fix: repair vault now flattens type folders and migrates legacy frontmatter

Repair Vault command now runs flatten_vault() and migrate_is_a_to_type()
before restoring themes and config, ensuring vaults adopt flat structure.
Also fixes config.md type definition to use `type: Type` instead of
legacy `Is A: Type`.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

docs/ARCHITECTURE.md

@@ -673,7 +673,7 @@ The vault backend (`src-tauri/src/vault/`) is split into focused submodules:
 | `create_vault_theme` | Create markdown theme note |
 | `ensure_vault_themes` | Seed default themes if missing |
 | `restore_default_themes` | Restore all default themes |
-| `repair_vault` | Restore default themes + missing config files |
+| `repair_vault` | Flatten vault structure, migrate legacy frontmatter, restore themes + config |
 
 ### AI & MCP
 

src-tauri/src/commands.rs

@@ -552,6 +552,10 @@ pub fn restore_default_themes(vault_path: String) -> Result<String, String> {
 #[tauri::command]
 pub fn repair_vault(vault_path: String) -> Result<String, String> {
     let vault_path = expand_tilde(&vault_path);
+    // Migrate legacy is_a/Is A frontmatter → type
+    vault::migrate_is_a_to_type(&vault_path)?;
+    // Flatten vault: move notes from type-based subfolders to root
+    vault::flatten_vault(&vault_path)?;
     // Migrate legacy theme/ directory to root, then repair themes
     theme::migrate_theme_dir_to_root(&vault_path);
     theme::restore_default_themes(&vault_path)?;
@@ -788,4 +792,49 @@ mod tests {
         let result = get_default_vault_path();
         assert!(result.is_ok());
     }
+
+    #[test]
+    fn test_repair_vault_flattens_type_folders() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let vault = dir.path();
+        let note_dir = vault.join("note");
+        std::fs::create_dir_all(&note_dir).unwrap();
+        std::fs::write(
+            note_dir.join("hello.md"),
+            "---\nis_a: Note\n---\n# Hello\n",
+        )
+        .unwrap();
+
+        let result = repair_vault(vault.to_str().unwrap().to_string());
+        assert!(result.is_ok());
+        // Note moved from note/ subfolder to root
+        assert!(vault.join("hello.md").exists());
+        assert!(!note_dir.join("hello.md").exists());
+        // Legacy is_a migrated to type
+        let content = std::fs::read_to_string(vault.join("hello.md")).unwrap();
+        assert!(content.contains("type: Note"));
+        assert!(!content.contains("is_a:"));
+    }
+
+    #[test]
+    fn test_repair_vault_creates_config_and_theme_files() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let vault = dir.path();
+
+        let result = repair_vault(vault.to_str().unwrap().to_string());
+        assert!(result.is_ok());
+        // Config files at root
+        assert!(vault.join("AGENTS.md").exists());
+        assert!(vault.join("config.md").exists());
+        // Theme files at root (flat structure)
+        assert!(vault.join("default-theme.md").exists());
+        assert!(vault.join("dark-theme.md").exists());
+        assert!(vault.join("minimal-theme.md").exists());
+        assert!(vault.join("theme.md").exists());
+        // No type/themes subfolders
+        assert!(!vault.join("theme").exists());
+        assert!(!vault.join("config").exists());
+        // .gitignore
+        assert!(vault.join(".gitignore").exists());
+    }
 }

src-tauri/src/vault/config_seed.rs

@@ -6,7 +6,7 @@ use super::getting_started::AGENTS_MD;
 /// Content for `config.md` — gives the Config type a sidebar icon and label.
 const CONFIG_TYPE_DEFINITION: &str = "\
 ---
-Is A: Type
+type: Type
 icon: gear-six
 color: gray
 order: 90
@@ -174,7 +174,7 @@ mod tests {
 
         assert!(vault.join("config.md").exists());
         let content = fs::read_to_string(vault.join("config.md")).unwrap();
-        assert!(content.contains("Is A: Type"));
+        assert!(content.contains("type: Type"));
         assert!(content.contains("icon: gear-six"));
     }
 

src/hooks/useCommandRegistry.ts

@@ -269,7 +269,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
       { id: 'install-mcp', label: mcpStatus === 'installed' ? 'Restore MCP Server' : 'Install MCP Server', group: 'Settings', keywords: ['mcp', 'claude', 'ai', 'tools', 'install', 'restore', 'fix', 'repair'], enabled: true, execute: () => onInstallMcp?.() },
       { id: 'reindex-vault', label: 'Reindex Vault', group: 'Settings', keywords: ['reindex', 'index', 'search', 'rebuild', 'refresh'], enabled: !!onReindexVault, execute: () => onReindexVault?.() },
       { id: 'reload-vault', label: 'Reload Vault', group: 'Settings', keywords: ['reload', 'refresh', 'rescan', 'sync', 'filesystem', 'cache'], enabled: !!onReloadVault, execute: () => onReloadVault?.() },
-      { id: 'repair-vault', label: 'Repair Vault', group: 'Settings', keywords: ['repair', 'fix', 'restore', 'config', 'agents', 'themes', 'missing', 'reset'], enabled: !!onRepairVault, execute: () => onRepairVault?.() },
+      { id: 'repair-vault', label: 'Repair Vault', group: 'Settings', keywords: ['repair', 'fix', 'restore', 'config', 'agents', 'themes', 'missing', 'reset', 'flatten', 'structure'], enabled: !!onRepairVault, execute: () => onRepairVault?.() },
 
       // Type-aware: "New [Type]" and "List [Type]"
       ...buildTypeCommands(vaultTypes, onCreateNoteOfType, onSelect),

tests/smoke/repair-vault-flat-structure.spec.ts

@@ -0,0 +1,44 @@
+import { test, expect } from '@playwright/test'
+
+test.describe('Repair Vault — flat structure', () => {
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/')
+    await page.waitForLoadState('networkidle')
+  })
+
+  test('repair vault executes without errors', async ({ page }) => {
+    const errors: string[] = []
+    page.on('console', msg => {
+      if (msg.type() === 'error') errors.push(msg.text())
+    })
+
+    // Open command palette and run Repair Vault
+    await page.keyboard.press('Meta+k')
+    await page.waitForTimeout(300)
+    await page.keyboard.type('repair vault')
+    await page.waitForTimeout(300)
+    await page.keyboard.press('Enter')
+    await page.waitForTimeout(1000)
+
+    // No console errors related to repair_vault
+    const repairErrors = errors.filter(e => e.includes('repair_vault'))
+    expect(repairErrors).toHaveLength(0)
+  })
+
+  test('app loads without type folder structure errors', async ({ page }) => {
+    const main = page.locator('#root')
+    await expect(main).toBeVisible()
+
+    const errors: string[] = []
+    page.on('console', msg => {
+      if (msg.type() === 'error') errors.push(msg.text())
+    })
+    await page.waitForTimeout(1000)
+
+    // No errors about move_note_to_type_folder or type folder operations
+    const folderErrors = errors.filter(
+      e => e.includes('move_note_to_type_folder') || e.includes('type_folder'),
+    )
+    expect(folderErrors).toHaveLength(0)
+  })
+})