/store/messageHandlers/graphControls/patch.ts
@@ -13,6 +13,7 @@ export function createGraphControlsStatePatch(
 ): PartialState {
   const next: PartialState = {};
 
+  assignChangedGraphControl(next, 'filterAccounting', state.filterAccounting, payload.filterAccounting);
   assignChangedGraphControl(next, 'graphNodeTypes', state.graphNodeTypes, payload.nodeTypes);
   assignChangedGraphControl(next, 'graphEdgeTypes', state.graphEdgeTypes, payload.edgeTypes);
   assignChangedGraphControl(next, 'nodeColors', state.nodeColors, payload.nodeColors);
diff --git a/packages/extension/src/webview/store/messageTypes.ts b/packages/extension/src/webview/store/messageTypes.ts
index da8c21b6b9..d4b1c7acfa 100644
--- a/packages/extension/src/webview/store/messageTypes.ts
+++ b/packages/extension/src/webview/store/messageTypes.ts
@@ -12,6 +12,7 @@ import type {
 import type { IGroup } from '../../shared/settings/groups';
 import type { BidirectionalEdgeMode, DirectionMode, NodeSizeMode } from '../../shared/settings/modes';
 import type { IPhysicsSettings } from '../../shared/settings/physics';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import type {
   PendingGroupUpdates,
   PendingUserGroupsUpdate,
@@ -52,6 +53,7 @@ export interface IStoreFields {
   optimisticLegendUpdates: PendingGroupUpdates;
   optimisticUserLegends: PendingUserGroupsUpdate | null;
   filterPatterns: string[];
+  filterAccounting: WorkspaceFilterAccounting;
   pluginFilterPatterns: string[];
   pluginFilterGroups: IPluginFilterPatternGroup[];
   disabledCustomFilterPatterns: string[];
diff --git a/packages/extension/src/webview/store/state.ts b/packages/extension/src/webview/store/state.ts
index ea04729a56..6c86444a2b 100644
--- a/packages/extension/src/webview/store/state.ts
+++ b/packages/extension/src/webview/store/state.ts
@@ -17,6 +17,7 @@ import type {
 import type { IGroup } from '../../shared/settings/groups';
 import type { BidirectionalEdgeMode, DirectionMode, NodeSizeMode } from '../../shared/settings/modes';
 import type { IPhysicsSettings } from '../../shared/settings/physics';
+import type { WorkspaceFilterAccounting } from '@codegraphy-dev/core';
 import type {
   PendingGroupUpdates,
   PendingUserGroupsUpdate,
@@ -56,6 +57,7 @@ export interface GraphState {
   optimisticLegendUpdates: PendingGroupUpdates;
   optimisticUserLegends: PendingUserGroupsUpdate | null;
   filterPatterns: string[];
+  filterAccounting: WorkspaceFilterAccounting;
   pluginFilterPatterns: string[];
   pluginFilterGroups: IPluginFilterPatternGroup[];
   disabledCustomFilterPatterns: string[];
diff --git a/packages/extension/tests/extension/graphView/analysis/execution/fixtures.ts b/packages/extension/tests/extension/graphView/analysis/execution/fixtures.ts
index bde935fef0..4946bda518 100644
--- a/packages/extension/tests/extension/graphView/analysis/execution/fixtures.ts
+++ b/packages/extension/tests/extension/graphView/analysis/execution/fixtures.ts
@@ -26,6 +26,7 @@ export function createExecutionAnalyzer(
     initialize: vi.fn(async () => undefined),
     syncWorkspacePlugins: vi.fn(async () => undefined),
     hasIndex: vi.fn(() => true),
+    getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
     hasRecoverableGraphState: vi.fn(() => true),
     analyze: vi.fn(async () => ({ nodes: [], edges: [] })),
     refreshIndex: vi.fn(async () => ({ nodes: [], edges: [] })),
diff --git a/packages/extension/tests/extension/graphView/analysis/execution/incremental.test.ts b/packages/extension/tests/extension/graphView/analysis/execution/incremental.test.ts
index f112955607..8fa294ddc6 100644
--- a/packages/extension/tests/extension/graphView/analysis/execution/incremental.test.ts
+++ b/packages/extension/tests/extension/graphView/analysis/execution/incremental.test.ts
@@ -13,6 +13,7 @@ function createState(
     analyzer: {
       analyze: vi.fn(),
       hasIndex: vi.fn(() => true),
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       hasRecoverableGraphState: vi.fn(() => true),
       initialize: vi.fn(),
       loadCachedGraph: vi.fn(async () => ({ nodes: [], edges: [] })),
diff --git a/packages/extension/tests/extension/graphView/analysis/lifecycle.test.ts b/packages/extension/tests/extension/graphView/analysis/lifecycle.test.ts
index f0f6a55786..7af5397dd7 100644
--- a/packages/extension/tests/extension/graphView/analysis/lifecycle.test.ts
+++ b/packages/extension/tests/extension/graphView/analysis/lifecycle.test.ts
@@ -31,6 +31,7 @@ function createAnalyzer(overrides: Partial<NonNullable<GraphViewProviderAnalysis
     initialize: vi.fn(async () => undefined),
     syncWorkspacePlugins: vi.fn(async () => undefined),
     hasIndex: vi.fn(() => true),
+    getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
     hasRecoverableGraphState: vi.fn(() => true),
     analyze: vi.fn(async () => ({ nodes: [], edges: [] })),
     registry: {
diff --git a/packages/extension/tests/extension/graphView/controls/definitions/snapshot.test.ts b/packages/extension/tests/extension/graphView/controls/definitions/snapshot.test.ts
index 66619f9a96..7489f9b233 100644
--- a/packages/extension/tests/extension/graphView/controls/definitions/snapshot.test.ts
+++ b/packages/extension/tests/extension/graphView/controls/definitions/snapshot.test.ts
@@ -16,6 +16,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: [] },
     );
 
@@ -56,6 +57,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       {
         nodeTypes: ['symbol:function', 'symbol:struct', 'symbol:enum', 'symbol:constant'],
         edgeTypes: [],
@@ -108,6 +110,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: ['import', 'reexport'] },
     );
 
@@ -140,6 +143,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: ['symbol:function'], edgeTypes: [] },
     );
 
@@ -182,6 +186,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       {
         nodeTypes: [
           'symbol:function',
@@ -254,6 +259,7 @@ describe('extension/graphView/controls/snapshot', () => {
           defaultVisible: true,
         },
       ],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: ['import', 'plugin:route'] },
     );
 
@@ -289,6 +295,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: ['reference'] },
     );
 
@@ -317,6 +324,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
     );
 
     expect(snapshot.edgeTypes.map((edgeType) => edgeType.id)).toEqual([
@@ -347,6 +355,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: ['include', 'call', 'contains', 'inherit', 'overrides'] },
     );
 
@@ -382,6 +391,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: ['using', 'type', 'call', 'inherit', 'implements', 'contains'] },
     );
 
@@ -421,6 +431,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: [] },
     );
 
@@ -482,6 +493,7 @@ describe('extension/graphView/controls/snapshot', () => {
           },
         },
       ],
+      { kind: 'unavailable' },
       { nodeTypes: ['route'], edgeTypes: ['plugin:route'] },
     );
 
@@ -541,6 +553,7 @@ describe('extension/graphView/controls/snapshot', () => {
       },
       [],
       [],
+      { kind: 'unavailable' },
       { nodeTypes: [], edgeTypes: [] },
     );
 
diff --git a/packages/extension/tests/extension/graphView/controls/send.test.ts b/packages/extension/tests/extension/graphView/controls/send.test.ts
index fd36cafe61..071c1b487d 100644
--- a/packages/extension/tests/extension/graphView/controls/send.test.ts
+++ b/packages/extension/tests/extension/graphView/controls/send.test.ts
@@ -20,6 +20,7 @@ describe('extension/graphView/controls/send', () => {
         ],
       },
       {
+        getFilterAccounting: () => ({ kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 }),
         registry: {
           listNodeTypes: () => [
             null,
@@ -55,6 +56,11 @@ describe('extension/graphView/controls/send', () => {
 
     const payload = sendMessage.mock.calls[0][0].payload;
     expect(payload).toBeDefined();
+    expect(payload.filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 3,
+      gitIgnoredPathCount: 2,
+    });
     expect(payload.nodeTypes.some((nodeType: { id: string }) => nodeType.id === 'bad-node')).toBe(false);
     expect(payload.edgeTypes.some((edgeType: { id: string }) => edgeType.id === 'bad-edge')).toBe(false);
   });
@@ -68,6 +74,7 @@ describe('extension/graphView/controls/send', () => {
         edges: [{ id: 'src/app.ts->src/lib.ts#import', from: 'src/app.ts', to: 'src/lib.ts', kind: 'import', sources: [] }],
       },
       {
+        getFilterAccounting: () => ({ kind: 'unavailable' }),
         registry: {
           listNodeTypes: 'not-a-function',
           listEdgeTypes: () => 'not-an-array',
@@ -92,6 +99,7 @@ describe('extension/graphView/controls/send', () => {
         edges: [],
       },
       {
+        getFilterAccounting: () => ({ kind: 'unavailable' }),
         registry: {
           listEdgeTypes: () => [
             { id: 'plugin:route', label: 'Route', defaultColor: '#10B981', defaultVisible: true },
@@ -137,6 +145,7 @@ describe('extension/graphView/controls/send', () => {
         ],
       },
       {
+        getFilterAccounting: () => ({ kind: 'unavailable' }),
         registry: {
           listEdgeTypes: () => [],
           listGraphScopeCapabilities: () => ({
@@ -181,7 +190,7 @@ describe('extension/graphView/controls/send', () => {
         nodes: [{ id: 'game/player.gd', label: 'Player', color: '#111111', nodeType: 'file' }],
         edges: [],
       },
-      { registry },
+      { getFilterAccounting: () => ({ kind: 'unavailable' }), registry },
       sendMessage,
       { get: <T>(_key: string, defaultValue: T): T => defaultValue },
       disabledPlugins,
@@ -212,6 +221,7 @@ describe('extension/graphView/controls/send', () => {
         ],
       },
       {
+        getFilterAccounting: () => ({ kind: 'unavailable' }),
         registry: {
           listEdgeTypes: () => [],
           listGraphScopeCapabilities: () => ({ nodeTypes: [], edgeTypes: [] }),
@@ -246,12 +256,14 @@ describe('extension/graphView/controls/send', () => {
 
     const payload = sendMessage.mock.calls[0][0].payload;
     expect(payload).toBeDefined();
+    expect(payload.filterAccounting).toEqual({ kind: 'unavailable' });
     expect(payload.nodeTypes.map((nodeType: { id: string }) => nodeType.id)).toEqual(STRUCTURAL_NODE_TYPE_IDS);
     expect(payload.edgeTypes.some((edgeType: { id: string }) => edgeType.id === 'plugin:route')).toBe(false);
   });
 
   it('keeps the snapshot payload intact when building the outbound message', () => {
     const snapshot: IGraphControlsSnapshot = {
+      filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
       nodeTypes: [{ id: 'file', label: 'File', defaultColor: '#A1A1AA', defaultVisible: true }],
       edgeTypes: [{ id: 'import', label: 'Import', defaultColor: '#60A5FA', defaultVisible: true }],
       nodeColors: { file: '#A1A1AA' },
diff --git a/packages/extension/tests/extension/graphView/provider/analysis/handlers.test.ts b/packages/extension/tests/extension/graphView/provider/analysis/handlers.test.ts
index 47c9c531af..52fcd6f878 100644
--- a/packages/extension/tests/extension/graphView/provider/analysis/handlers.test.ts
+++ b/packages/extension/tests/extension/graphView/provider/analysis/handlers.test.ts
@@ -73,7 +73,13 @@ describe('graphView/provider/analysis/handlers', () => {
   });
 
   it('builds execution handlers that update provider state and delegate callbacks', () => {
-    const source = createSource();
+    const source = createSource({
+      _analyzer: { getFilterAccounting: vi.fn(() => ({
+        kind: 'current',
+        excludedFileCount: 3,
+        gitIgnoredPathCount: 2,
+      })) } as never,
+    });
     const dependencies = createDependencies();
     const callbacks = {
       isAnalysisStale: vi.fn(() => true),
@@ -151,6 +157,7 @@ describe('graphView/provider/analysis/handlers', () => {
       sendMessage({
         type: 'GRAPH_CONTROLS_UPDATED',
         payload: {
+          filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
           nodeTypes: [],
           edgeTypes: [],
           nodeColors: {},
@@ -179,6 +186,7 @@ describe('graphView/provider/analysis/handlers', () => {
     expect(source._sendMessage).toHaveBeenCalledWith({
       type: 'GRAPH_CONTROLS_UPDATED',
       payload: {
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         nodeTypes: [],
         edgeTypes: [],
         nodeColors: {},
@@ -189,6 +197,7 @@ describe('graphView/provider/analysis/handlers', () => {
     expect(source._sendMessage).toHaveBeenNthCalledWith(1, {
       type: 'GRAPH_CONTROLS_UPDATED',
       payload: {
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         nodeTypes: [],
         edgeTypes: [],
         nodeColors: {},
diff --git a/packages/extension/tests/extension/graphView/provider/settingsState.test.ts b/packages/extension/tests/extension/graphView/provider/settingsState.test.ts
index 6f14db84a6..4f4e6eaa0b 100644
--- a/packages/extension/tests/extension/graphView/provider/settingsState.test.ts
+++ b/packages/extension/tests/extension/graphView/provider/settingsState.test.ts
@@ -265,7 +265,14 @@ describe('graphView/provider/settingsState', () => {
 
   it('sends all settings with the current state, analyzer filters, and side-effect callbacks', () => {
     const source = createSource({
-      _analyzer: { getPluginFilterPatterns: vi.fn(() => ['plugin/**']) },
+      _analyzer: {
+        getFilterAccounting: vi.fn(() => ({
+          kind: 'current' as const,
+          excludedFileCount: 4,
+          gitIgnoredPathCount: 2,
+        })),
+        getPluginFilterPatterns: vi.fn(() => ['plugin/**']),
+      },
     });
     const snapshot = { snapshot: true } as never;
     const message = {
@@ -303,6 +310,16 @@ describe('graphView/provider/settingsState', () => {
     expect(source._computeMergedGroups).toHaveBeenCalledOnce();
     expect(source._sendGroupsUpdated).toHaveBeenCalledOnce();
     expect(source._sendMessage).toHaveBeenCalledWith(message);
+    expect(source._sendMessage).toHaveBeenCalledWith(expect.objectContaining({
+      type: 'GRAPH_CONTROLS_UPDATED',
+      payload: expect.objectContaining({
+        filterAccounting: {
+          kind: 'current',
+          excludedFileCount: 4,
+          gitIgnoredPathCount: 2,
+        },
+      }),
+    }));
     expect(source._userGroups).toEqual([{ id: 'group.updated' }]);
     expect(source._filterPatterns).toEqual(['updated/**']);
   });
@@ -311,7 +328,10 @@ describe('graphView/provider/settingsState', () => {
     const source = createSource({
       _userGroups: [{ id: 'group.current' } as never],
       _filterPatterns: ['current/**'],
-      _analyzer: { getPluginFilterPatterns: vi.fn(() => ['plugin/**']) },
+      _analyzer: {
+        getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
+        getPluginFilterPatterns: vi.fn(() => ['plugin/**']),
+      },
     });
     const snapshotGroups = [{ id: 'group.snapshot' } as never];
     const snapshotFilterPatterns = ['snapshot/**'];
diff --git a/packages/extension/tests/extension/graphView/provider/settingsStateDefaultDependencies.test.ts b/packages/extension/tests/extension/graphView/provider/settingsStateDefaultDependencies.test.ts
index 8cdadbd23e..a4fb744390 100644
--- a/packages/extension/tests/extension/graphView/provider/settingsStateDefaultDependencies.test.ts
+++ b/packages/extension/tests/extension/graphView/provider/settingsStateDefaultDependencies.test.ts
@@ -198,7 +198,10 @@ describe('graphView/provider/settingsState default dependencies', () => {
 
   it('sends settings through the default provider message bridge', () => {
     const source = createSource({
-      _analyzer: { getPluginFilterPatterns: vi.fn(() => ['plugin/**']) },
+      _analyzer: {
+        getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
+        getPluginFilterPatterns: vi.fn(() => ['plugin/**']),
+      },
     });
     const settingsMessage = {
       type: 'SETTINGS_UPDATED',
@@ -253,7 +256,10 @@ describe('graphView/provider/settingsState default dependencies', () => {
 
   it('sends all settings through the default snapshot bridge', () => {
     const source = createSource({
-      _analyzer: { getPluginFilterPatterns: vi.fn(() => ['plugin/**']) },
+      _analyzer: {
+        getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
+        getPluginFilterPatterns: vi.fn(() => ['plugin/**']),
+      },
     });
     const allSettingsMessage = {
       type: 'ALL_SETTINGS_UPDATED',
diff --git a/packages/extension/tests/extension/graphViewProvider.errorHandling.test.ts b/packages/extension/tests/extension/graphViewProvider.errorHandling.test.ts
index 3f61d24de0..f144a20674 100644
--- a/packages/extension/tests/extension/graphViewProvider.errorHandling.test.ts
+++ b/packages/extension/tests/extension/graphViewProvider.errorHandling.test.ts
@@ -47,6 +47,7 @@ describe('GraphViewProvider error handling', () => {
         hasIndex(): boolean;
         initialize(): Promise<void>;
         discoverGraph(): Promise<IGraphData>;
+        getFilterAccounting(): { kind: 'unavailable' };
         registry: { notifyPostAnalyze(graph: IGraphData): void };
       };
     })._analyzer = {
@@ -54,6 +55,7 @@ describe('GraphViewProvider error handling', () => {
       hasIndex: () => true,
       initialize: vi.fn().mockResolvedValue(undefined),
       discoverGraph: vi.fn().mockResolvedValue({ nodes: [], edges: [] }),
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       registry: {
         notifyPostAnalyze: () => {},
       },
@@ -78,6 +80,7 @@ describe('GraphViewProvider error handling', () => {
     (provider as unknown as {
       _analyzer: {
         analyze: () => Promise<IGraphData>;
+        getFilterAccounting(): { kind: 'unavailable' };
         registry: {
           extensionPlugins: {
             list(): unknown[];
@@ -89,6 +92,7 @@ describe('GraphViewProvider error handling', () => {
       };
     })._analyzer = {
       analyze: vi.fn().mockRejectedValueOnce(new Error('analysis failed')),
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       registry: {
         extensionPlugins: {
           list: () => [],
diff --git a/packages/extension/tests/extension/graphViewProvider.lifecycle.test.ts b/packages/extension/tests/extension/graphViewProvider.lifecycle.test.ts
index b3093d7937..4fd9ff38c6 100644
--- a/packages/extension/tests/extension/graphViewProvider.lifecycle.test.ts
+++ b/packages/extension/tests/extension/graphViewProvider.lifecycle.test.ts
@@ -139,8 +139,16 @@ describe('GraphViewProvider lifecycle', () => {
     vi.spyOn(internals._fileInfoMethods, '_sendFavorites').mockImplementation(() => {});
 
     (provider as unknown as {
-      _analyzer: { clearCache: () => void; hasIndex: () => boolean };
-    })._analyzer = { clearCache, hasIndex: () => true };
+      _analyzer: {
+        clearCache: () => void;
+        getFilterAccounting(): { kind: 'unavailable' };
+        hasIndex: () => boolean;
+      };
+    })._analyzer = {
+      clearCache,
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
+      hasIndex: () => true,
+    };
 
     await provider.clearCacheAndRefresh();
 
@@ -229,9 +237,15 @@ describe('GraphViewProvider lifecycle', () => {
     vi.spyOn(internals._pluginMethods, '_sendGroupsUpdated').mockImplementation(() => {});
 
     (provider as unknown as {
-      _analyzer: { analyze: () => Promise<IGraphData> };
+      _analyzer: {
+        analyze: () => Promise<IGraphData>;
+        getFilterAccounting(): { kind: 'unavailable' };
+      };
       _analyzerInitialized: boolean;
-    })._analyzer = { analyze: vi.fn() };
+    })._analyzer = {
+      analyze: vi.fn(),
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
+    };
     (provider as unknown as { _analyzerInitialized: boolean })._analyzerInitialized = true;
     (provider as unknown as { _analysisRequestId: number })._analysisRequestId = 1;
 
diff --git a/packages/extension/tests/extension/graphViewProvider.viewState.test.ts b/packages/extension/tests/extension/graphViewProvider.viewState.test.ts
index c680a46a64..d908fd2c39 100644
--- a/packages/extension/tests/extension/graphViewProvider.viewState.test.ts
+++ b/packages/extension/tests/extension/graphViewProvider.viewState.test.ts
@@ -292,6 +292,7 @@ describe('GraphViewProvider view state and internal helpers', () => {
     const notifyGraphRebuild = vi.fn();
     (provider as unknown as {
       _analyzer: {
+        getFilterAccounting(): { kind: 'unavailable' };
         rebuildGraph: typeof rebuildGraph;
         registry: {
           list(): [];
@@ -302,6 +303,7 @@ describe('GraphViewProvider view state and internal helpers', () => {
         };
       };
     })._analyzer = {
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       rebuildGraph,
       registry: {
         list: () => [],
diff --git a/packages/extension/tests/extension/pipeline/lifecycle.test.ts b/packages/extension/tests/extension/pipeline/lifecycle.test.ts
index 9916f9be9e..809ef0e6f4 100644
--- a/packages/extension/tests/extension/pipeline/lifecycle.test.ts
+++ b/packages/extension/tests/extension/pipeline/lifecycle.test.ts
@@ -367,13 +367,14 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
     } as unknown as vscode.ExtensionContext);
 
     vi.spyOn(repoMetaModule, 'readCodeGraphyRepoMeta').mockReturnValue({
-      version: 1,
+      version: 2,
       lastIndexedAt: '2026-04-08T00:00:00.000Z',
       lastIndexedCommit: 'abc123',
       pluginBuildSignature: 'plugin-build-signature',
       pluginSignature: 'plugin-signature',
       settingsSignature: 'settings-signature',
       pendingChangedFiles: [],
+      filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
     });
     vi.spyOn(
       analyzer as unknown as {
@@ -396,13 +397,14 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
     expect(analyzer.hasIndex()).toBe(true);
 
     vi.spyOn(repoMetaModule, 'readCodeGraphyRepoMeta').mockReturnValue({
-      version: 1,
+      version: 2,
       lastIndexedAt: null,
       lastIndexedCommit: null,
       pluginBuildSignature: null,
       pluginSignature: null,
       settingsSignature: null,
       pendingChangedFiles: [],
+      filterAccounting: { kind: 'unavailable' },
     });
     expect(analyzer.hasIndex()).toBe(false);
   });
@@ -543,7 +545,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       },
     } as unknown as vscode.ExtensionContext);
     writeWorkspaceMetaFixture(workspaceRoot, {
-      version: 1,
+      version: 2,
       lastIndexedAt: '2026-04-08T00:00:00.000Z',
       pluginBuildSignature: null,
       pluginSignature: 'old-plugin-signature',
@@ -551,6 +553,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       analysisVersion: WORKSPACE_ANALYSIS_CACHE_VERSION,
       pendingChangedFiles: [],
       failedPluginIds: [],
+      filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
     });
     vi.spyOn(
       analyzer as unknown as {
@@ -584,7 +587,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       },
     } as unknown as vscode.ExtensionContext);
     writeWorkspaceMetaFixture(workspaceRoot, {
-      version: 1,
+      version: 2,
       lastIndexedAt: '2026-04-08T00:00:00.000Z',
       pluginBuildSignature: null,
       pluginSignature: 'plugin-signature',
@@ -592,6 +595,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       analysisVersion: WORKSPACE_ANALYSIS_CACHE_VERSION,
       pendingChangedFiles: [],
       failedPluginIds: [],
+      filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
     });
     vi.spyOn(
       analyzer as unknown as {
@@ -625,7 +629,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       },
     } as unknown as vscode.ExtensionContext);
     writeWorkspaceMetaFixture(workspaceRoot, {
-      version: 1,
+      version: 2,
       lastIndexedAt: '2026-04-08T00:00:00.000Z',
       pluginBuildSignature: null,
       pluginSignature: 'plugin-signature',
@@ -633,6 +637,7 @@ describe('WorkspacePipeline lifecycle', { timeout: 30000 }, () => {
       analysisVersion: 'old-analysis-version',
       pendingChangedFiles: [],
       failedPluginIds: [],
+      filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
     });
     vi.spyOn(
       analyzer as unknown as {
diff --git a/packages/extension/tests/extension/pipeline/pluginFilterAccounting.integration.test.ts b/packages/extension/tests/extension/pipeline/pluginFilterAccounting.integration.test.ts
new file mode 100644
index 0000000000..52605996c4
--- /dev/null
+++ b/packages/extension/tests/extension/pipeline/pluginFilterAccounting.integration.test.ts
@@ -0,0 +1,114 @@
+import { afterEach, describe, expect, it } from 'vitest';
+import { execFileSync } from 'node:child_process';
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import { z } from 'zod';
+import { FileDiscovery, parseCodeGraphyPluginPackageManifest } from '@codegraphy-dev/core';
+import { getWorkspacePipelinePluginFilterPatterns } from '../../../src/extension/pipeline/plugins/bootstrap/filters';
+import { unknownRecordSchema } from '../../../src/shared/values';
+
+interface FilterPluginInfo {
+  plugin: {
+    id: string;
+    name: string;
+    defaultFilters: string[];
+  };
+}
+
+const tempDirectories: string[] = [];
+
+function createMixedWorkspace(): string {
+  const workspaceRoot = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraphy-filter-accounting-'));
+  tempDirectories.push(workspaceRoot);
+  execFileSync('git', ['init', '-q'], { cwd: workspaceRoot });
+
+  const files: Record<string, string> = {
+    '.gitignore': 'ignored/**\n',
+    'src/app.ts': 'export const app = true;\n',
+    '.next/app.js': 'export const app = true;\n',
+    'scripts/player.gd': 'extends Node\n',
+    'scripts/player.gd.uid': 'uid://player\n',
+    'Assets/Player.prefab': '%YAML 1.1\n',
+    'Assets/Player.prefab.meta': 'guid: player\n',
+    'ignored/ignored.meta': 'guid: ignored\n',
+  };
+
+  for (const [relativePath, content] of Object.entries(files)) {
+    const filePath = path.join(workspaceRoot, relativePath);
+    fs.mkdirSync(path.dirname(filePath), { recursive: true });
+    fs.writeFileSync(filePath, content);
+  }
+
+  return workspaceRoot;
+}
+
+function readCorePlugin(packageName: string): FilterPluginInfo {
+  const packageJsonPath = path.resolve(__dirname, `../../../../${packageName}/package.json`);
+  const manifest = parseCodeGraphyPluginPackageManifest(
+    JSON.parse(fs.readFileSync(packageJsonPath, 'utf8')),
+  );
+  if (!manifest) throw new Error(`Invalid plugin package: ${packageName}`);
+  const descriptor = manifest.plugins.find(plugin => plugin.host === 'core');
+  if (!descriptor) throw new Error(`Core plugin descriptor not found: ${packageName}`);
+  const metadata = unknownRecordSchema.parse(descriptor.data);
+  const defaultFilters = z.array(z.string()).parse(metadata.defaultFilters);
+  if (!descriptor.id) throw new Error(`Core plugin ID not found: ${packageName}`);
+  if (!descriptor.name) throw new Error(`Core plugin name not found: ${packageName}`);
+
+  return {
+    plugin: {
+      id: descriptor.id,
+      name: descriptor.name,
+      defaultFilters,
+    },
+  };
+}
+
+afterEach(() => {
+  for (const directory of tempDirectories.splice(0)) {
+    fs.rmSync(directory, { recursive: true, force: true });
+  }
+});
+
+describe('plugin Filter accounting', () => {
+  it('tracks shipped TypeScript, Godot, and Unity defaults as plugins become active', async () => {
+    const workspaceRoot = createMixedWorkspace();
+    const plugins = [
+      readCorePlugin('plugin-typescript'),
+      readCorePlugin('plugin-godot'),
+      readCorePlugin('plugin-unity'),
+    ];
+    const source = { list: () => plugins };
+    const discovery = new FileDiscovery();
+
+    const typescriptOnly = await discovery.discover({
+      rootPath: workspaceRoot,
+      filter: getWorkspacePipelinePluginFilterPatterns(
+        source,
+        new Set(['codegraphy.gdscript', 'codegraphy.unity']),
+      ),
+    });
+    expect(typescriptOnly.filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 1,
+      gitIgnoredPathCount: 2,
+    });
+
+    const allPlugins = await discovery.discover({
+      rootPath: workspaceRoot,
+      filter: getWorkspacePipelinePluginFilterPatterns(source),
+    });
+    expect(allPlugins.filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 3,
+      gitIgnoredPathCount: 2,
+    });
+    expect(allPlugins.files.map(file => file.relativePath)).toEqual(expect.arrayContaining([
+      'Assets/Player.prefab',
+      'scripts/player.gd',
+      'src/app.ts',
+    ]));
+    expect(allPlugins.gitIgnoredPaths).toContain('ignored');
+  });
+});
diff --git a/packages/extension/tests/extension/pipeline/service/cache/index.test.ts b/packages/extension/tests/extension/pipeline/service/cache/index.test.ts
index 3a9d059fe6..5c516b9132 100644
--- a/packages/extension/tests/extension/pipeline/service/cache/index.test.ts
+++ b/packages/extension/tests/extension/pipeline/service/cache/index.test.ts
@@ -17,13 +17,14 @@ describe('pipeline/service/cache/index', () => {
   const tempRoots = new Set<string>();
 
   const meta = (overrides: Partial<ICodeGraphyRepoMeta> = {}): ICodeGraphyRepoMeta => ({
-    version: 1,
+    version: 2,
     lastIndexedAt: '2026-01-01T00:00:00.000Z',
     lastIndexedCommit: 'abc123',
     pluginBuildSignature: null,
     pluginSignature: 'plugin-signature',
     settingsSignature: 'settings-signature',
     pendingChangedFiles: [],
+    filterAccounting: { kind: 'unavailable' },
     ...overrides,
   });
 
@@ -120,6 +121,7 @@ describe('pipeline/service/cache/index', () => {
     const warn = vi.fn();
     const persistIndexMetadata = vi.fn();
     const dependencies = {
+      getFilterAccounting: vi.fn(() => ({ kind: 'current' as const, excludedFileCount: 3, gitIgnoredPathCount: 2 })),
       getPluginBuildSignature: vi.fn(() => 'next-plugin-build-signature'),
       getPluginSignature: vi.fn(() => 'next-plugin-signature'),
       getSettingsSignature: vi.fn(() => 'next-settings-signature'),
@@ -130,6 +132,7 @@ describe('pipeline/service/cache/index', () => {
     await persistWorkspacePipelineIndexMetadata('/workspace', dependencies);
 
     expect(persistIndexMetadata).toHaveBeenCalledWith('/workspace', {
+      filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
       pluginBuildSignature: 'next-plugin-build-signature',
       pluginSignature: 'next-plugin-signature',
       settingsSignature: 'next-settings-signature',
@@ -140,6 +143,7 @@ describe('pipeline/service/cache/index', () => {
   it('records the current commit when index metadata is persisted', async () => {
     const persistIndexMetadata = vi.fn();
     const dependencies = {
+      getFilterAccounting: vi.fn(() => ({ kind: 'current' as const, excludedFileCount: 3, gitIgnoredPathCount: 2 })),
       getCurrentCommitSha: vi.fn(() => 'def456'),
       getPluginBuildSignature: vi.fn(() => 'next-plugin-build-signature'),
       getPluginSignature: vi.fn(() => 'next-plugin-signature'),
@@ -151,6 +155,7 @@ describe('pipeline/service/cache/index', () => {
     await persistWorkspacePipelineIndexMetadata('/workspace', dependencies);
 
     expect(persistIndexMetadata).toHaveBeenCalledWith('/workspace', {
+      filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
       lastIndexedCommit: 'def456',
       pluginBuildSignature: 'next-plugin-build-signature',
       pluginSignature: 'next-plugin-signature',
@@ -166,6 +171,7 @@ describe('pipeline/service/cache/index', () => {
     }));
     const persistIndexMetadata = vi.fn();
     const dependencies = {
+      getFilterAccounting: vi.fn(() => ({ kind: 'current' as const, excludedFileCount: 3, gitIgnoredPathCount: 2 })),
       getPluginBuildSignature: vi.fn(() => 'plugin-build-signature'),
       getPluginSignature: vi.fn(() => 'plugin-signature'),
       getSettingsSignature: vi.fn(() => 'settings-signature'),
@@ -176,6 +182,7 @@ describe('pipeline/service/cache/index', () => {
     await persistWorkspacePipelineIndexMetadata('/workspace', dependencies);
 
     expect(persistIndexMetadata).toHaveBeenCalledWith('/workspace', {
+      filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
       pluginBuildSignature: 'plugin-build-signature',
       pluginSignature: 'plugin-signature',
       settingsSignature: 'settings-signature',
@@ -189,6 +196,7 @@ describe('pipeline/service/cache/index', () => {
       throw error;
     });
     const dependencies = {
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       getPluginBuildSignature: vi.fn(() => 'next-plugin-build-signature'),
       getPluginSignature: vi.fn(() => 'next-plugin-signature'),
       getSettingsSignature: vi.fn(() => 'next-settings-signature'),
@@ -214,6 +222,7 @@ describe('pipeline/service/cache/index', () => {
     const warn = vi.fn();
 
     await expect(persistWorkspacePipelineIndexMetadata('/workspace', {
+      getFilterAccounting: vi.fn(() => ({ kind: 'unavailable' as const })),
       getPluginBuildSignature: vi.fn(() => null),
       getPluginSignature: vi.fn(() => null),
       getSettingsSignature: vi.fn(() => 'settings-signature'),
diff --git a/packages/extension/tests/extension/pipeline/service/cachedGraph.test.ts b/packages/extension/tests/extension/pipeline/service/cachedGraph.test.ts
index a32ac54d87..fc85c74dfc 100644
--- a/packages/extension/tests/extension/pipeline/service/cachedGraph.test.ts
+++ b/packages/extension/tests/extension/pipeline/service/cachedGraph.test.ts
@@ -3,6 +3,7 @@ import {
   type AnalysisCacheTier,
   hasRequiredAnalysisCacheTiers,
   projectFileAnalysisConnections,
+  readCodeGraphyWorkspaceMeta,
   throwIfWorkspaceAnalysisAborted,
   type FileDiscovery,
   type IDiscoveredFile,
@@ -19,6 +20,7 @@ vi.mock('@codegraphy-dev/core', async (importOriginal) => {
     ...actual,
     hasRequiredAnalysisCacheTiers: vi.fn(),
     projectFileAnalysisConnections: vi.fn(),
+    readCodeGraphyWorkspaceMeta: vi.fn(actual.readCodeGraphyWorkspaceMeta),
     throwIfWorkspaceAnalysisAborted: vi.fn(),
   };
 });
@@ -146,6 +148,7 @@ interface CachedGraphState {
   _lastFileConnections: Map<string, unknown>;
   _lastGitIgnoredPaths: string[];
   _lastWorkspaceRoot: string;
+  _filterAccounting: import('@codegraphy-dev/core').WorkspaceFilterAccounting;
 }
 
 function cachedGraphState(facade: TestCachedGraphFacade): CachedGraphState {
@@ -175,6 +178,17 @@ describe('extension/pipeline/service/cachedGraph', () => {
     vi.clearAllMocks();
     vi.mocked(hasWorkspacePipelineIndex).mockReturnValue(false);
     vi.mocked(hasRequiredAnalysisCacheTiers).mockReturnValue(true);
+    vi.mocked(readCodeGraphyWorkspaceMeta).mockReturnValue({
+      version: 2,
+      lastIndexedAt: null,
+      pluginSignature: null,
+      pluginBuildSignature: null,
+      settingsSignature: null,
+      analysisVersion: null,
+      pendingChangedFiles: [],
+      failedPluginIds: [],
+      filterAccounting: { kind: 'unavailable' },
+    });
     setupCachedDiscovery();
   });
 
@@ -232,6 +246,33 @@ describe('extension/pipeline/service/cachedGraph', () => {
 
   });
 
+  it('restores authoritative discovery accounting when excluded files never entered the cache', async () => {
+    vi.mocked(readCodeGraphyWorkspaceMeta).mockReturnValue({
+      version: 2,
+      lastIndexedAt: '2026-08-06T12:00:00.000Z',
+      pluginSignature: 'plugins',
+      pluginBuildSignature: 'build',
+      settingsSignature: 'settings',
+      analysisVersion: 'analysis',
+      pendingChangedFiles: [],
+      failedPluginIds: [],
+      filterAccounting: { kind: 'current', excludedFileCount: 4, gitIgnoredPathCount: 2 },
+    });
+    const restartedFacade = new TestCachedGraphFacade();
+
+    await restartedFacade.loadCachedGraph();
+
+    expect(cachedGraphState(restartedFacade)._filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 4,
+      gitIgnoredPathCount: 2,
+    });
+    expect(createCachedWorkspaceDiscoveryState).toHaveBeenCalledWith(
+      '/workspace',
+      ['src/cached.ts'],
+    );
+  });
+
   it('marks replayed state recoverable only when it came from a persisted index', async () => {
     const facade = new TestCachedGraphFacade();
 
diff --git a/packages/extension/tests/extension/pipeline/service/refresh/modes/gitignoreMetadata.test.ts b/packages/extension/tests/extension/pipeline/service/refresh/modes/gitignoreMetadata.test.ts
index 8e692aed92..6583c11b93 100644
--- a/packages/extension/tests/extension/pipeline/service/refresh/modes/gitignoreMetadata.test.ts
+++ b/packages/extension/tests/extension/pipeline/service/refresh/modes/gitignoreMetadata.test.ts
@@ -52,6 +52,7 @@ function createFacade(
     _lastDiscoveredFiles: [createFile('old.ts')],
     _lastFileAnalysis: new Map([['src/a.ts', { filePath: '/workspace/src/a.ts' }]]),
     _lastFileConnections: new Map([['src/a.ts', [{ from: 'src/a.ts', to: 'src/b.ts' }]]]),
+    _filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 1 },
     _lastGitIgnoredPaths: ['old-ignore'],
     _lastGraphData: createGraph('last'),
     _lastWorkspaceRoot: '/old-workspace',
@@ -95,19 +96,15 @@ describe('extension/pipeline/service/refresh/modes/gitignoreMetadata', () => {
     const files = [createFile('src/new.ts')];
     const disabledPlugins = new Set(['plugin.disabled']);
     const signal = new AbortController().signal;
-    const persistError = new Error('metadata failed');
-    const warn = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
     const facade = createFacade({
       _buildGraphDataFromAnalysis: vi.fn(() => graph),
-      _persistIndexMetadata: vi.fn(async () => {
-        throw persistError;
-      }),
     });
     vi.mocked(discoverRefreshWorkspaceFiles).mockResolvedValue({
       config: { showOrphans: false },
       discoveryResult: {
         directories: undefined,
         files,
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         gitIgnoredPaths: undefined,
       },
     } as never);
@@ -119,7 +116,6 @@ describe('extension/pipeline/service/refresh/modes/gitignoreMetadata', () => {
         signal,
       }),
     ).resolves.toBe(graph);
-    await Promise.resolve();
 
     expect(discoverRefreshWorkspaceFiles).toHaveBeenCalledWith({
       configReader: facade._config,
@@ -135,21 +131,21 @@ describe('extension/pipeline/service/refresh/modes/gitignoreMetadata', () => {
     expect(facade.getPluginFilterPatterns).toHaveBeenCalledWith(disabledPlugins);
     expect(facade._lastDiscoveredDirectories).toEqual([]);
     expect(facade._lastDiscoveredFiles).toBe(files);
+    expect(facade._filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 3,
+      gitIgnoredPathCount: 2,
+    });
     expect(facade._lastGitIgnoredPaths).toEqual([]);
     expect(facade._lastWorkspaceRoot).toBe('/workspace');
     expect(facade._lastFileAnalysis).toEqual(new Map());
     expect(facade._lastFileConnections).toEqual(new Map());
     expect(facade._persistIndexMetadata).toHaveBeenCalledOnce();
-    expect(warn).toHaveBeenCalledWith(
-      '[CodeGraphy] Failed to persist gitignore metadata refresh.',
-      persistError,
-    );
     expect(facade._buildGraphDataFromAnalysis).toHaveBeenCalledWith(
       new Map(),
       '/workspace',
       false,
       disabledPlugins,
     );
-    warn.mockRestore();
   });
 });
diff --git a/packages/extension/tests/extension/pipeline/service/refresh/modes/pluginFiles.test.ts b/packages/extension/tests/extension/pipeline/service/refresh/modes/pluginFiles.test.ts
index 503a1241e9..308c946a29 100644
--- a/packages/extension/tests/extension/pipeline/service/refresh/modes/pluginFiles.test.ts
+++ b/packages/extension/tests/extension/pipeline/service/refresh/modes/pluginFiles.test.ts
@@ -54,6 +54,7 @@ function createFacade(
     _lastDiscoveredFiles: [],
     _lastFileAnalysis: new Map(),
     _lastFileConnections: new Map(),
+    _filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 1 },
     _lastGitIgnoredPaths: ['old-ignore'],
     _lastGraphData: createGraph('last'),
     _lastWorkspaceRoot: '/workspace',
@@ -122,6 +123,7 @@ describe('extension/pipeline/service/refresh/modes/pluginFiles', () => {
       discoveryResult: {
         directories: undefined,
         files,
+        filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 0 },
         gitIgnoredPaths: undefined,
       },
     } as never);
@@ -149,6 +151,11 @@ describe('extension/pipeline/service/refresh/modes/pluginFiles', () => {
     const getPluginFilterPatterns = vi.mocked(discoverRefreshWorkspaceFiles).mock.calls[0][0].getPluginFilterPatterns;
     expect(getPluginFilterPatterns(disabledPlugins)).toEqual(['plugin/**']);
     expect(facade.getPluginFilterPatterns).toHaveBeenCalledWith(disabledPlugins);
+    expect(facade._filterAccounting).toEqual({
+      kind: 'current',
+      excludedFileCount: 1,
+      gitIgnoredPathCount: 0,
+    });
     expect(facade._lastGitIgnoredPaths).toEqual([]);
     expect(createWorkspaceIndexRefreshSource).toHaveBeenCalledWith(facade, disabledPlugins);
     expect(facade._registry.list).toHaveBeenCalledOnce();
diff --git a/packages/extension/tests/extension/pipeline/service/runtime/discovery.test.ts b/packages/extension/tests/extension/pipeline/service/runtime/discovery.test.ts
index aac42bab0c..6d0ab8692b 100644
--- a/packages/extension/tests/extension/pipeline/service/runtime/discovery.test.ts
+++ b/packages/extension/tests/extension/pipeline/service/runtime/discovery.test.ts
@@ -25,6 +25,7 @@ describe('pipeline/service/discovery', () => {
         durationMs: 12,
         files: [{ relativePath: 'src/a.ts' }],
         cacheFilePaths: ['src/a.ts', 'example-python/app.py'],
+        filterAccounting: { kind: 'current' as const, excludedFileCount: 1, gitIgnoredPathCount: 1 },
         gitIgnoredPaths: ['example-python/app.py'],
         limitReached: false,
         totalFound: undefined,
@@ -39,6 +40,7 @@ describe('pipeline/service/discovery', () => {
       directories: ['src/new-folder'],
       durationMs: 12,
       files: [{ relativePath: 'src/a.ts' }],
+      filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 1 },
       gitIgnoredPaths: ['example-python/app.py'],
       limitReached: false,
       totalFound: 1,
diff --git a/packages/extension/tests/extension/repoSettings/freshness/index.test.ts b/packages/extension/tests/extension/repoSettings/freshness/index.test.ts
index e7bea6042c..7e52d63d9c 100644
--- a/packages/extension/tests/extension/repoSettings/freshness/index.test.ts
+++ b/packages/extension/tests/extension/repoSettings/freshness/index.test.ts
@@ -6,13 +6,14 @@ import { evaluateCodeGraphyIndexStatus } from '../../../../src/extension/repoSet
 import type { ICodeGraphyRepoMeta } from '../../../../src/extension/repoSettings/meta';
 
 const indexedMeta: ICodeGraphyRepoMeta = {
-  version: 1,
+  version: 2,
   lastIndexedAt: '2026-04-27T12:00:00.000Z',
   lastIndexedCommit: 'abc123',
   pluginBuildSignature: 'plugin-build',
   pluginSignature: 'plugins',
   settingsSignature: 'settings',
   pendingChangedFiles: [],
+  filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
 };
 
 describe('repoSettings/freshness/index', () => {
diff --git a/packages/extension/tests/extension/repoSettings/freshness/reasons.test.ts b/packages/extension/tests/extension/repoSettings/freshness/reasons.test.ts
index aa6eabd6ac..380e7d5182 100644
--- a/packages/extension/tests/extension/repoSettings/freshness/reasons.test.ts
+++ b/packages/extension/tests/extension/repoSettings/freshness/reasons.test.ts
@@ -3,13 +3,14 @@ import { collectStaleReasons } from '../../../../src/extension/repoSettings/fres
 import type { ICodeGraphyRepoMeta } from '../../../../src/extension/repoSettings/meta';
 
 const indexedMeta: ICodeGraphyRepoMeta = {
-  version: 1,
+  version: 2,
   lastIndexedAt: '2026-04-27T12:00:00.000Z',
   lastIndexedCommit: 'abc123',
   pluginBuildSignature: 'plugin-build',
   pluginSignature: 'plugins',
   settingsSignature: 'settings',
   pendingChangedFiles: [],
+  filterAccounting: { kind: 'current', excludedFileCount: 2, gitIgnoredPathCount: 1 },
 };
 
 describe('repoSettings/freshness/reasons', () => {
diff --git a/packages/extension/tests/extension/repoSettings/meta.test.ts b/packages/extension/tests/extension/repoSettings/meta.test.ts
index f02120d27c..b836f3a1bc 100644
--- a/packages/extension/tests/extension/repoSettings/meta.test.ts
+++ b/packages/extension/tests/extension/repoSettings/meta.test.ts
@@ -47,7 +47,7 @@ describe('extension/repoSettings/meta', () => {
     expect(path.basename(getCodeGraphyRepoMetaPath('/workspace/project'))).toBe('meta.json');
   });
 
-  it('merges partial persisted meta with the default fields', () => {
+  it('resets incomplete persisted metadata to the current default snapshot', () => {
     const workspaceRoot = createTempWorkspace();
     tempDirectories.push(workspaceRoot);
     const metaPath = getCodeGraphyRepoMetaPath(workspaceRoot);
@@ -63,13 +63,14 @@ describe('extension/repoSettings/meta', () => {
     );
 
     expect(readCodeGraphyRepoMeta(workspaceRoot)).toEqual({
-      version: 1,
+      version: 2,
       lastIndexedAt: null,
-      lastIndexedCommit: 'abc123',
+      lastIndexedCommit: null,
       pluginBuildSignature: null,
       pluginSignature: null,
       settingsSignature: null,
-      pendingChangedFiles: ['src/app.ts'],
+      pendingChangedFiles: [],
+      filterAccounting: { kind: 'unavailable' },
     });
   });
 
@@ -82,7 +83,9 @@ describe('extension/repoSettings/meta', () => {
     fs.writeFileSync(
       metaPath,
       JSON.stringify({
+        version: 2,
         lastIndexedCommit: 'abc123',
+        filterAccounting: { kind: 'unavailable' },
       }, null, 2),
       'utf8',
     );
@@ -110,13 +113,14 @@ describe('extension/repoSettings/meta', () => {
     );
 
     expect(readCodeGraphyRepoMeta(workspaceRoot)).toEqual({
-      version: 1,
+      version: 2,
       lastIndexedAt: null,
-      lastIndexedCommit: 'abc123',
+      lastIndexedCommit: null,
       pluginBuildSignature: null,
       pluginSignature: null,
       settingsSignature: null,
-      pendingChangedFiles: ['src/app.ts', 'src/index.ts'],
+      pendingChangedFiles: [],
+      filterAccounting: { kind: 'unavailable' },
     });
   });
 
diff --git a/packages/extension/tests/playwright-vscode/filter-accounting.spec.ts b/packages/extension/tests/playwright-vscode/filter-accounting.spec.ts
new file mode 100644
index 0000000000..1877cd1511
--- /dev/null
+++ b/packages/extension/tests/playwright-vscode/filter-accounting.spec.ts
@@ -0,0 +1,75 @@
+import { expect, test } from '@playwright/test';
+import fs from 'node:fs';
+import path from 'node:path';
+import { clickToolbarButton, getGraphCounts } from '../acceptance/graphView/canvas';
+import {
+  copyExampleWorkspace,
+  createWorkspaceTempRoot,
+} from '../acceptance/graphView/workspace';
+import {
+  cleanupVSCode,
+  launchVSCodeWithWorkspace,
+  openGraphView,
+  waitForGraphFrame,
+} from '../acceptance/graphView/vscode';
+
+test('reports plugin default Filter effects in an Extension Development Host', async ({}, testInfo) => {
+  const workspaceTempRoot = createWorkspaceTempRoot();
+  const workspacePath = copyExampleWorkspace(workspaceTempRoot, 'example-typescript', {
+    pluginPackages: [],
+  });
+  const filteredFilePath = path.join(workspacePath, '.next', 'generated.js');
+  fs.mkdirSync(path.dirname(filteredFilePath), { recursive: true });
+  fs.writeFileSync(filteredFilePath, 'export const generated = true;\n');
+  const proofDirectory = process.env.CODEGRAPHY_VISUAL_PROOF_DIR ?? testInfo.outputDir;
+  fs.mkdirSync(proofDirectory, { recursive: true });
+  const vscode = await launchVSCodeWithWorkspace(workspacePath, {
+    pluginPackageRelativePaths: ['packages/plugin-typescript'],
+  });
+
+  try {
+    await openGraphView(vscode.page);
+    const frame = await waitForGraphFrame(vscode.page);
+    await indexWorkspace(frame);
+    const beforeCounts = await getGraphCounts(frame);
+
+    await frame.getByRole('button', { name: /^Filters,/ }).click();
+    await expect(frame.getByText('Before analysis: 0 workspace files excluded')).toBeVisible();
+    await expect(frame.getByText('In Graph View: 0 Nodes excluded')).toBeVisible();
+    await frame.locator('[data-codegraphy-surface="app"]').screenshot({
+      path: path.join(proofDirectory, 'trello-242-before.png'),
+    });
+
+    await frame.getByRole('button', { name: /^Filters,/ }).click();
+    await clickToolbarButton(frame, 'Plugins');
+    await frame.getByRole('switch', { name: 'TypeScript/JavaScript' }).click();
+    await expect(frame.getByRole('switch', { name: 'TypeScript/JavaScript' })).toBeChecked();
+    await expect(frame.getByRole('progressbar', { name: 'Indexing progress' })).toBeHidden({ timeout: 30_000 });
+    await clickToolbarButton(frame, 'Plugins');
+    await frame.getByTitle('Re-index Workspace').click();
+    await expect(frame.getByRole('progressbar', { name: 'Indexing progress' })).toBeHidden({ timeout: 30_000 });
+    await expect.poll(() => getGraphCounts(frame)).toEqual({
+      nodes: beforeCounts.nodes - 1,
+      edges: expect.any(Number),
+    });
+
+    await frame.getByRole('button', { name: /^Filters,/ }).click();
+    await expect(frame.getByText('Before analysis: 1 workspace file excluded')).toBeVisible();
+    await expect(frame.getByText('In Graph View: 0 Nodes excluded')).toBeVisible();
+    await frame.locator('[data-codegraphy-surface="app"]').screenshot({
+      path: path.join(proofDirectory, 'trello-242-after.png'),
+    });
+  } finally {
+    await cleanupVSCode(vscode);
+    fs.rmSync(workspaceTempRoot, { recursive: true, force: true });
+  }
+});
+
+async function indexWorkspace(frame: Parameters<typeof getGraphCounts>[0]): Promise<void> {
+  const indexButton = frame.getByRole('button', { name: 'Index Workspace' });
+  await expect(indexButton).toBeVisible();
+  await indexButton.click();
+  await expect(
+    frame.getByRole('progressbar', { name: 'Indexing progress' }),
+  ).toBeHidden({ timeout: 30_000 });
+}
diff --git a/packages/extension/tests/webview/app/shell/view/visibleGraph.test.tsx b/packages/extension/tests/webview/app/shell/view/visibleGraph.test.tsx
index fdf94090b4..af5699ee42 100644
--- a/packages/extension/tests/webview/app/shell/view/visibleGraph.test.tsx
+++ b/packages/extension/tests/webview/app/shell/view/visibleGraph.test.tsx
@@ -149,6 +149,7 @@ describe('App visible graph',()=>{
           { pluginId: 'plugin.one', pluginName: 'Plugin One', patterns: ['**/generated/**'] },
         ],
         pluginFilterPatterns: ['**/generated/**'],
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 1 },
         disabledPluginFilterPatterns: [],
         showOrphans: true,
       });
@@ -156,11 +157,13 @@ describe('App visible graph',()=>{
       render(<App />);
   
       fireEvent.click(screen.getByRole('button', { name: 'Filters, 1 enabled' }));
-      expect(screen.getByText('1 excluded from graph')).toBeInTheDocument();
+      expect(screen.getByText('Before analysis: 3 workspace files excluded')).toBeInTheDocument();
+      expect(screen.getByText('In Graph View: 1 Node excluded')).toBeInTheDocument();
   
       fireEvent.click(screen.getByLabelText('Disable plugin Plugin One filters'));
   
-      expect(screen.getByText('0 excluded from graph')).toBeInTheDocument();
+      expect(screen.getByText('Before analysis: 3 workspace files excluded')).toBeInTheDocument();
+      expect(screen.getByText('In Graph View: 0 Nodes excluded')).toBeInTheDocument();
     });
 
   it('should hide graph corner controls while a right-side popup is open', async () => {
diff --git a/packages/extension/tests/webview/searchBar/filters/popover.test.tsx b/packages/extension/tests/webview/searchBar/filters/popover.test.tsx
index d19b56b95b..44b5e6a04b 100644
--- a/packages/extension/tests/webview/searchBar/filters/popover.test.tsx
+++ b/packages/extension/tests/webview/searchBar/filters/popover.test.tsx
@@ -14,7 +14,8 @@ function renderPopover(overrides: Partial<React.ComponentProps<typeof FilterPopo
     disabledCustomPatterns: [],
     disabledPluginPatterns: [],
     customPatterns: ['existing/**'],
-    excludedCount: 4,
+    filterAccounting: { kind: 'current', excludedFileCount: 4, gitIgnoredPathCount: 2 },
+    excludedNodeCount: 2,
     onDisabledCustomPatternsChange: vi.fn(),
     onDisabledPluginPatternsChange: vi.fn(),
     onOpenChange: vi.fn(),
@@ -40,12 +41,32 @@ describe('searchBar/filters/popover', () => {
 
     expect(screen.getByText('Filters')).toBeInTheDocument();
     expect(screen.getByText('2 enabled')).toBeInTheDocument();
-    expect(screen.getByText('4 excluded from graph')).toBeInTheDocument();
+    expect(screen.getByText('Before analysis: 4 workspace files excluded')).toBeInTheDocument();
+    expect(screen.getByText('In Graph View: 2 Nodes excluded')).toBeInTheDocument();
     expect(screen.getByText('Custom')).toBeInTheDocument();
     expect(screen.getByText('Plugin defaults')).toBeInTheDocument();
     expect(screen.getByRole('button', { name: 'Filters, 2 enabled' }).className).toContain('bg-secondary');
   });
 
+  it('reports pre-analysis File and Graph View Node exclusions without reconciling overlap', () => {
+    renderPopover({
+      filterAccounting: { kind: 'current', excludedFileCount: 1, gitIgnoredPathCount: 1 },
+      excludedNodeCount: 1,
+    });
+
+    expect(screen.getByText('Before analysis: 1 workspace file excluded')).toBeInTheDocument();
+    expect(screen.getByText('In Graph View: 1 Node excluded')).toBeInTheDocument();
+    expect(screen.queryByText(/2 .*excluded/)).not.toBeInTheDocument();
+  });
+
+  it('does not report zero when persisted discovery accounting is unavailable', () => {
+    renderPopover({ filterAccounting: { kind: 'unavailable' } });
+
+    expect(screen.getByText(
+      'Before analysis: re-index to calculate excluded workspace files',
+    )).toBeInTheDocument();
+  });
+
   it('opens and closes from its own trigger when uncontrolled', () => {
     const props = renderPopover({ onOpenChange: vi.fn(), open: undefined });
 
diff --git a/packages/extension/tests/webview/store/messageHandlers/graph/controls.test.ts b/packages/extension/tests/webview/store/messageHandlers/graph/controls.test.ts
index f58a62ba7e..b108c076dd 100644
--- a/packages/extension/tests/webview/store/messageHandlers/graph/controls.test.ts
+++ b/packages/extension/tests/webview/store/messageHandlers/graph/controls.test.ts
@@ -36,6 +36,7 @@ describe('graph message handlers: controls',()=>{
 
   it('maps graph controls and favorites payloads', () => {
       const controls: IGraphControlsSnapshot = {
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         nodeTypes: [{ id: 'file', label: 'File', defaultColor: '#A1A1AA', defaultVisible: true }],
         edgeTypes: [{ id: 'import', label: 'Import', defaultColor: '#64748B', defaultVisible: true }],
         nodeColors: { file: '#A1A1AA' },
@@ -47,6 +48,7 @@ describe('graph message handlers: controls',()=>{
         type: 'GRAPH_CONTROLS_UPDATED',
         payload: controls,
       })).toEqual({
+        filterAccounting: controls.filterAccounting,
         graphNodeTypes: controls.nodeTypes,
         graphEdgeTypes: controls.edgeTypes,
         nodeColors: controls.nodeColors,
@@ -64,6 +66,7 @@ describe('graph message handlers: controls',()=>{
 
   it('skips graph controls updates when extension echoes the current controls', () => {
       const controls: IGraphControlsSnapshot = {
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         nodeTypes: [{ id: 'file', label: 'File', defaultColor: '#A1A1AA', defaultVisible: true }],
         edgeTypes: [{ id: 'import', label: 'Import', defaultColor: '#64748B', defaultVisible: true }],
         nodeColors: { file: '#A1A1AA' },
@@ -71,6 +74,7 @@ describe('graph message handlers: controls',()=>{
         edgeVisibility: { import: false },
       };
       const state = createState({
+        filterAccounting: controls.filterAccounting,
         graphNodeTypes: controls.nodeTypes,
         graphEdgeTypes: controls.edgeTypes,
         nodeColors: controls.nodeColors,
@@ -78,6 +82,7 @@ describe('graph message handlers: controls',()=>{
         edgeVisibility: controls.edgeVisibility,
       });
       const echoedControls: IGraphControlsSnapshot = {
+        filterAccounting: { ...controls.filterAccounting },
         nodeTypes: [...controls.nodeTypes],
         edgeTypes: [...controls.edgeTypes],
         nodeColors: { ...controls.nodeColors },
@@ -93,6 +98,7 @@ describe('graph message handlers: controls',()=>{
 
   it('returns only changed graph control fields when extension echoes partial changes', () => {
       const controls: IGraphControlsSnapshot = {
+        filterAccounting: { kind: 'current', excludedFileCount: 3, gitIgnoredPathCount: 2 },
         nodeTypes: [{ id: 'file', label: 'File', defaultColor: '#A1A1AA', defaultVisible: true }],
         edgeTypes: [{ id: 'import', label: 'Import', defaultColor: '#64748B', defaultVisible: true }],
         nodeColors: { file: '#A1A1AA' },
@@ -100,6 +106,7 @@ describe('graph message handlers: controls',()=>{
         edgeVisibility: { import: false },
       };
       const state = createState({
+        filterAccounting: controls.filterAccounting,
         graphNodeTypes: controls.nodeTypes,
         graphEdgeTypes: controls.edgeTypes,
         nodeColors: controls.nodeColors,
@@ -108,6 +115,7 @@ describe('graph message handlers: controls',()=>{
       });
       const nextEdgeVisibility = { import: true };
       const echoedControls: IGraphControlsSnapshot = {
+        filterAccounting: { kind: 'current', excludedFileCount: 4, gitIgnoredPathCount: 2 },
         nodeTypes: [...controls.nodeTypes],
         edgeTypes: [...controls.edgeTypes],
         nodeColors: { ...controls.nodeColors },
@@ -118,6 +126,9 @@ describe('graph message handlers: controls',()=>{
       expect(handleGraphControlsUpdated(
         { type: 'GRAPH_CONTROLS_UPDATED', payload: echoedControls },
         { getState: () => state },
-      )).toEqual({ edgeVisibility: nextEdgeVisibility });
+      )).toEqual({
+        edgeVisibility: nextEdgeVisibility,
+        filterAccounting: { kind: 'current', excludedFileCount: 4, gitIgnoredPathCount: 2 },
+      });
     });
 });
diff --git a/packages/extension/tests/webview/store/messageHandlers/graph/fixture.ts b/packages/extension/tests/webview/store/messageHandlers/graph/fixture.ts
index d2833f4d09..a4f8869edb 100644
--- a/packages/extension/tests/webview/store/messageHandlers/graph/fixture.ts
+++ b/packages/extension/tests/webview/store/messageHandlers/graph/fixture.ts
@@ -37,6 +37,7 @@ export function createState(
     optimisticLegendUpdates: {},
     optimisticUserLegends: null,
     filterPatterns: [],
+    filterAccounting: { kind: 'unavailable' },
     pluginFilterPatterns: [],
     pluginFilterGroups: [],
     disabledCustomFilterPatterns: [],
diff --git a/packages/extension/tests/webview/store/messageHandlers/graph/settings.test.ts b/packages/extension/tests/webview/store/messageHandlers/graph/settings.test.ts
index a77d7fe1db..8e105e9449 100644
--- a/packages/extension/tests/webview/store/messageHandlers/graph/settings.test.ts
+++ b/packages/extension/tests/webview/store/messageHandlers/graph/settings.test.ts
@@ -43,6 +43,7 @@ describe('graph message handlers: settings',()=>{
         disabledCustomFilterPatterns: ['custom/**'],
         disabledPluginFilterPatterns: [],
       });
+
     });
 
   it('maps depth, direction, physics, labels, max-files, and active-file payloads', () => {