diff --git a/packages/core/src/services/fileDiscoveryService.test.ts b/packages/core/src/services/fileDiscoveryService.test.ts
index 9a56435bdc..de7c561e4d 100644
--- a/packages/core/src/services/fileDiscoveryService.test.ts
+++ b/packages/core/src/services/fileDiscoveryService.test.ts
@@ -136,6 +136,43 @@ describe('FileDiscoveryService', () => {
     });
   });
 
+  describe('filterFilesWithReport', () => {
+    beforeEach(async () => {
+      await fs.mkdir(path.join(projectRoot, '.git'));
+      await createTestFile('.gitignore', 'node_modules/');
+      await createTestFile('.geminiignore', '*.log');
+    });
+
+    it('should return filtered paths and correct ignored count', () => {
+      const files = [
+        'src/index.ts',
+        'node_modules/package/index.js',
+        'debug.log',
+        'README.md',
+      ].map((f) => path.join(projectRoot, f));
+
+      const service = new FileDiscoveryService(projectRoot);
+      const report = service.filterFilesWithReport(files);
+
+      expect(report.filteredPaths).toEqual(
+        ['src/index.ts', 'README.md'].map((f) => path.join(projectRoot, f)),
+      );
+      expect(report.ignoredCount).toBe(2);
+    });
+
+    it('should handle no ignored files', () => {
+      const files = ['src/index.ts', 'README.md'].map((f) =>
+        path.join(projectRoot, f),
+      );
+
+      const service = new FileDiscoveryService(projectRoot);
+      const report = service.filterFilesWithReport(files);
+
+      expect(report.filteredPaths).toEqual(files);
+      expect(report.ignoredCount).toBe(0);
+    });
+  });
+
   describe('shouldGitIgnoreFile & shouldGeminiIgnoreFile', () => {
     beforeEach(async () => {
       await fs.mkdir(path.join(projectRoot, '.git'));
diff --git a/packages/core/src/services/fileDiscoveryService.ts b/packages/core/src/services/fileDiscoveryService.ts
index 4620362685..dbec5f1ffa 100644
--- a/packages/core/src/services/fileDiscoveryService.ts
+++ b/packages/core/src/services/fileDiscoveryService.ts
@@ -18,8 +18,7 @@ export interface FilterFilesOptions {
 
 export interface FilterReport {
   filteredPaths: string[];
-  gitIgnoredCount: number;
-  geminiIgnoredCount: number;
+  ignoredCount: number;
 }
 
 export class FileDiscoveryService {
@@ -70,28 +69,12 @@ export class FileDiscoveryService {
       respectGeminiIgnore: true,
     },
   ): FilterReport {
-    const filteredPaths: string[] = [];
-    let gitIgnoredCount = 0;
-    let geminiIgnoredCount = 0;
-
-    for (const filePath of filePaths) {
-      if (opts.respectGitIgnore && this.shouldGitIgnoreFile(filePath)) {
-        gitIgnoredCount++;
-        continue;
-      }
-
-      if (opts.respectGeminiIgnore && this.shouldGeminiIgnoreFile(filePath)) {
-        geminiIgnoredCount++;
-        continue;
-      }
-
-      filteredPaths.push(filePath);
-    }
+    const filteredPaths = this.filterFiles(filePaths, opts);
+    const ignoredCount = filePaths.length - filteredPaths.length;
 
     return {
       filteredPaths,
-      gitIgnoredCount,
-      geminiIgnoredCount,
+      ignoredCount,
     };
   }
 
diff --git a/packages/core/src/tools/glob.ts b/packages/core/src/tools/glob.ts
index 2ac2fd89c2..0dbd71e479 100644
--- a/packages/core/src/tools/glob.ts
+++ b/packages/core/src/tools/glob.ts
@@ -169,7 +169,7 @@ class GlobToolInvocation extends BaseToolInvocation<
         path.relative(this.config.getTargetDir(), p.fullpath()),
       );
 
-      const { filteredPaths, gitIgnoredCount, geminiIgnoredCount } =
+      const { filteredPaths, ignoredCount } =
         fileDiscovery.filterFilesWithReport(relativePaths, {
           respectGitIgnore:
             this.params?.respect_git_ignore ??
@@ -196,11 +196,8 @@ class GlobToolInvocation extends BaseToolInvocation<
         } else {
           message += ` within ${searchDirectories.length} workspace directories`;
         }
-        if (gitIgnoredCount > 0) {
-          message += ` (${gitIgnoredCount} files were git-ignored)`;
-        }
-        if (geminiIgnoredCount > 0) {
-          message += ` (${geminiIgnoredCount} files were gemini-ignored)`;
+        if (ignoredCount > 0) {
+          message += ` (${ignoredCount} files were ignored)`;
         }
         return {
           llmContent: message,
@@ -231,11 +228,8 @@ class GlobToolInvocation extends BaseToolInvocation<
       } else {
         resultMessage += ` across ${searchDirectories.length} workspace directories`;
       }
-      if (gitIgnoredCount > 0) {
-        resultMessage += ` (${gitIgnoredCount} additional files were git-ignored)`;
-      }
-      if (geminiIgnoredCount > 0) {
-        resultMessage += ` (${geminiIgnoredCount} additional files were gemini-ignored)`;
+      if (ignoredCount > 0) {
+        resultMessage += ` (${ignoredCount} additional files were ignored)`;
       }
       resultMessage += `, sorted by modification time (newest first):\n${fileListDescription}`;
 
diff --git a/packages/core/src/tools/ls.test.ts b/packages/core/src/tools/ls.test.ts
index f48f8cde23..1cda0c9e7e 100644
--- a/packages/core/src/tools/ls.test.ts
+++ b/packages/core/src/tools/ls.test.ts
@@ -149,7 +149,7 @@ describe('LSTool', () => {
       expect(result.llmContent).toContain('file1.txt');
       expect(result.llmContent).not.toContain('file2.log');
       // .git is always ignored by default.
-      expect(result.returnDisplay).toBe('Listed 2 item(s). (2 git-ignored)');
+      expect(result.returnDisplay).toBe('Listed 2 item(s). (2 ignored)');
     });
 
     it('should respect geminiignore patterns', async () => {
@@ -161,7 +161,7 @@ describe('LSTool', () => {
 
       expect(result.llmContent).toContain('file1.txt');
       expect(result.llmContent).not.toContain('file2.log');
-      expect(result.returnDisplay).toBe('Listed 2 item(s). (1 gemini-ignored)');
+      expect(result.returnDisplay).toBe('Listed 2 item(s). (1 ignored)');
     });
 
     it('should handle non-directory paths', async () => {
diff --git a/packages/core/src/tools/ls.ts b/packages/core/src/tools/ls.ts
index 9699be5d60..7aac367e50 100644
--- a/packages/core/src/tools/ls.ts
+++ b/packages/core/src/tools/ls.ts
@@ -173,7 +173,7 @@ class LSToolInvocation extends BaseToolInvocation<LSToolParams, ToolResult> {
       );
 
       const fileDiscovery = this.config.getFileService();
-      const { filteredPaths, gitIgnoredCount, geminiIgnoredCount } =
+      const { filteredPaths, ignoredCount } =
         fileDiscovery.filterFilesWithReport(relativePaths, {
           respectGitIgnore:
             this.params.file_filtering_options?.respect_git_ignore ??
@@ -222,20 +222,13 @@ class LSToolInvocation extends BaseToolInvocation<LSToolParams, ToolResult> {
         .join('\n');
 
       let resultMessage = `Directory listing for ${this.params.path}:\n${directoryContent}`;
-      const ignoredMessages = [];
-      if (gitIgnoredCount > 0) {
-        ignoredMessages.push(`${gitIgnoredCount} git-ignored`);
-      }
-      if (geminiIgnoredCount > 0) {
-        ignoredMessages.push(`${geminiIgnoredCount} gemini-ignored`);
-      }
-      if (ignoredMessages.length > 0) {
-        resultMessage += `\n\n(${ignoredMessages.join(', ')})`;
+      if (ignoredCount > 0) {
+        resultMessage += `\n\n(${ignoredCount} ignored)`;
       }
 
       let displayMessage = `Listed ${entries.length} item(s).`;
-      if (ignoredMessages.length > 0) {
-        displayMessage += ` (${ignoredMessages.join(', ')})`;
+      if (ignoredCount > 0) {
+        displayMessage += ` (${ignoredCount} ignored)`;
       }
 
       return {
diff --git a/packages/core/src/tools/read-many-files.ts b/packages/core/src/tools/read-many-files.ts
index 88d2660c1b..5681647cb5 100644
--- a/packages/core/src/tools/read-many-files.ts
+++ b/packages/core/src/tools/read-many-files.ts
@@ -225,7 +225,7 @@ ${finalExclusionPatternsForDescription
       );
 
       const fileDiscovery = this.config.getFileService();
-      const { filteredPaths, gitIgnoredCount, geminiIgnoredCount } =
+      const { filteredPaths, ignoredCount } =
         fileDiscovery.filterFilesWithReport(relativeEntries, {
           respectGitIgnore:
             this.params.file_filtering_options?.respect_git_ignore ??
@@ -253,19 +253,11 @@ ${finalExclusionPatternsForDescription
         filesToConsider.add(fullPath);
       }
 
-      // Add info about git-ignored files if any were filtered
-      if (gitIgnoredCount > 0) {
+      // Add info about ignored files if any were filtered
+      if (ignoredCount > 0) {
         skippedFiles.push({
-          path: `${gitIgnoredCount} file(s)`,
-          reason: 'git ignored',
-        });
-      }
-
-      // Add info about gemini-ignored files if any were filtered
-      if (geminiIgnoredCount > 0) {
-        skippedFiles.push({
-          path: `${geminiIgnoredCount} file(s)`,
-          reason: 'gemini ignored',
+          path: `${ignoredCount} file(s)`,
+          reason: 'ignored by project ignore files',
         });
       }
     } catch (error) {