1 files changed, 57 insertions, 12 deletions
diff --git a/packages/cli/src/ui/hooks/atCommandProcessor.ts b/packages/cli/src/ui/hooks/atCommandProcessor.ts
index 7fe68f10..983abc62 100644
--- a/packages/cli/src/ui/hooks/atCommandProcessor.ts
+++ b/packages/cli/src/ui/hooks/atCommandProcessor.ts
@@ -136,12 +136,17 @@ export async function handleAtCommand({
 
   // Get centralized file discovery service
   const fileDiscovery = config.getFileService();
-  const respectGitIgnore = config.getFileFilteringRespectGitIgnore();
+
+  const respectFileIgnore = config.getFileFilteringOptions();
 
   const pathSpecsToRead: string[] = [];
   const atPathToResolvedSpecMap = new Map<string, string>();
   const contentLabelsForDisplay: string[] = [];
-  const ignoredPaths: string[] = [];
+  const ignoredByReason: Record<string, string[]> = {
+    git: [],
+    gemini: [],
+    both: [],
+  };
 
   const toolRegistry = await config.getToolRegistry();
   const readManyFilesTool = toolRegistry.getTool('read_many_files');
@@ -182,10 +187,31 @@ export async function handleAtCommand({
     }
 
     // Check if path should be ignored based on filtering options
-    if (fileDiscovery.shouldIgnoreFile(pathName, { respectGitIgnore })) {
-      const reason = respectGitIgnore ? 'git-ignored' : 'custom-ignored';
-      onDebugMessage(`Path ${pathName} is ${reason} and will be skipped.`);
-      ignoredPaths.push(pathName);
+
+    const gitIgnored =
+      respectFileIgnore.respectGitIgnore &&
+      fileDiscovery.shouldIgnoreFile(pathName, {
+        respectGitIgnore: true,
+        respectGeminiIgnore: false,
+      });
+    const geminiIgnored =
+      respectFileIgnore.respectGeminiIgnore &&
+      fileDiscovery.shouldIgnoreFile(pathName, {
+        respectGitIgnore: false,
+        respectGeminiIgnore: true,
+      });
+
+    if (gitIgnored || geminiIgnored) {
+      const reason =
+        gitIgnored && geminiIgnored ? 'both' : gitIgnored ? 'git' : 'gemini';
+      ignoredByReason[reason].push(pathName);
+      const reasonText =
+        reason === 'both'
+          ? 'ignored by both git and gemini'
+          : reason === 'git'
+            ? 'git-ignored'
+            : 'gemini-ignored';
+      onDebugMessage(`Path ${pathName} is ${reasonText} and will be skipped.`);
       continue;
     }
 
@@ -319,11 +345,26 @@ export async function handleAtCommand({
   initialQueryText = initialQueryText.trim();
 
   // Inform user about ignored paths
-  if (ignoredPaths.length > 0) {
-    const ignoreType = respectGitIgnore ? 'git-ignored' : 'custom-ignored';
-    onDebugMessage(
-      `Ignored ${ignoredPaths.length} ${ignoreType} files: ${ignoredPaths.join(', ')}`,
-    );
+  const totalIgnored =
+    ignoredByReason.git.length +
+    ignoredByReason.gemini.length +
+    ignoredByReason.both.length;
+
+  if (totalIgnored > 0) {
+    const messages = [];
+    if (ignoredByReason.git.length) {
+      messages.push(`Git-ignored: ${ignoredByReason.git.join(', ')}`);
+    }
+    if (ignoredByReason.gemini.length) {
+      messages.push(`Gemini-ignored: ${ignoredByReason.gemini.join(', ')}`);
+    }
+    if (ignoredByReason.both.length) {
+      messages.push(`Ignored by both: ${ignoredByReason.both.join(', ')}`);
+    }
+
+    const message = `Ignored ${totalIgnored} files:\n${messages.join('\n')}`;
+    console.log(message);
+    onDebugMessage(message);
   }
 
   // Fallback for lone "@" or completely invalid @-commands resulting in empty initialQueryText
@@ -347,7 +388,11 @@ export async function handleAtCommand({
 
   const toolArgs = {
     paths: pathSpecsToRead,
-    respect_git_ignore: respectGitIgnore, // Use configuration setting
+    file_filtering_options: {
+      respect_git_ignore: respectFileIgnore.respectGitIgnore,
+      respect_gemini_ignore: respectFileIgnore.respectGeminiIgnore,
+    },
+    // Use configuration setting
   };
   let toolCallDisplay: IndividualToolCallDisplay;