diff --git a/apps/desktop/src/store/tinybase/persister/human/load.ts b/apps/desktop/src/store/tinybase/persister/human/load.ts
index 2b6ba85089..1d2dfab746 100644
--- a/apps/desktop/src/store/tinybase/persister/human/load.ts
+++ b/apps/desktop/src/store/tinybase/persister/human/load.ts
@@ -1,6 +1,6 @@
 import type { HumanStorage } from "@hypr/store";
 
-import { cleanupOrphanFiles, loadAllEntities } from "../markdown-utils";
+import { loadAllEntities } from "../markdown-utils";
 import { frontmatterToHuman } from "./utils";
 
 const LABEL = "HumanPersister";
@@ -11,10 +11,3 @@ export async function loadAllHumans(
 ): Promise<Record<string, HumanStorage>> {
   return loadAllEntities(dataDir, DIR_NAME, LABEL, frontmatterToHuman);
 }
-
-export async function cleanupOrphanHumanFiles(
-  dataDir: string,
-  validHumanIds: Set<string>,
-): Promise<void> {
-  return cleanupOrphanFiles(dataDir, DIR_NAME, validHumanIds, LABEL);
-}
diff --git a/apps/desktop/src/store/tinybase/persister/human/persister.ts b/apps/desktop/src/store/tinybase/persister/human/persister.ts
index 1e8788d9ab..ff87186b46 100644
--- a/apps/desktop/src/store/tinybase/persister/human/persister.ts
+++ b/apps/desktop/src/store/tinybase/persister/human/persister.ts
@@ -4,9 +4,11 @@ import type {
   OptionalSchemas,
 } from "tinybase/with-schemas";
 
+import { commands as folderCommands } from "@hypr/plugin-folder";
+
 import { createSessionDirPersister, getDataDir } from "../utils";
 import { collectHumanWriteOps, type HumanCollectorResult } from "./collect";
-import { cleanupOrphanHumanFiles, loadAllHumans } from "./load";
+import { loadAllHumans } from "./load";
 import { migrateHumansJsonIfNeeded } from "./migrate";
 
 export function createHumanPersister<Schemas extends OptionalSchemas>(
@@ -24,9 +26,13 @@ export function createHumanPersister<Schemas extends OptionalSchemas>(
       }
       return [{ humans }, {}] as unknown as Content<Schemas>;
     },
-    postSave: async (dataDir, result) => {
+    postSave: async (_dataDir, result) => {
       const { validHumanIds } = result as HumanCollectorResult;
-      await cleanupOrphanHumanFiles(dataDir, validHumanIds);
+      await folderCommands.cleanupOrphanFiles(
+        "humans",
+        "md",
+        Array.from(validHumanIds),
+      );
     },
   });
 }
diff --git a/apps/desktop/src/store/tinybase/persister/markdown-utils.ts b/apps/desktop/src/store/tinybase/persister/markdown-utils.ts
index 226f36dc85..36718444b8 100644
--- a/apps/desktop/src/store/tinybase/persister/markdown-utils.ts
+++ b/apps/desktop/src/store/tinybase/persister/markdown-utils.ts
@@ -91,48 +91,6 @@ export async function loadAllEntities<T>(
   return result;
 }
 
-export async function cleanupOrphanFiles(
-  dataDir: string,
-  dirName: string,
-  validIds: Set<string>,
-  label: string,
-): Promise<void> {
-  const paths = createEntityPaths(dirName);
-  const entityDir = paths.getDir(dataDir);
-
-  let entries: { name: string; isDirectory: boolean }[];
-  try {
-    entries = await readDir(entityDir);
-  } catch (error) {
-    if (isFileNotFoundError(error)) {
-      return;
-    }
-    throw error;
-  }
-
-  for (const entry of entries) {
-    if (entry.isDirectory) continue;
-    if (!entry.name.endsWith(".md")) continue;
-
-    const entityId = entry.name.replace(/\.md$/, "");
-    if (!isUUID(entityId)) continue;
-
-    if (!validIds.has(entityId)) {
-      try {
-        const filePath = paths.getFilePath(dataDir, entityId);
-        await remove(filePath);
-      } catch (error) {
-        if (!isFileNotFoundError(error)) {
-          console.error(
-            `[${label}] Failed to remove orphan file ${entry.name}:`,
-            error,
-          );
-        }
-      }
-    }
-  }
-}
-
 export async function migrateJsonToMarkdown<T>(
   dataDir: string,
   jsonFilename: string,
diff --git a/apps/desktop/src/store/tinybase/persister/organization/load.ts b/apps/desktop/src/store/tinybase/persister/organization/load.ts
index 778dd6535a..d37b974c51 100644
--- a/apps/desktop/src/store/tinybase/persister/organization/load.ts
+++ b/apps/desktop/src/store/tinybase/persister/organization/load.ts
@@ -1,6 +1,6 @@
 import type { OrganizationStorage } from "@hypr/store";
 
-import { cleanupOrphanFiles, loadAllEntities } from "../markdown-utils";
+import { loadAllEntities } from "../markdown-utils";
 import { frontmatterToOrganization } from "./utils";
 
 const LABEL = "OrganizationPersister";
@@ -11,10 +11,3 @@ export async function loadAllOrganizations(
 ): Promise<Record<string, OrganizationStorage>> {
   return loadAllEntities(dataDir, DIR_NAME, LABEL, frontmatterToOrganization);
 }
-
-export async function cleanupOrphanOrganizationFiles(
-  dataDir: string,
-  validOrgIds: Set<string>,
-): Promise<void> {
-  return cleanupOrphanFiles(dataDir, DIR_NAME, validOrgIds, LABEL);
-}
diff --git a/apps/desktop/src/store/tinybase/persister/organization/persister.ts b/apps/desktop/src/store/tinybase/persister/organization/persister.ts
index acabb988a8..a002991be2 100644
--- a/apps/desktop/src/store/tinybase/persister/organization/persister.ts
+++ b/apps/desktop/src/store/tinybase/persister/organization/persister.ts
@@ -4,12 +4,14 @@ import type {
   OptionalSchemas,
 } from "tinybase/with-schemas";
 
+import { commands as folderCommands } from "@hypr/plugin-folder";
+
 import { createSessionDirPersister, getDataDir } from "../utils";
 import {
   collectOrganizationWriteOps,
   type OrganizationCollectorResult,
 } from "./collect";
-import { cleanupOrphanOrganizationFiles, loadAllOrganizations } from "./load";
+import { loadAllOrganizations } from "./load";
 import { migrateOrganizationsJsonIfNeeded } from "./migrate";
 
 export function createOrganizationPersister<Schemas extends OptionalSchemas>(
@@ -27,9 +29,13 @@ export function createOrganizationPersister<Schemas extends OptionalSchemas>(
       }
       return [{ organizations }, {}] as unknown as Content<Schemas>;
     },
-    postSave: async (dataDir, result) => {
+    postSave: async (_dataDir, result) => {
       const { validOrgIds } = result as OrganizationCollectorResult;
-      await cleanupOrphanOrganizationFiles(dataDir, validOrgIds);
+      await folderCommands.cleanupOrphanFiles(
+        "organizations",
+        "md",
+        Array.from(validOrgIds),
+      );
     },
   });
 }
diff --git a/apps/desktop/src/store/tinybase/persister/prompts/load.ts b/apps/desktop/src/store/tinybase/persister/prompts/load.ts
index 075c0dba83..c1b1cac924 100644
--- a/apps/desktop/src/store/tinybase/persister/prompts/load.ts
+++ b/apps/desktop/src/store/tinybase/persister/prompts/load.ts
@@ -1,6 +1,6 @@
 import type { PromptStorage } from "@hypr/store";
 
-import { cleanupOrphanFiles, loadAllEntities } from "../markdown-utils";
+import { loadAllEntities } from "../markdown-utils";
 import { frontmatterToPrompt } from "./utils";
 
 const LABEL = "PromptPersister";
@@ -11,10 +11,3 @@ export async function loadAllPrompts(
 ): Promise<Record<string, PromptStorage>> {
   return loadAllEntities(dataDir, DIR_NAME, LABEL, frontmatterToPrompt);
 }
-
-export async function cleanupOrphanPromptFiles(
-  dataDir: string,
-  validPromptIds: Set<string>,
-): Promise<void> {
-  return cleanupOrphanFiles(dataDir, DIR_NAME, validPromptIds, LABEL);
-}
diff --git a/apps/desktop/src/store/tinybase/persister/prompts/persister.ts b/apps/desktop/src/store/tinybase/persister/prompts/persister.ts
index 077e9daeef..59492822fe 100644
--- a/apps/desktop/src/store/tinybase/persister/prompts/persister.ts
+++ b/apps/desktop/src/store/tinybase/persister/prompts/persister.ts
@@ -4,9 +4,11 @@ import type {
   OptionalSchemas,
 } from "tinybase/with-schemas";
 
+import { commands as folderCommands } from "@hypr/plugin-folder";
+
 import { createSessionDirPersister, getDataDir } from "../utils";
 import { collectPromptWriteOps, type PromptCollectorResult } from "./collect";
-import { cleanupOrphanPromptFiles, loadAllPrompts } from "./load";
+import { loadAllPrompts } from "./load";
 import { migratePromptsJsonIfNeeded } from "./migrate";
 
 export function createPromptPersister<Schemas extends OptionalSchemas>(
@@ -24,9 +26,13 @@ export function createPromptPersister<Schemas extends OptionalSchemas>(
       }
       return [{ prompts }, {}] as unknown as Content<Schemas>;
     },
-    postSave: async (dataDir, result) => {
+    postSave: async (_dataDir, result) => {
       const { validPromptIds } = result as PromptCollectorResult;
-      await cleanupOrphanPromptFiles(dataDir, validPromptIds);
+      await folderCommands.cleanupOrphanFiles(
+        "prompts",
+        "md",
+        Array.from(validPromptIds),
+      );
     },
   });
 }
diff --git a/apps/desktop/src/store/tinybase/persister/session/load.ts b/apps/desktop/src/store/tinybase/persister/session/load.ts
index f6d8905bad..2297b7134c 100644
--- a/apps/desktop/src/store/tinybase/persister/session/load.ts
+++ b/apps/desktop/src/store/tinybase/persister/session/load.ts
@@ -1,5 +1,5 @@
 import { sep } from "@tauri-apps/api/path";
-import { exists, readDir, readTextFile, remove } from "@tauri-apps/plugin-fs";
+import { exists, readDir, readTextFile } from "@tauri-apps/plugin-fs";
 
 import type {
   MappingSessionParticipantStorage,
@@ -8,7 +8,6 @@ import type {
   Tag,
 } from "@hypr/store";
 
-import { isFileNotFoundError, isUUID } from "../utils";
 import type { SessionMetaJson } from "./collect";
 
 export type LoadedData = {
@@ -114,66 +113,3 @@ export async function loadAllSessionMeta(dataDir: string): Promise<LoadedData> {
 
   return result;
 }
-
-async function collectSessionDirsRecursively(
-  sessionsDir: string,
-  currentPath: string,
-  result: Array<{ path: string; name: string }>,
-): Promise<void> {
-  const s = sep();
-  const fullPath = currentPath
-    ? [sessionsDir, currentPath].join(s)
-    : sessionsDir;
-
-  let entries: { name: string; isDirectory: boolean }[];
-  try {
-    entries = await readDir(fullPath);
-  } catch {
-    return;
-  }
-
-  for (const entry of entries) {
-    if (!entry.isDirectory) continue;
-
-    const entryPath = currentPath
-      ? [currentPath, entry.name].join(s)
-      : entry.name;
-    const metaPath = [sessionsDir, entryPath, "_meta.json"].join(s);
-    const hasMetaJson = await exists(metaPath);
-
-    if (hasMetaJson) {
-      result.push({ path: [sessionsDir, entryPath].join(s), name: entry.name });
-    } else {
-      await collectSessionDirsRecursively(sessionsDir, entryPath, result);
-    }
-  }
-}
-
-export async function cleanupOrphanSessionDirs(
-  dataDir: string,
-  validSessionIds: Set<string>,
-): Promise<void> {
-  const sessionsDir = [dataDir, "sessions"].join(sep());
-  const existingDirs: Array<{ path: string; name: string }> = [];
-
-  try {
-    await collectSessionDirsRecursively(sessionsDir, "", existingDirs);
-  } catch {
-    return;
-  }
-
-  for (const dir of existingDirs) {
-    if (isUUID(dir.name) && !validSessionIds.has(dir.name)) {
-      try {
-        await remove(dir.path, { recursive: true });
-      } catch (e) {
-        if (!isFileNotFoundError(e)) {
-          console.error(
-            `[SessionPersister] Failed to remove orphan dir ${dir.path}:`,
-            e,
-          );
-        }
-      }
-    }
-  }
-}
diff --git a/apps/desktop/src/store/tinybase/persister/session/persister.ts b/apps/desktop/src/store/tinybase/persister/session/persister.ts
index 25e43ce4b9..7d13fd9d19 100644
--- a/apps/desktop/src/store/tinybase/persister/session/persister.ts
+++ b/apps/desktop/src/store/tinybase/persister/session/persister.ts
@@ -4,9 +4,11 @@ import type {
   OptionalSchemas,
 } from "tinybase/with-schemas";
 
+import { commands as folderCommands } from "@hypr/plugin-folder";
+
 import { createSessionDirPersister, getDataDir } from "../utils";
 import { collectSessionWriteOps, type SessionCollectorResult } from "./collect";
-import { cleanupOrphanSessionDirs, loadAllSessionMeta } from "./load";
+import { loadAllSessionMeta } from "./load";
 
 export function createSessionPersister<Schemas extends OptionalSchemas>(
   store: MergeableStore<Schemas>,
@@ -33,9 +35,13 @@ export function createSessionPersister<Schemas extends OptionalSchemas>(
         return undefined;
       }
     },
-    postSave: async (dataDir, result) => {
+    postSave: async (_dataDir, result) => {
       const { validSessionIds } = result as SessionCollectorResult;
-      await cleanupOrphanSessionDirs(dataDir, validSessionIds);
+      await folderCommands.cleanupOrphanDirs(
+        "sessions",
+        "_meta.json",
+        Array.from(validSessionIds),
+      );
     },
   });
 }
diff --git a/plugins/folder/build.rs b/plugins/folder/build.rs
index c067cd1de5..dbaba0bf87 100644
--- a/plugins/folder/build.rs
+++ b/plugins/folder/build.rs
@@ -4,6 +4,8 @@ const COMMANDS: &[&str] = &[
     "create_folder",
     "rename_folder",
     "delete_folder",
+    "cleanup_orphan_files",
+    "cleanup_orphan_dirs",
 ];
 
 fn main() {
diff --git a/plugins/folder/js/bindings.gen.ts b/plugins/folder/js/bindings.gen.ts
index cdd228370b..ea7989f860 100644
--- a/plugins/folder/js/bindings.gen.ts
+++ b/plugins/folder/js/bindings.gen.ts
@@ -45,6 +45,22 @@ async deleteFolder(folderPath: string) : Promise<Result<null, string>> {
     if(e instanceof Error) throw e;
     else return { status: "error", error: e  as any };
 }
+},
+async cleanupOrphanFiles(subdir: string, extension: string, validIds: string[]) : Promise<Result<number, string>> {
+    try {
+    return { status: "ok", data: await TAURI_INVOKE("plugin:folder|cleanup_orphan_files", { subdir, extension, validIds }) };
+} catch (e) {
+    if(e instanceof Error) throw e;
+    else return { status: "error", error: e  as any };
+}
+},
+async cleanupOrphanDirs(subdir: string, markerFile: string, validIds: string[]) : Promise<Result<number, string>> {
+    try {
+    return { status: "ok", data: await TAURI_INVOKE("plugin:folder|cleanup_orphan_dirs", { subdir, markerFile, validIds }) };
+} catch (e) {
+    if(e instanceof Error) throw e;
+    else return { status: "error", error: e  as any };
+}
 }
 }
 
diff --git a/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_dirs.toml b/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_dirs.toml
new file mode 100644
index 0000000000..e33bb08326
--- /dev/null
+++ b/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_dirs.toml
@@ -0,0 +1,13 @@
+# Automatically generated - DO NOT EDIT!
+
+"$schema" = "../../schemas/schema.json"
+
+[[permission]]
+identifier = "allow-cleanup-orphan-dirs"
+description = "Enables the cleanup_orphan_dirs command without any pre-configured scope."
+commands.allow = ["cleanup_orphan_dirs"]
+
+[[permission]]
+identifier = "deny-cleanup-orphan-dirs"
+description = "Denies the cleanup_orphan_dirs command without any pre-configured scope."
+commands.deny = ["cleanup_orphan_dirs"]
diff --git a/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_files.toml b/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_files.toml
new file mode 100644
index 0000000000..4ba885592b
--- /dev/null
+++ b/plugins/folder/permissions/autogenerated/commands/cleanup_orphan_files.toml
@@ -0,0 +1,13 @@
+# Automatically generated - DO NOT EDIT!
+
+"$schema" = "../../schemas/schema.json"
+
+[[permission]]
+identifier = "allow-cleanup-orphan-files"
+description = "Enables the cleanup_orphan_files command without any pre-configured scope."
+commands.allow = ["cleanup_orphan_files"]
+
+[[permission]]
+identifier = "deny-cleanup-orphan-files"
+description = "Denies the cleanup_orphan_files command without any pre-configured scope."
+commands.deny = ["cleanup_orphan_files"]
diff --git a/plugins/folder/permissions/autogenerated/reference.md b/plugins/folder/permissions/autogenerated/reference.md
index 70d75fa62b..c981503911 100644
--- a/plugins/folder/permissions/autogenerated/reference.md
+++ b/plugins/folder/permissions/autogenerated/reference.md
@@ -9,6 +9,8 @@ Default permissions for the plugin
 - `allow-create-folder`
 - `allow-rename-folder`
 - `allow-delete-folder`
+- `allow-cleanup-orphan-files`
+- `allow-cleanup-orphan-dirs`
 
 ## Permission Table
 
@@ -19,6 +21,58 @@ Default permissions for the plugin
 </tr>
 
 
+<tr>
+<td>
+
+`folder:allow-cleanup-orphan-dirs`
+
+</td>
+<td>
+
+Enables the cleanup_orphan_dirs command without any pre-configured scope.
+
+</td>
+</tr>
+
+<tr>
+<td>
+
+`folder:deny-cleanup-orphan-dirs`
+
+</td>
+<td>
+
+Denies the cleanup_orphan_dirs command without any pre-configured scope.
+
+</td>
+</tr>
+
+<tr>
+<td>
+
+`folder:allow-cleanup-orphan-files`
+
+</td>
+<td>
+
+Enables the cleanup_orphan_files command without any pre-configured scope.
+
+</td>
+</tr>
+
+<tr>
+<td>
+
+`folder:deny-cleanup-orphan-files`
+
+</td>
+<td>
+
+Denies the cleanup_orphan_files command without any pre-configured scope.
+
+</td>
+</tr>
+
 <tr>
 <td>
 
diff --git a/plugins/folder/permissions/default.toml b/plugins/folder/permissions/default.toml
index f8b964d133..095f1e7d92 100644
--- a/plugins/folder/permissions/default.toml
+++ b/plugins/folder/permissions/default.toml
@@ -6,4 +6,6 @@ permissions = [
     "allow-create-folder",
     "allow-rename-folder",
     "allow-delete-folder",
+    "allow-cleanup-orphan-files",
+    "allow-cleanup-orphan-dirs",
 ]
diff --git a/plugins/folder/permissions/schemas/schema.json b/plugins/folder/permissions/schemas/schema.json
index 74680ac934..791cb67dbd 100644
--- a/plugins/folder/permissions/schemas/schema.json
+++ b/plugins/folder/permissions/schemas/schema.json
@@ -294,6 +294,30 @@
     "PermissionKind": {
       "type": "string",
       "oneOf": [
+        {
+          "description": "Enables the cleanup_orphan_dirs command without any pre-configured scope.",
+          "type": "string",
+          "const": "allow-cleanup-orphan-dirs",
+          "markdownDescription": "Enables the cleanup_orphan_dirs command without any pre-configured scope."
+        },
+        {
+          "description": "Denies the cleanup_orphan_dirs command without any pre-configured scope.",
+          "type": "string",
+          "const": "deny-cleanup-orphan-dirs",
+          "markdownDescription": "Denies the cleanup_orphan_dirs command without any pre-configured scope."
+        },
+        {
+          "description": "Enables the cleanup_orphan_files command without any pre-configured scope.",
+          "type": "string",
+          "const": "allow-cleanup-orphan-files",
+          "markdownDescription": "Enables the cleanup_orphan_files command without any pre-configured scope."
+        },
+        {
+          "description": "Denies the cleanup_orphan_files command without any pre-configured scope.",
+          "type": "string",
+          "const": "deny-cleanup-orphan-files",
+          "markdownDescription": "Denies the cleanup_orphan_files command without any pre-configured scope."
+        },
         {
           "description": "Enables the create_folder command without any pre-configured scope.",
           "type": "string",
@@ -355,10 +379,10 @@
           "markdownDescription": "Denies the rename_folder command without any pre-configured scope."
         },
         {
-          "description": "Default permissions for the plugin\n#### This default permission set includes:\n\n- `allow-list-folders`\n- `allow-move-session`\n- `allow-create-folder`\n- `allow-rename-folder`\n- `allow-delete-folder`",
+          "description": "Default permissions for the plugin\n#### This default permission set includes:\n\n- `allow-list-folders`\n- `allow-move-session`\n- `allow-create-folder`\n- `allow-rename-folder`\n- `allow-delete-folder`\n- `allow-cleanup-orphan-files`\n- `allow-cleanup-orphan-dirs`",
           "type": "string",
           "const": "default",
-          "markdownDescription": "Default permissions for the plugin\n#### This default permission set includes:\n\n- `allow-list-folders`\n- `allow-move-session`\n- `allow-create-folder`\n- `allow-rename-folder`\n- `allow-delete-folder`"
+          "markdownDescription": "Default permissions for the plugin\n#### This default permission set includes:\n\n- `allow-list-folders`\n- `allow-move-session`\n- `allow-create-folder`\n- `allow-rename-folder`\n- `allow-delete-folder`\n- `allow-cleanup-orphan-files`\n- `allow-cleanup-orphan-dirs`"
         }
       ]
     }
diff --git a/plugins/folder/src/commands.rs b/plugins/folder/src/commands.rs
index 5c12a0fd53..88a4ed3a20 100644
--- a/plugins/folder/src/commands.rs
+++ b/plugins/folder/src/commands.rs
@@ -53,3 +53,29 @@ pub(crate) async fn delete_folder<R: tauri::Runtime>(
         .delete_folder(&folder_path)
         .map_err(|e| e.to_string())
 }
+
+#[tauri::command]
+#[specta::specta]
+pub(crate) async fn cleanup_orphan_files<R: tauri::Runtime>(
+    app: tauri::AppHandle<R>,
+    subdir: String,
+    extension: String,
+    valid_ids: Vec<String>,
+) -> Result<u32, String> {
+    app.folder()
+        .cleanup_orphan_files(&subdir, &extension, valid_ids)
+        .map_err(|e| e.to_string())
+}
+
+#[tauri::command]
+#[specta::specta]
+pub(crate) async fn cleanup_orphan_dirs<R: tauri::Runtime>(
+    app: tauri::AppHandle<R>,
+    subdir: String,
+    marker_file: String,
+    valid_ids: Vec<String>,
+) -> Result<u32, String> {
+    app.folder()
+        .cleanup_orphan_dirs(&subdir, &marker_file, valid_ids)
+        .map_err(|e| e.to_string())
+}
diff --git a/plugins/folder/src/ext.rs b/plugins/folder/src/ext.rs
index f88341b8b3..063643d7a7 100644
--- a/plugins/folder/src/ext.rs
+++ b/plugins/folder/src/ext.rs
@@ -1,10 +1,12 @@
-use std::collections::HashMap;
+use std::collections::{HashMap, HashSet};
 use std::path::PathBuf;
 
 use tauri_plugin_path2::Path2PluginExt;
 
 use crate::types::ListFoldersResult;
-use crate::utils::{find_session_dir, scan_directory_recursive};
+use crate::utils::{
+    cleanup_dirs_recursive, cleanup_files_in_dir, find_session_dir, scan_directory_recursive,
+};
 
 pub struct Folder<'a, R: tauri::Runtime, M: tauri::Manager<R>> {
     manager: &'a M,
@@ -12,14 +14,16 @@ pub struct Folder<'a, R: tauri::Runtime, M: tauri::Manager<R>> {
 }
 
 impl<'a, R: tauri::Runtime, M: tauri::Manager<R>> Folder<'a, R, M> {
-    fn sessions_dir(&self) -> Result<PathBuf, crate::Error> {
-        let base = self
-            .manager
+    fn base_dir(&self) -> Result<PathBuf, crate::Error> {
+        self.manager
             .app_handle()
             .path2()
             .base()
-            .map_err(|e| crate::Error::Path(e.to_string()))?;
-        Ok(base.join("sessions"))
+            .map_err(|e| crate::Error::Path(e.to_string()))
+    }
+
+    fn sessions_dir(&self) -> Result<PathBuf, crate::Error> {
+        Ok(self.base_dir()?.join("sessions"))
     }
 
     pub fn list_folders(&self) -> Result<ListFoldersResult, crate::Error> {
@@ -128,6 +132,28 @@ impl<'a, R: tauri::Runtime, M: tauri::Manager<R>> Folder<'a, R, M> {
         tracing::info!("Deleted folder: {:?}", folder);
         Ok(())
     }
+
+    pub fn cleanup_orphan_files(
+        &self,
+        subdir: &str,
+        extension: &str,
+        valid_ids: Vec<String>,
+    ) -> Result<u32, crate::Error> {
+        let dir = self.base_dir()?.join(subdir);
+        let valid_set: HashSet<String> = valid_ids.into_iter().collect();
+        Ok(cleanup_files_in_dir(&dir, extension, &valid_set)?)
+    }
+
+    pub fn cleanup_orphan_dirs(
+        &self,
+        subdir: &str,
+        marker_file: &str,
+        valid_ids: Vec<String>,
+    ) -> Result<u32, crate::Error> {
+        let dir = self.base_dir()?.join(subdir);
+        let valid_set: HashSet<String> = valid_ids.into_iter().collect();
+        Ok(cleanup_dirs_recursive(&dir, marker_file, &valid_set)?)
+    }
 }
 
 pub trait FolderPluginExt<R: tauri::Runtime> {
diff --git a/plugins/folder/src/lib.rs b/plugins/folder/src/lib.rs
index 37b08128c8..713ebd3418 100644
--- a/plugins/folder/src/lib.rs
+++ b/plugins/folder/src/lib.rs
@@ -21,6 +21,8 @@ fn make_specta_builder<R: tauri::Runtime>() -> tauri_specta::Builder<R> {
             commands::create_folder::<tauri::Wry>,
             commands::rename_folder::<tauri::Wry>,
             commands::delete_folder::<tauri::Wry>,
+            commands::cleanup_orphan_files::<tauri::Wry>,
+            commands::cleanup_orphan_dirs::<tauri::Wry>,
         ])
         .error_handling(tauri_specta::ErrorHandlingMode::Result)
 }
diff --git a/plugins/folder/src/utils.rs b/plugins/folder/src/utils.rs
index 8f39246b78..f13844a8a6 100644
--- a/plugins/folder/src/utils.rs
+++ b/plugins/folder/src/utils.rs
@@ -1,3 +1,4 @@
+use std::collections::HashSet;
 use std::path::{Path, PathBuf};
 
 use uuid::Uuid;
@@ -101,6 +102,116 @@ pub fn scan_directory_recursive(
     }
 }
 
+pub fn cleanup_files_in_dir(
+    dir: &Path,
+    extension: &str,
+    valid_ids: &HashSet<String>,
+) -> std::io::Result<u32> {
+    if !dir.exists() {
+        return Ok(0);
+    }
+
+    let mut removed = 0;
+
+    for entry in std::fs::read_dir(dir)?.flatten() {
+        let path = entry.path();
+        if !path.is_file() {
+            continue;
+        }
+
+        let Some(stem) = path.file_stem().and_then(|n| n.to_str()) else {
+            continue;
+        };
+
+        if path.extension().and_then(|e| e.to_str()) != Some(extension) {
+            continue;
+        }
+
+        if !is_uuid(stem) {
+            continue;
+        }
+
+        if !valid_ids.contains(stem) {
+            if let Err(e) = std::fs::remove_file(&path) {
+                tracing::warn!("Failed to remove orphan file {:?}: {}", path, e);
+            } else {
+                tracing::debug!("Removed orphan file: {:?}", path);
+                removed += 1;
+            }
+        }
+    }
+
+    Ok(removed)
+}
+
+pub fn cleanup_dirs_recursive(
+    base_dir: &Path,
+    marker_file: &str,
+    valid_ids: &HashSet<String>,
+) -> std::io::Result<u32> {
+    if !base_dir.exists() {
+        return Ok(0);
+    }
+
+    let orphans = collect_orphan_dirs(base_dir, marker_file, valid_ids);
+
+    let mut removed = 0;
+    for dir in orphans {
+        if let Err(e) = std::fs::remove_dir_all(&dir) {
+            tracing::warn!("Failed to remove orphan dir {:?}: {}", dir, e);
+        } else {
+            tracing::info!("Removed orphan dir: {:?}", dir);
+            removed += 1;
+        }
+    }
+
+    Ok(removed)
+}
+
+fn collect_orphan_dirs(
+    base_dir: &Path,
+    marker_file: &str,
+    valid_ids: &HashSet<String>,
+) -> Vec<PathBuf> {
+    let mut orphans = Vec::new();
+    collect_orphan_dirs_recursive(base_dir, base_dir, marker_file, valid_ids, &mut orphans);
+    orphans
+}
+
+fn collect_orphan_dirs_recursive(
+    base_dir: &Path,
+    current_dir: &Path,
+    marker_file: &str,
+    valid_ids: &HashSet<String>,
+    orphans: &mut Vec<PathBuf>,
+) {
+    let entries = match std::fs::read_dir(current_dir) {
+        Ok(entries) => entries,
+        Err(_) => return,
+    };
+
+    for entry in entries.flatten() {
+        let path = entry.path();
+        if !path.is_dir() {
+            continue;
+        }
+
+        let Some(name) = path.file_name().and_then(|n| n.to_str()) else {
+            continue;
+        };
+
+        let has_marker = path.join(marker_file).exists();
+
+        if has_marker {
+            if is_uuid(name) && !valid_ids.contains(name) {
+                orphans.push(path);
+            }
+        } else if !is_uuid(name) {
+            collect_orphan_dirs_recursive(base_dir, &path, marker_file, valid_ids, orphans);
+        }
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;