diff --git a/src/agents/sessions/package-manager.test.ts b/src/agents/sessions/package-manager.test.ts
index 68b4f70c00f2..39c088386932 100644
--- a/src/agents/sessions/package-manager.test.ts
+++ b/src/agents/sessions/package-manager.test.ts
@@ -133,14 +133,32 @@ describe("DefaultPackageManager", () => {
     const insidePrompt = join(configRoot, "prompts", "inside.md");
     const insideTheme = join(configRoot, "themes", "inside.json");
     const insideExtension = join(configRoot, "extensions", "inside.ts");
+    const ignoredPrompt = join(configRoot, "prompts", "ignored.md");
+    const ignoredTheme = join(configRoot, "themes", "ignored.json");
+    const hiddenPrompt = join(configRoot, "prompts", ".hidden.md");
+    const hiddenTheme = join(configRoot, "themes", ".hidden.json");
+    const nestedPrompt = join(configRoot, "prompts", "nested", "nested.md");
+    const nestedTheme = join(configRoot, "themes", "nested", "nested.json");
+    const wrongPromptType = join(configRoot, "prompts", "wrong.json");
+    const wrongThemeType = join(configRoot, "themes", "wrong.md");
     await mkdir(join(root, ".git"));
-    await mkdir(join(configRoot, "prompts"), { recursive: true });
-    await mkdir(join(configRoot, "themes"), { recursive: true });
+    await mkdir(join(configRoot, "prompts", "nested"), { recursive: true });
+    await mkdir(join(configRoot, "themes", "nested"), { recursive: true });
     await mkdir(join(configRoot, "extensions"), { recursive: true });
     await mkdir(outsideRoot, { recursive: true });
     await writeFile(insidePrompt, "# Inside\n", "utf-8");
     await writeFile(insideTheme, "{}\n", "utf-8");
     await writeFile(insideExtension, "export default {};\n", "utf-8");
+    await writeFile(ignoredPrompt, "# Ignored\n", "utf-8");
+    await writeFile(ignoredTheme, "{}\n", "utf-8");
+    await writeFile(nestedPrompt, "# Nested\n", "utf-8");
+    await writeFile(nestedTheme, "{}\n", "utf-8");
+    await writeFile(hiddenPrompt, "# Hidden\n", "utf-8");
+    await writeFile(hiddenTheme, "{}\n", "utf-8");
+    await writeFile(wrongPromptType, "{}\n", "utf-8");
+    await writeFile(wrongThemeType, "# Wrong\n", "utf-8");
+    await writeFile(join(configRoot, "prompts", ".ignore"), "ignored.md\n", "utf-8");
+    await writeFile(join(configRoot, "themes", ".ignore"), "ignored.json\n", "utf-8");
     await writeFile(join(outsideRoot, "outside.md"), "# Outside\n", "utf-8");
     await writeFile(join(outsideRoot, "outside.json"), "{}\n", "utf-8");
     await writeFile(join(outsideRoot, "outside.ts"), "export default {};\n", "utf-8");
@@ -161,12 +179,22 @@ describe("DefaultPackageManager", () => {
     });
 
     const resolved = await manager.resolve();
+    const promptPaths = resolved.prompts.map((prompt) => prompt.path);
+    const themePaths = resolved.themes.map((theme) => theme.path);
 
-    expect(resolved.prompts.map((prompt) => prompt.path)).toContain(insidePrompt);
-    expect(resolved.themes.map((theme) => theme.path)).toContain(insideTheme);
+    expect(promptPaths).toContain(insidePrompt);
+    expect(themePaths).toContain(insideTheme);
+    expect(promptPaths).not.toContain(ignoredPrompt);
+    expect(themePaths).not.toContain(ignoredTheme);
+    expect(promptPaths).not.toContain(nestedPrompt);
+    expect(themePaths).not.toContain(nestedTheme);
+    expect(promptPaths).not.toContain(hiddenPrompt);
+    expect(themePaths).not.toContain(hiddenTheme);
+    expect(promptPaths).not.toContain(wrongPromptType);
+    expect(themePaths).not.toContain(wrongThemeType);
     expect(resolved.extensions.map((extension) => extension.path)).toContain(insideExtension);
-    expect(resolved.prompts.some((prompt) => prompt.path.includes("linked"))).toBe(false);
-    expect(resolved.themes.some((theme) => theme.path.includes("linked"))).toBe(false);
+    expect(promptPaths.some((promptPath) => promptPath.includes("linked"))).toBe(false);
+    expect(themePaths.some((themePath) => themePath.includes("linked"))).toBe(false);
     expect(resolved.extensions.some((extension) => extension.path.includes("linked"))).toBe(false);
   });
 
diff --git a/src/agents/sessions/package-manager.ts b/src/agents/sessions/package-manager.ts
index 814af2099c78..5c867d84dc46 100644
--- a/src/agents/sessions/package-manager.ts
+++ b/src/agents/sessions/package-manager.ts
@@ -110,6 +110,7 @@ interface PackageFilter {
 }
 
 type ResourceType = "extensions" | "skills" | "prompts" | "themes";
+type TopLevelAutoResourceType = Extract<ResourceType, "prompts" | "themes">;
 
 const RESOURCE_TYPES: ResourceType[] = ["extensions", "skills", "prompts", "themes"];
 
@@ -351,7 +352,10 @@ function collectAncestorAgentsSkillDirs(startDir: string): string[] {
   return skillDirs;
 }
 
-function collectAutoPromptEntries(dir: string): string[] {
+function collectTopLevelAutoResourceEntries(
+  dir: string,
+  resourceType: TopLevelAutoResourceType,
+): string[] {
   const entries: string[] = [];
   if (!existsSync(dir)) {
     return entries;
@@ -388,55 +392,7 @@ function collectAutoPromptEntries(dir: string): string[] {
         continue;
       }
 
-      if (isFile && entry.name.endsWith(".md")) {
-        entries.push(fullPath);
-      }
-    }
-  } catch {
-    // Ignore errors
-  }
-
-  return entries;
-}
-
-function collectAutoThemeEntries(dir: string): string[] {
-  const entries: string[] = [];
-  if (!existsSync(dir)) {
-    return entries;
-  }
-
-  const ig = ignore();
-  addIgnoreRules(ig, dir, dir);
-
-  try {
-    const dirEntries = readdirSync(dir, { withFileTypes: true });
-    for (const entry of dirEntries) {
-      if (entry.name.startsWith(".")) {
-        continue;
-      }
-      if (entry.name === "node_modules") {
-        continue;
-      }
-
-      const fullPath = join(dir, entry.name);
-      if (!isRealPathWithinRoot(dir, fullPath)) {
-        continue;
-      }
-      let isFile = entry.isFile();
-      if (entry.isSymbolicLink()) {
-        try {
-          isFile = statSync(fullPath).isFile();
-        } catch {
-          continue;
-        }
-      }
-
-      const relPath = toPosixPath(relative(dir, fullPath));
-      if (ig.ignores(relPath)) {
-        continue;
-      }
-
-      if (isFile && entry.name.endsWith(".json")) {
+      if (isFile && FILE_PATTERNS[resourceType].test(entry.name)) {
         entries.push(fullPath);
       }
     }
@@ -1415,14 +1371,14 @@ export class DefaultPackageManager implements PackageManager {
 
     addResources(
       "prompts",
-      collectAutoPromptEntries(projectDirs.prompts),
+      collectTopLevelAutoResourceEntries(projectDirs.prompts, "prompts"),
       projectMetadata,
       projectOverrides.prompts,
       projectBaseDir,
     );
     addResources(
       "themes",
-      collectAutoThemeEntries(projectDirs.themes),
+      collectTopLevelAutoResourceEntries(projectDirs.themes, "themes"),
       projectMetadata,
       projectOverrides.themes,
       projectBaseDir,
@@ -1462,14 +1418,14 @@ export class DefaultPackageManager implements PackageManager {
 
     addResources(
       "prompts",
-      collectAutoPromptEntries(userDirs.prompts),
+      collectTopLevelAutoResourceEntries(userDirs.prompts, "prompts"),
       userMetadata,
       userOverrides.prompts,
       globalBaseDir,
     );
     addResources(
       "themes",
-      collectAutoThemeEntries(userDirs.themes),
+      collectTopLevelAutoResourceEntries(userDirs.themes, "themes"),
       userMetadata,
       userOverrides.themes,
       globalBaseDir,