fix: vault cache misses files in new directories, breaking theme restore

Root cause: git_uncommitted_files() used `git status --porcelain` which
reports new untracked directories as `?? theme/` instead of listing
individual files inside. The .md filter skipped directory entries, so
files in newly-created directories (theme/default.md, etc.) were
invisible to the cache system.

Fix: additionally use `git ls-files --others --exclude-standard` which
lists individual untracked files, resolving directories to their
contents.

Also:
- Add type/theme.md definition (icon: palette) to restore and getting-started vault
- Seed theme/*.md vault notes in getting-started vault
- Fix mock create_vault_theme to add entries for dev mode

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src-tauri/src/lib.rs

@@ -49,6 +49,8 @@ fn run_startup_tasks() {
     theme::seed_default_themes(vp_str);
     // Seed theme/ with built-in vault theme notes if missing
     theme::seed_vault_themes(vp_str);
+    // Seed type/theme.md so the Theme type has an icon in the sidebar
+    let _ = theme::ensure_theme_type_definition(vp_str);
 
     // Register Laputa MCP server in Claude Code and Cursor configs
     match mcp::register_mcp(vp_str) {

src-tauri/src/theme/defaults.rs

@@ -329,3 +329,15 @@ editor-max-width: 680\n\
 # Minimal Theme\n\
 \n\
 High contrast, minimal chrome. Monospace typography throughout.\n";
+
+/// Type definition for the Theme note type.
+pub const THEME_TYPE_DEFINITION: &str = "---\n\
+Is A: Type\n\
+icon: palette\n\
+color: purple\n\
+order: 50\n\
+---\n\
+\n\
+# Theme\n\
+\n\
+A visual theme for Laputa. Each theme defines CSS custom properties that control colors, typography, and spacing.\n";

src-tauri/src/theme/mod.rs

@@ -10,7 +10,8 @@ use std::path::Path;
 pub use create::{create_theme, create_vault_theme};
 pub use defaults::*;
 pub use seed::{
-    ensure_vault_themes, restore_default_themes, seed_default_themes, seed_vault_themes,
+    ensure_theme_type_definition, ensure_vault_themes, restore_default_themes,
+    seed_default_themes, seed_vault_themes,
 };
 
 /// A theme file parsed from _themes/*.json in the vault.

src-tauri/src/theme/seed.rs

@@ -104,9 +104,26 @@ pub fn restore_default_themes(vault_path: &str) -> Result<String, String> {
     // Seed theme/ markdown notes (reuses ensure_vault_themes for consistency)
     ensure_vault_themes(vault_path)?;
 
+    // Seed type/theme.md so the Theme type has an icon and label in the sidebar
+    ensure_theme_type_definition(vault_path)?;
+
     Ok("Default themes restored".to_string())
 }
 
+/// Create `type/theme.md` if it doesn't exist (gives the Theme type a sidebar icon/color).
+pub fn ensure_theme_type_definition(vault_path: &str) -> Result<(), String> {
+    let type_dir = Path::new(vault_path).join("type");
+    fs::create_dir_all(&type_dir)
+        .map_err(|e| format!("Failed to create type directory: {e}"))?;
+    let path = type_dir.join("theme.md");
+    let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+    if needs_write {
+        fs::write(&path, THEME_TYPE_DEFINITION)
+            .map_err(|e| format!("Failed to write type/theme.md: {e}"))?;
+    }
+    Ok(())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -244,6 +261,46 @@ mod tests {
         assert!(vault.join("theme").join("default.md").exists());
         assert!(vault.join("theme").join("dark.md").exists());
         assert!(vault.join("theme").join("minimal.md").exists());
+        assert!(
+            vault.join("type").join("theme.md").exists(),
+            "restore must create type/theme.md"
+        );
+        let type_content = fs::read_to_string(vault.join("type").join("theme.md")).unwrap();
+        assert!(type_content.contains("Is A: Type"));
+        assert!(type_content.contains("icon: palette"));
+    }
+
+    #[test]
+    fn test_ensure_theme_type_definition_creates_file() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_theme_type_definition(vp).unwrap();
+        let path = vault.join("type").join("theme.md");
+        assert!(path.exists());
+        let content = fs::read_to_string(&path).unwrap();
+        assert!(content.contains("Is A: Type"));
+        assert!(content.contains("icon: palette"));
+    }
+
+    #[test]
+    fn test_ensure_theme_type_definition_is_idempotent() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let type_dir = vault.join("type");
+        fs::create_dir_all(&type_dir).unwrap();
+        let custom = "---\nIs A: Type\nicon: swatches\ncolor: green\n---\n# Theme\n";
+        fs::write(type_dir.join("theme.md"), custom).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_theme_type_definition(vp).unwrap();
+        let content = fs::read_to_string(type_dir.join("theme.md")).unwrap();
+        assert!(
+            content.contains("swatches"),
+            "existing content must be preserved"
+        );
     }
 
     #[test]

src-tauri/src/vault/cache.rs

@@ -79,15 +79,10 @@ fn git_changed_files(vault: &Path, from_hash: &str, to_hash: &str) -> Vec<String
         .map(|s| collect_md_paths_from_diff(&s))
         .unwrap_or_default();
 
-    // Use ls-files for untracked files so that newly-seeded directories are picked up
-    // as individual files rather than as a single "?? dirname/" entry.
+    // Include uncommitted changes (modified, staged, and untracked files).
     let uncommitted = git_uncommitted_files(vault);
-    // Also include modified-but-unstaged files via status --porcelain.
-    let modified = run_git(vault, &["status", "--porcelain"])
-        .map(|s| collect_md_paths_from_porcelain(&s))
-        .unwrap_or_default();
 
-    for path in uncommitted.into_iter().chain(modified) {
+    for path in uncommitted.into_iter() {
         if !files.contains(&path) {
             files.push(path);
         }
@@ -97,9 +92,33 @@ fn git_changed_files(vault: &Path, from_hash: &str, to_hash: &str) -> Vec<String
 }
 
 fn git_uncommitted_files(vault: &Path) -> Vec<String> {
-    run_git(vault, &["status", "--porcelain"])
+    // Modified/staged tracked files from git status --porcelain
+    let mut files: Vec<String> = run_git(vault, &["status", "--porcelain"])
         .map(|s| collect_md_paths_from_porcelain(&s))
-        .unwrap_or_default()
+        .unwrap_or_default();
+
+    // Untracked files via ls-files (lists individual files, not just directories).
+    // git status --porcelain shows `?? dir/` for new directories, hiding individual
+    // files inside — ls-files resolves them so the cache picks up all new .md files.
+    let untracked = run_git(
+        vault,
+        &["ls-files", "--others", "--exclude-standard"],
+    )
+    .map(|s| {
+        s.lines()
+            .filter(|l| !l.is_empty() && l.ends_with(".md"))
+            .map(|l| l.to_string())
+            .collect::<Vec<_>>()
+    })
+    .unwrap_or_default();
+
+    for path in untracked {
+        if !files.contains(&path) {
+            files.push(path);
+        }
+    }
+
+    files
 }
 
 fn load_cache(vault: &Path) -> Option<VaultCache> {
@@ -541,4 +560,66 @@ mod tests {
         assert!(titles.contains(&"Existing"));
         assert!(titles.contains(&"New Note"));
     }
+
+    #[test]
+    fn test_update_same_commit_new_files_in_new_subdirectory() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path();
+
+        std::process::Command::new("git")
+            .args(["init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.email", "test@test.com"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.name", "Test"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        create_test_file(vault, "existing.md", "# Existing\n");
+        std::process::Command::new("git")
+            .args(["add", "."])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["commit", "-m", "init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Prime cache
+        let entries = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries.len(), 1);
+
+        // Create files in a new subdirectory (simulates restore_default_themes)
+        create_test_file(
+            vault,
+            "theme/default.md",
+            "---\nIs A: Theme\n---\n# Default Theme\n",
+        );
+        create_test_file(
+            vault,
+            "theme/dark.md",
+            "---\nIs A: Theme\n---\n# Dark Theme\n",
+        );
+
+        // Cache same commit — files in new subdirectory must appear
+        let entries2 = scan_vault_cached(vault).unwrap();
+        assert_eq!(
+            entries2.len(),
+            3,
+            "must pick up files in new untracked subdirectory"
+        );
+        let titles: Vec<&str> = entries2.iter().map(|e| e.title.as_str()).collect();
+        assert!(titles.contains(&"Existing"));
+        assert!(titles.contains(&"Default Theme"));
+        assert!(titles.contains(&"Dark Theme"));
+    }
 }

src-tauri/src/vault/getting_started.rs

@@ -133,6 +133,10 @@ const SAMPLE_FILES: &[SampleFile] = &[
         rel_path: "type/topic.md",
         content: "---\nIs A: Type\nicon: tag\ncolor: yellow\norder: 4\n---\n\n# Topic\n\nA Topic is a subject area or interest category that groups related notes, projects, and people.\n",
     },
+    SampleFile {
+        rel_path: "type/theme.md",
+        content: "---\nIs A: Type\nicon: palette\ncolor: purple\norder: 50\n---\n\n# Theme\n\nA visual theme for Laputa. Each theme defines CSS custom properties that control colors, typography, and spacing.\n",
+    },
     SampleFile {
         rel_path: "note/welcome-to-laputa.md",
         content: r#"---
@@ -394,7 +398,7 @@ pub fn create_getting_started_vault(target_path: &str) -> Result<String, String>
             .map_err(|e| format!("Failed to write {}: {}", sample.rel_path, e))?;
     }
 
-    // Seed built-in themes
+    // Seed built-in themes (both JSON legacy and vault-based markdown notes)
     let themes_dir = vault_dir.join("_themes");
     fs::create_dir_all(&themes_dir)
         .map_err(|e| format!("Failed to create _themes directory: {e}"))?;
@@ -405,6 +409,16 @@ pub fn create_getting_started_vault(target_path: &str) -> Result<String, String>
     fs::write(themes_dir.join("minimal.json"), crate::theme::MINIMAL_THEME)
         .map_err(|e| format!("Failed to write minimal theme: {e}"))?;
 
+    let theme_notes_dir = vault_dir.join("theme");
+    fs::create_dir_all(&theme_notes_dir)
+        .map_err(|e| format!("Failed to create theme directory: {e}"))?;
+    fs::write(theme_notes_dir.join("default.md"), crate::theme::DEFAULT_VAULT_THEME)
+        .map_err(|e| format!("Failed to write default vault theme: {e}"))?;
+    fs::write(theme_notes_dir.join("dark.md"), crate::theme::DARK_VAULT_THEME)
+        .map_err(|e| format!("Failed to write dark vault theme: {e}"))?;
+    fs::write(theme_notes_dir.join("minimal.md"), crate::theme::MINIMAL_VAULT_THEME)
+        .map_err(|e| format!("Failed to write minimal vault theme: {e}"))?;
+
     crate::git::init_repo(target_path)?;
 
     Ok(vault_dir
@@ -507,8 +521,8 @@ mod tests {
         create_getting_started_vault(vault_path.to_str().unwrap()).unwrap();
 
         let entries = crate::vault::scan_vault(&vault_path).unwrap();
-        // SAMPLE_FILES + AGENTS.md
-        assert_eq!(entries.len(), SAMPLE_FILES.len() + 1);
+        // SAMPLE_FILES + AGENTS.md + 3 vault theme notes (theme/default.md, dark.md, minimal.md)
+        assert_eq!(entries.len(), SAMPLE_FILES.len() + 1 + 3);
     }
 
     #[test]
@@ -583,12 +597,21 @@ mod tests {
         let vault_path = dir.path().join("theme-vault");
         create_getting_started_vault(vault_path.to_str().unwrap()).unwrap();
 
+        // JSON legacy themes
         assert!(vault_path.join("_themes/default.json").exists());
         assert!(vault_path.join("_themes/dark.json").exists());
         assert!(vault_path.join("_themes/minimal.json").exists());
 
         let themes = crate::theme::list_themes(vault_path.to_str().unwrap()).unwrap();
         assert_eq!(themes.len(), 3);
+
+        // Vault-based theme notes
+        assert!(vault_path.join("theme/default.md").exists());
+        assert!(vault_path.join("theme/dark.md").exists());
+        assert!(vault_path.join("theme/minimal.md").exists());
+
+        // Theme type definition
+        assert!(vault_path.join("type/theme.md").exists());
     }
 
     #[test]