refactor: extract useEditorSaveWithLinks and useNavigationGestures from App.tsx (#186)

App.tsx had 539 lines and 112 git touches in 30 days — highest churn in
the codebase. Two self-contained hooks were defined inline with no
dependency on App internals:

- useEditorSaveWithLinks: wraps useEditorSave to also extract and update
  outgoing wikilinks on save. Moved to src/hooks/useEditorSaveWithLinks.ts.

- useNavigationGestures: registers mouse button 3/4 back/forward and
  macOS trackpad horizontal swipe listeners. Moved to
  src/hooks/useNavigationGestures.ts.

App.tsx shrinks from 539 → 473 lines (-66 lines). Both hooks are now
independently testable and reusable.

Co-authored-by: Test <test@test.com>

design/search-bundle-qmd.pen

@@ -0,0 +1 @@
+{"children":[{"id":"status-bar-indexing","type":"frame","name":"StatusBar - Indexing Progress States","layout":"vertical","x":0,"y":0,"width":1400,"height":400,"gap":24,"padding":24,"fill":"#F7F6F3","children":[{"id":"title","type":"text","content":"StatusBar Indexing Progress - search-bundle-qmd","fontSize":20,"fontWeight":"600","fill":"#37352F"},{"id":"desc","type":"text","content":"The indexing badge appears in the StatusBar left section, after the pending changes badge. It shows the current indexing phase with a spinner icon (Loader2) during active phases and a Search icon when complete.","fontSize":14,"fill":"#9B9A97","width":900},{"id":"states","type":"frame","name":"States","layout":"vertical","gap":16,"width":1350,"children":[{"id":"state-idle","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-idle","type":"text","content":"idle:","fontSize":12,"fontWeight":"600","fill":"#9B9A97","width":100},{"id":"val-idle","type":"text","content":"(hidden - no badge shown)","fontSize":12,"fill":"#9B9A97"}]},{"id":"state-installing","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-install","type":"text","content":"installing:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-install","type":"text","content":"| [spinner] Installing search\u2026","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-scanning","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-scan","type":"text","content":"scanning:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-scan","type":"text","content":"| [spinner] Indexing\u2026 342/1,057","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-embedding","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-embed","type":"text","content":"embedding:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-embed","type":"text","content":"| [spinner] Embedding\u2026 50/200","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-complete","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-done","type":"text","content":"complete:","fontSize":12,"fontWeight":"600","fill":"#22c55e","width":100},{"id":"val-done","type":"text","content":"| [search icon] Index ready  (auto-dismisses after 5s)","fontSize":12,"fill":"#22c55e"}]},{"id":"state-error","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-err","type":"text","content":"error:","fontSize":12,"fontWeight":"600","fill":"#f97316","width":100},{"id":"val-err","type":"text","content":"| [search icon] Index error  (orange accent)","fontSize":12,"fill":"#f97316"}]}]},{"id":"flow","type":"frame","name":"Flow","layout":"vertical","gap":8,"width":1350,"children":[{"id":"flow-title","type":"text","content":"Auto-indexing Flow","fontSize":16,"fontWeight":"600","fill":"#37352F"},{"id":"flow-desc","type":"text","content":"1. Vault opens \u2192 useIndexing checks index status via get_index_status\n2. If qmd missing or collection missing or pending embeds \u2192 triggers start_indexing\n3. Rust emits indexing-progress events (installing \u2192 scanning \u2192 embedding \u2192 complete)\n4. StatusBar shows IndexingBadge with spinner + phase label + progress counts\n5. On file save \u2192 trigger_incremental_index runs qmd update in background\n6. Complete phase auto-dismisses after 5 seconds","fontSize":13,"fill":"#37352F","width":900}]}]}],"variables":{}}

design/sync-conflict-resolution.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

src-tauri/src/git.rs

@@ -461,6 +461,61 @@ fn parse_updated_files(stdout: &str) -> Vec<String> {
         .collect()
 }
 
+/// Resolve a single conflict file by choosing "ours" or "theirs" strategy,
+/// then stage the result.
+pub fn git_resolve_conflict(vault_path: &str, file: &str, strategy: &str) -> Result<(), String> {
+    let vault = Path::new(vault_path);
+
+    let checkout_flag = match strategy {
+        "ours" => "--ours",
+        "theirs" => "--theirs",
+        _ => {
+            return Err(format!(
+                "Invalid strategy '{}': must be 'ours' or 'theirs'",
+                strategy
+            ))
+        }
+    };
+
+    run_git(vault, &["checkout", checkout_flag, "--", file])?;
+    run_git(vault, &["add", "--", file])?;
+
+    Ok(())
+}
+
+/// Commit after all merge conflicts have been resolved.
+pub fn git_commit_conflict_resolution(vault_path: &str) -> Result<String, String> {
+    let vault = Path::new(vault_path);
+
+    // Verify no remaining conflicts
+    let remaining = get_conflict_files(vault_path)?;
+    if !remaining.is_empty() {
+        return Err(format!(
+            "Cannot commit: {} file(s) still have unresolved conflicts",
+            remaining.len()
+        ));
+    }
+
+    let commit = Command::new("git")
+        .args(["commit", "-m", "Resolve merge conflicts"])
+        .current_dir(vault)
+        .output()
+        .map_err(|e| format!("Failed to run git commit: {}", e))?;
+
+    if !commit.status.success() {
+        let stderr = String::from_utf8_lossy(&commit.stderr);
+        let stdout = String::from_utf8_lossy(&commit.stdout);
+        let detail = if stderr.trim().is_empty() {
+            stdout
+        } else {
+            stderr
+        };
+        return Err(format!("git commit failed: {}", detail.trim()));
+    }
+
+    Ok(String::from_utf8_lossy(&commit.stdout).to_string())
+}
+
 /// Push to remote.
 pub fn git_push(vault_path: &str) -> Result<String, String> {
     let vault = Path::new(vault_path);
@@ -1217,6 +1272,113 @@ mod tests {
         );
     }
 
+    /// Set up a pair of clones that have a merge conflict on the same file.
+    /// Returns (bare, clone_a, clone_b) where clone_b has an unresolved conflict.
+    fn setup_conflict_pair() -> (TempDir, TempDir, TempDir) {
+        let (bare_dir, clone_a_dir, clone_b_dir) = setup_remote_pair();
+
+        let vp_a = clone_a_dir.path().to_str().unwrap();
+        let vp_b = clone_b_dir.path().to_str().unwrap();
+
+        // A creates the file and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Original\n").unwrap();
+        git_commit(vp_a, "create conflict.md").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B pulls to get the file
+        git_pull(vp_b).unwrap();
+
+        // A modifies and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Version A\n").unwrap();
+        git_commit(vp_a, "A's change").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B modifies the same file locally and commits
+        fs::write(clone_b_dir.path().join("conflict.md"), "# Version B\n").unwrap();
+        git_commit(vp_b, "B's change").unwrap();
+
+        // B pulls — this causes a merge conflict
+        let result = git_pull(vp_b).unwrap();
+        assert_eq!(result.status, "conflict");
+
+        (bare_dir, clone_a_dir, clone_b_dir)
+    }
+
+    #[test]
+    fn test_resolve_conflict_ours() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        let conflicts = get_conflict_files(vp_b).unwrap();
+        assert!(conflicts.contains(&"conflict.md".to_string()));
+
+        git_resolve_conflict(vp_b, "conflict.md", "ours").unwrap();
+
+        let remaining = get_conflict_files(vp_b).unwrap();
+        assert!(remaining.is_empty());
+
+        let content = fs::read_to_string(clone_b.path().join("conflict.md")).unwrap();
+        assert_eq!(content, "# Version B\n");
+    }
+
+    #[test]
+    fn test_resolve_conflict_theirs() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        git_resolve_conflict(vp_b, "conflict.md", "theirs").unwrap();
+
+        let remaining = get_conflict_files(vp_b).unwrap();
+        assert!(remaining.is_empty());
+
+        let content = fs::read_to_string(clone_b.path().join("conflict.md")).unwrap();
+        assert_eq!(content, "# Version A\n");
+    }
+
+    #[test]
+    fn test_resolve_conflict_invalid_strategy() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        let result = git_resolve_conflict(vp_b, "conflict.md", "invalid");
+        assert!(result.is_err());
+        assert!(result.unwrap_err().contains("Invalid strategy"));
+    }
+
+    #[test]
+    fn test_commit_conflict_resolution() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // Resolve all conflicts first
+        git_resolve_conflict(vp_b, "conflict.md", "ours").unwrap();
+
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_ok());
+
+        // Verify the merge commit exists
+        let log = Command::new("git")
+            .args(["log", "--oneline", "-1"])
+            .current_dir(clone_b.path())
+            .output()
+            .unwrap();
+        let log_str = String::from_utf8_lossy(&log.stdout);
+        assert!(log_str.contains("Resolve merge conflicts"));
+    }
+
+    #[test]
+    fn test_commit_conflict_resolution_fails_with_unresolved() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // Don't resolve — try to commit directly
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_err());
+        assert!(result
+            .unwrap_err()
+            .contains("still have unresolved conflicts"));
+    }
+
     #[test]
     fn test_parse_github_repo_path_non_github() {
         assert_eq!(

src-tauri/src/indexing.rs

@@ -0,0 +1,486 @@
+use serde::Serialize;
+use std::path::Path;
+use std::process::Command;
+use std::sync::Mutex;
+
+static QMD_PATH_CACHE: Mutex<Option<String>> = Mutex::new(None);
+
+/// Locate the qmd binary, checking known locations and PATH.
+/// Caches the result for subsequent calls.
+pub fn find_qmd_binary() -> Option<String> {
+    if let Ok(guard) = QMD_PATH_CACHE.lock() {
+        if let Some(ref cached) = *guard {
+            return Some(cached.clone());
+        }
+    }
+
+    let result = find_qmd_binary_uncached();
+
+    if let Some(ref path) = result {
+        if let Ok(mut guard) = QMD_PATH_CACHE.lock() {
+            *guard = Some(path.clone());
+        }
+    }
+
+    result
+}
+
+fn find_qmd_binary_uncached() -> Option<String> {
+    let candidates = [
+        dirs::home_dir().map(|h| h.join(".bun/bin/qmd").to_string_lossy().to_string()),
+        Some("/usr/local/bin/qmd".to_string()),
+        Some("/opt/homebrew/bin/qmd".to_string()),
+    ];
+    for candidate in candidates.into_iter().flatten() {
+        if Path::new(&candidate).exists() {
+            return Some(candidate);
+        }
+    }
+    // Fallback: try PATH
+    Command::new("which")
+        .arg("qmd")
+        .output()
+        .ok()
+        .and_then(|o| {
+            if o.status.success() {
+                Some(String::from_utf8_lossy(&o.stdout).trim().to_string())
+            } else {
+                None
+            }
+        })
+}
+
+/// Clear the cached qmd path (e.g. after auto-install).
+pub fn clear_qmd_cache() {
+    if let Ok(mut guard) = QMD_PATH_CACHE.lock() {
+        *guard = None;
+    }
+}
+
+#[derive(Debug, Serialize, Clone)]
+pub struct IndexStatus {
+    pub available: bool,
+    pub qmd_installed: bool,
+    pub collection_exists: bool,
+    pub indexed_count: usize,
+    pub embedded_count: usize,
+    pub pending_embed: usize,
+}
+
+/// Check whether the vault has a qmd index and its status.
+pub fn check_index_status(vault_path: &str) -> IndexStatus {
+    let qmd_bin = match find_qmd_binary() {
+        Some(b) => b,
+        None => {
+            return IndexStatus {
+                available: false,
+                qmd_installed: false,
+                collection_exists: false,
+                indexed_count: 0,
+                embedded_count: 0,
+                pending_embed: 0,
+            }
+        }
+    };
+
+    let vault_name = vault_dir_name(vault_path);
+    let output = Command::new(&qmd_bin).args(["status"]).output();
+
+    match output {
+        Ok(o) if o.status.success() => {
+            let stdout = String::from_utf8_lossy(&o.stdout);
+            parse_status_for_vault(&stdout, &vault_name)
+        }
+        _ => IndexStatus {
+            available: false,
+            qmd_installed: true,
+            collection_exists: false,
+            indexed_count: 0,
+            embedded_count: 0,
+            pending_embed: 0,
+        },
+    }
+}
+
+fn vault_dir_name(vault_path: &str) -> String {
+    Path::new(vault_path)
+        .file_name()
+        .and_then(|n| n.to_str())
+        .unwrap_or("laputa")
+        .to_lowercase()
+}
+
+fn parse_status_for_vault(status_output: &str, vault_name: &str) -> IndexStatus {
+    let mut collection_exists = false;
+    let mut indexed_count = 0;
+    let mut embedded_count = 0;
+    let mut pending_embed = 0;
+
+    // Look for collection section matching vault name
+    let mut in_vault_section = false;
+    for line in status_output.lines() {
+        let trimmed = line.trim();
+        // Collection headers look like: "  laputa (qmd://laputa/)"
+        if trimmed.contains(&format!("qmd://{vault_name}/")) {
+            collection_exists = true;
+            in_vault_section = true;
+            continue;
+        }
+        // New collection section starts
+        if trimmed.contains("qmd://") && !trimmed.contains(vault_name) {
+            in_vault_section = false;
+            continue;
+        }
+        if in_vault_section {
+            if let Some(count_str) = extract_count_from_line(trimmed, "Files:") {
+                indexed_count = count_str;
+            }
+        }
+    }
+
+    // Global counts from the Documents section
+    for line in status_output.lines() {
+        let trimmed = line.trim();
+        if trimmed.starts_with("Total:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                if embedded_count == 0 && indexed_count == 0 {
+                    indexed_count = n;
+                }
+            }
+        } else if trimmed.starts_with("Vectors:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                embedded_count = n;
+            }
+        } else if trimmed.starts_with("Pending:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                pending_embed = n;
+            }
+        }
+    }
+
+    IndexStatus {
+        available: true,
+        qmd_installed: true,
+        collection_exists,
+        indexed_count,
+        embedded_count,
+        pending_embed,
+    }
+}
+
+fn extract_count_from_line(line: &str, prefix: &str) -> Option<usize> {
+    if !line.starts_with(prefix) {
+        return None;
+    }
+    extract_first_number(line)
+}
+
+fn extract_first_number(s: &str) -> Option<usize> {
+    s.split_whitespace()
+        .find_map(|word| word.parse::<usize>().ok())
+}
+
+/// Ensure a qmd collection exists for this vault. Creates one if missing.
+pub fn ensure_collection(vault_path: &str) -> Result<(), String> {
+    let qmd_bin = find_qmd_binary().ok_or("qmd not installed")?;
+    let vault_name = vault_dir_name(vault_path);
+
+    // Check if collection already exists
+    let output = Command::new(&qmd_bin)
+        .args(["collection", "list"])
+        .output()
+        .map_err(|e| format!("Failed to list collections: {e}"))?;
+
+    if output.status.success() {
+        let stdout = String::from_utf8_lossy(&output.stdout);
+        if stdout.contains(&format!("qmd://{vault_name}/")) {
+            return Ok(());
+        }
+    }
+
+    // Create collection
+    Command::new(&qmd_bin)
+        .args([
+            "collection",
+            "add",
+            vault_path,
+            "--name",
+            &vault_name,
+            "--mask",
+            "**/*.md",
+        ])
+        .output()
+        .map_err(|e| format!("Failed to create collection: {e}"))?;
+
+    Ok(())
+}
+
+#[derive(Debug, Serialize, Clone)]
+pub struct IndexingProgress {
+    pub phase: String,
+    pub current: usize,
+    pub total: usize,
+    pub done: bool,
+    pub error: Option<String>,
+}
+
+/// Run full indexing: update + embed. Returns progress updates via callback.
+pub fn run_full_index<F>(vault_path: &str, on_progress: F) -> Result<(), String>
+where
+    F: Fn(IndexingProgress),
+{
+    let qmd_bin = find_qmd_binary().ok_or("qmd not installed")?;
+
+    ensure_collection(vault_path)?;
+
+    // Phase 1: update (scan files)
+    on_progress(IndexingProgress {
+        phase: "scanning".to_string(),
+        current: 0,
+        total: 0,
+        done: false,
+        error: None,
+    });
+
+    let update_output = Command::new(&qmd_bin)
+        .args(["update"])
+        .output()
+        .map_err(|e| format!("qmd update failed: {e}"))?;
+
+    if !update_output.status.success() {
+        let stderr = String::from_utf8_lossy(&update_output.stderr);
+        let err = format!("qmd update failed: {stderr}");
+        on_progress(IndexingProgress {
+            phase: "error".to_string(),
+            current: 0,
+            total: 0,
+            done: true,
+            error: Some(err.clone()),
+        });
+        return Err(err);
+    }
+
+    // Parse update output for counts
+    let update_stdout = String::from_utf8_lossy(&update_output.stdout);
+    let total = parse_indexed_count(&update_stdout);
+
+    on_progress(IndexingProgress {
+        phase: "scanning".to_string(),
+        current: total,
+        total,
+        done: false,
+        error: None,
+    });
+
+    // Phase 2: embed (generate vectors)
+    on_progress(IndexingProgress {
+        phase: "embedding".to_string(),
+        current: 0,
+        total,
+        done: false,
+        error: None,
+    });
+
+    let embed_output = Command::new(&qmd_bin)
+        .args(["embed"])
+        .output()
+        .map_err(|e| format!("qmd embed failed: {e}"))?;
+
+    if !embed_output.status.success() {
+        let stderr = String::from_utf8_lossy(&embed_output.stderr);
+        // Embedding failure is non-fatal — keyword search still works
+        log::warn!("qmd embed failed (keyword search still works): {stderr}");
+        on_progress(IndexingProgress {
+            phase: "complete".to_string(),
+            current: total,
+            total,
+            done: true,
+            error: Some("Embedding failed — keyword search only".to_string()),
+        });
+        return Ok(());
+    }
+
+    on_progress(IndexingProgress {
+        phase: "complete".to_string(),
+        current: total,
+        total,
+        done: true,
+        error: None,
+    });
+
+    Ok(())
+}
+
+fn parse_indexed_count(update_output: &str) -> usize {
+    // qmd update output typically contains lines like "Indexed 9078 files"
+    for line in update_output.lines() {
+        if let Some(n) = extract_first_number(line) {
+            return n;
+        }
+    }
+    0
+}
+
+/// Run incremental update for a single file change.
+pub fn run_incremental_update(vault_path: &str) -> Result<(), String> {
+    let qmd_bin = find_qmd_binary().ok_or("qmd not installed")?;
+
+    // Verify collection exists
+    let vault_name = vault_dir_name(vault_path);
+    let list_output = Command::new(&qmd_bin)
+        .args(["collection", "list"])
+        .output()
+        .map_err(|e| format!("Failed to list collections: {e}"))?;
+
+    if list_output.status.success() {
+        let stdout = String::from_utf8_lossy(&list_output.stdout);
+        if !stdout.contains(&format!("qmd://{vault_name}/")) {
+            // Collection doesn't exist yet — skip incremental, full index needed
+            return Ok(());
+        }
+    }
+
+    let output = Command::new(&qmd_bin)
+        .args(["update"])
+        .output()
+        .map_err(|e| format!("qmd incremental update failed: {e}"))?;
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        return Err(format!("qmd update failed: {stderr}"));
+    }
+
+    Ok(())
+}
+
+/// Attempt to auto-install qmd via bun. Returns Ok if successful.
+pub fn auto_install_qmd() -> Result<String, String> {
+    // Find bun
+    let bun = find_bun().ok_or("bun not installed — cannot auto-install qmd")?;
+
+    let output = Command::new(&bun)
+        .args(["install", "-g", "qmd"])
+        .output()
+        .map_err(|e| format!("Failed to install qmd: {e}"))?;
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        return Err(format!("qmd installation failed: {stderr}"));
+    }
+
+    // Clear cache so find_qmd_binary() re-discovers
+    clear_qmd_cache();
+
+    match find_qmd_binary() {
+        Some(path) => Ok(path),
+        None => Err("qmd installed but binary not found".to_string()),
+    }
+}
+
+fn find_bun() -> Option<String> {
+    let candidates = [
+        dirs::home_dir().map(|h| h.join(".bun/bin/bun").to_string_lossy().to_string()),
+        Some("/opt/homebrew/bin/bun".to_string()),
+        Some("/usr/local/bin/bun".to_string()),
+    ];
+    for candidate in candidates.into_iter().flatten() {
+        if Path::new(&candidate).exists() {
+            return Some(candidate);
+        }
+    }
+    Command::new("which")
+        .arg("bun")
+        .output()
+        .ok()
+        .and_then(|o| {
+            if o.status.success() {
+                Some(String::from_utf8_lossy(&o.stdout).trim().to_string())
+            } else {
+                None
+            }
+        })
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn vault_dir_name_extracts_last_segment() {
+        assert_eq!(vault_dir_name("/Users/luca/Laputa"), "laputa");
+        assert_eq!(vault_dir_name("/home/user/MyVault"), "myvault");
+    }
+
+    #[test]
+    fn vault_dir_name_fallback() {
+        assert_eq!(vault_dir_name(""), "laputa");
+    }
+
+    #[test]
+    fn extract_first_number_works() {
+        assert_eq!(
+            extract_first_number("Total: 9078 files indexed"),
+            Some(9078)
+        );
+        assert_eq!(extract_first_number("Vectors: 14676 embedded"), Some(14676));
+        assert_eq!(extract_first_number("no numbers here"), None);
+    }
+
+    #[test]
+    fn parse_status_finds_collection() {
+        let status = r#"
+QMD Status
+
+Index: /Users/luca/.cache/qmd/index.sqlite
+Size:  100.9 MB
+
+Documents
+  Total:    9115 files indexed
+  Vectors:  14676 embedded
+  Pending:  26 need embedding
+
+Collections
+  laputa (qmd://laputa/)
+    Pattern:  **/*.md
+    Files:    9078 (updated 20d ago)
+"#;
+        let result = parse_status_for_vault(status, "laputa");
+        assert!(result.collection_exists);
+        assert_eq!(result.indexed_count, 9078);
+        assert_eq!(result.embedded_count, 14676);
+        assert_eq!(result.pending_embed, 26);
+    }
+
+    #[test]
+    fn parse_status_missing_collection() {
+        let status = r#"
+QMD Status
+
+Documents
+  Total:    100 files indexed
+  Vectors:  50 embedded
+  Pending:  0
+
+Collections
+  other (qmd://other/)
+    Files:    100
+"#;
+        let result = parse_status_for_vault(status, "laputa");
+        assert!(!result.collection_exists);
+    }
+
+    #[test]
+    fn extract_count_from_line_works() {
+        assert_eq!(
+            extract_count_from_line("Files:    9078 (updated 20d ago)", "Files:"),
+            Some(9078)
+        );
+        assert_eq!(extract_count_from_line("Pattern:  **/*.md", "Files:"), None);
+    }
+
+    #[test]
+    fn parse_indexed_count_from_output() {
+        assert_eq!(parse_indexed_count("Indexed 342 files in 1.2s"), 342);
+        assert_eq!(parse_indexed_count("No output"), 0);
+    }
+}

src-tauri/src/lib.rs

@@ -3,6 +3,7 @@ pub mod claude_cli;
 pub mod frontmatter;
 pub mod git;
 pub mod github;
+pub mod indexing;
 pub mod mcp;
 pub mod menu;
 pub mod search;
@@ -21,6 +22,7 @@ use claude_cli::{AgentStreamRequest, ChatStreamRequest, ClaudeCliStatus, ClaudeS
 use frontmatter::FrontmatterValue;
 use git::{GitCommit, GitPullResult, LastCommitInfo, ModifiedFile};
 use github::{DeviceFlowPollResult, DeviceFlowStart, GitHubUser, GithubRepo};
+use indexing::{IndexStatus, IndexingProgress};
 use search::SearchResponse;
 use settings::Settings;
 use theme::{ThemeFile, VaultSettings};
@@ -131,6 +133,18 @@ fn git_pull(vault_path: String) -> Result<GitPullResult, String> {
     git::git_pull(&vault_path)
 }
 
+#[tauri::command]
+fn git_resolve_conflict(vault_path: String, file: String, strategy: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path);
+    git::git_resolve_conflict(&vault_path, &file, &strategy)
+}
+
+#[tauri::command]
+fn git_commit_conflict_resolution(vault_path: String) -> Result<String, String> {
+    let vault_path = expand_tilde(&vault_path);
+    git::git_commit_conflict_resolution(&vault_path)
+}
+
 #[tauri::command]
 fn git_push(vault_path: String) -> Result<String, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -341,6 +355,64 @@ async fn search_vault(
         .map_err(|e| format!("Search task failed: {}", e))?
 }
 
+#[tauri::command]
+fn get_index_status(vault_path: String) -> IndexStatus {
+    let vault_path = expand_tilde(&vault_path);
+    indexing::check_index_status(&vault_path)
+}
+
+#[tauri::command]
+async fn start_indexing(app_handle: tauri::AppHandle, vault_path: String) -> Result<(), String> {
+    use tauri::Emitter;
+    let vault_path = expand_tilde(&vault_path).into_owned();
+    tokio::task::spawn_blocking(move || {
+        // Auto-install qmd if not available
+        if indexing::find_qmd_binary().is_none() {
+            let _ = app_handle.emit(
+                "indexing-progress",
+                IndexingProgress {
+                    phase: "installing".to_string(),
+                    current: 0,
+                    total: 0,
+                    done: false,
+                    error: None,
+                },
+            );
+            match indexing::auto_install_qmd() {
+                Ok(_) => log::info!("qmd auto-installed successfully"),
+                Err(e) => {
+                    log::warn!("qmd auto-install failed: {e}");
+                    let _ = app_handle.emit(
+                        "indexing-progress",
+                        IndexingProgress {
+                            phase: "error".to_string(),
+                            current: 0,
+                            total: 0,
+                            done: true,
+                            error: Some(format!("qmd not available: {e}")),
+                        },
+                    );
+                    return Err(e);
+                }
+            }
+        }
+
+        indexing::run_full_index(&vault_path, |progress| {
+            let _ = app_handle.emit("indexing-progress", &progress);
+        })
+    })
+    .await
+    .map_err(|e| format!("Indexing task failed: {e}"))?
+}
+
+#[tauri::command]
+async fn trigger_incremental_index(vault_path: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path).into_owned();
+    tokio::task::spawn_blocking(move || indexing::run_incremental_update(&vault_path))
+        .await
+        .map_err(|e| format!("Incremental index failed: {e}"))?
+}
+
 struct WsBridgeChild(Mutex<Option<Child>>);
 
 #[tauri::command]
@@ -543,6 +615,8 @@ pub fn run() {
             get_last_commit_info,
             git_pull,
             git_push,
+            git_resolve_conflict,
+            git_commit_conflict_resolution,
             ai_chat,
             check_claude_cli,
             stream_claude_chat,
@@ -566,6 +640,9 @@ pub fn run() {
             github_device_flow_poll,
             github_get_user,
             search_vault,
+            get_index_status,
+            start_indexing,
+            trigger_incremental_index,
             create_getting_started_vault,
             check_vault_exists,
             get_default_vault_path,

src-tauri/src/search.rs

@@ -1,3 +1,4 @@
+use crate::indexing;
 use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
 use std::path::Path;
@@ -30,31 +31,6 @@ struct QmdResult {
     pub score: f64,
 }
 
-fn find_qmd_binary() -> Option<String> {
-    let candidates = [
-        dirs::home_dir().map(|h| h.join(".bun/bin/qmd").to_string_lossy().to_string()),
-        Some("/usr/local/bin/qmd".to_string()),
-        Some("/opt/homebrew/bin/qmd".to_string()),
-    ];
-    for candidate in candidates.into_iter().flatten() {
-        if Path::new(&candidate).exists() {
-            return Some(candidate);
-        }
-    }
-    // Fallback: try PATH
-    Command::new("which")
-        .arg("qmd")
-        .output()
-        .ok()
-        .and_then(|o| {
-            if o.status.success() {
-                Some(String::from_utf8_lossy(&o.stdout).trim().to_string())
-            } else {
-                None
-            }
-        })
-}
-
 fn qmd_uri_to_vault_path(uri: &str, vault_path: &str) -> String {
     // qmd://laputa/essay/foo.md → essay/foo.md
     let relative = uri
@@ -108,7 +84,7 @@ fn detect_collection_name(vault_path: &str) -> String {
 }
 
 fn detect_collection_name_uncached(vault_path: &str) -> String {
-    let qmd_bin = match find_qmd_binary() {
+    let qmd_bin = match indexing::find_qmd_binary() {
         Some(b) => b,
         None => return "laputa".to_string(),
     };
@@ -149,8 +125,8 @@ pub fn search_vault(
 ) -> Result<SearchResponse, String> {
     let start = Instant::now();
 
-    let qmd_bin =
-        find_qmd_binary().ok_or_else(|| "qmd binary not found. Install qmd first.".to_string())?;
+    let qmd_bin = indexing::find_qmd_binary()
+        .ok_or_else(|| "qmd binary not found. Install qmd first.".to_string())?;
 
     let collection = detect_collection_name(vault_path);
 

src/App.tsx

@@ -17,7 +17,6 @@ import { useMcpRegistration } from './hooks/useMcpRegistration'
 import { useVaultLoader } from './hooks/useVaultLoader'
 import { useSettings } from './hooks/useSettings'
 import { useNoteActions } from './hooks/useNoteActions'
-import { useEditorSave } from './hooks/useEditorSave'
 import { useCommitFlow } from './hooks/useCommitFlow'
 import { useViewMode } from './hooks/useViewMode'
 import { useEntryActions } from './hooks/useEntryActions'
@@ -28,14 +27,18 @@ import { useGitHistory } from './hooks/useGitHistory'
 import { useUpdater } from './hooks/useUpdater'
 import { useNavigationHistory } from './hooks/useNavigationHistory'
 import { useAutoSync } from './hooks/useAutoSync'
+import { useConflictResolver } from './hooks/useConflictResolver'
+import { useIndexing } from './hooks/useIndexing'
 import { useZoom } from './hooks/useZoom'
 import { useBuildNumber } from './hooks/useBuildNumber'
 import { useOnboarding } from './hooks/useOnboarding'
 import { useThemeManager } from './hooks/useThemeManager'
+import { useEditorSaveWithLinks } from './hooks/useEditorSaveWithLinks'
+import { useNavigationGestures } from './hooks/useNavigationGestures'
+import { ConflictResolverModal } from './components/ConflictResolverModal'
 import { UpdateBanner } from './components/UpdateBanner'
 import { invoke } from '@tauri-apps/api/core'
 import { isTauri, mockInvoke } from './mock-tauri'
-import { extractOutgoingLinks } from './utils/wikilinks'
 import type { SidebarSelection } from './types'
 import './App.css'
 
@@ -77,34 +80,6 @@ function useLayoutPanels() {
 }
 
 /** Wraps useEditorSave to also keep outgoingLinks in sync on save and on content change. */
-function useEditorSaveWithLinks(config: {
-  updateContent: (path: string, content: string) => void
-  updateEntry: (path: string, patch: Partial<import('./types').VaultEntry>) => void
-  setTabs: Parameters<typeof useEditorSave>[0]['setTabs']
-  setToastMessage: (msg: string | null) => void
-  onAfterSave: () => void
-  onNotePersisted?: (path: string) => void
-}) {
-  const { updateContent, updateEntry } = config
-  const saveContent = useCallback((path: string, content: string) => {
-    updateContent(path, content)
-    updateEntry(path, { outgoingLinks: extractOutgoingLinks(content) })
-  }, [updateContent, updateEntry])
-  const editor = useEditorSave({ updateVaultContent: saveContent, setTabs: config.setTabs, setToastMessage: config.setToastMessage, onAfterSave: config.onAfterSave, onNotePersisted: config.onNotePersisted })
-  const { handleContentChange: rawOnChange } = editor
-  const prevLinksKeyRef = useRef('')
-  const handleContentChange = useCallback((path: string, content: string) => {
-    rawOnChange(path, content)
-    const links = extractOutgoingLinks(content)
-    const key = links.join('\0')
-    if (key !== prevLinksKeyRef.current) {
-      prevLinksKeyRef.current = key
-      updateEntry(path, { outgoingLinks: links })
-    }
-  }, [rawOnChange, updateEntry])
-  return { ...editor, handleContentChange }
-}
-
 function App() {
   const [selection, setSelection] = useState<SidebarSelection>(DEFAULT_SELECTION)
   const layout = useLayoutPanels()
@@ -135,11 +110,40 @@ function App() {
     onVaultUpdated: vault.reloadVault,
     onConflict: (files) => {
       const names = files.map((f) => f.split('/').pop()).join(', ')
-      setToastMessage(`Conflict in ${names} — review needed`)
+      setToastMessage(`Conflict in ${names} — click to resolve`)
     },
     onToast: (msg) => setToastMessage(msg),
   })
 
+  // Ref bridges for conflict resolution callbacks (notes declared below)
+  const openConflictFileRef = useRef<(relativePath: string) => void>(() => {})
+
+  const indexing = useIndexing(resolvedPath)
+
+  const conflictResolver = useConflictResolver({
+    vaultPath: resolvedPath,
+    onResolved: () => {
+      dialogs.closeConflictResolver()
+      autoSync.resumePull()
+      vault.reloadVault()
+      autoSync.triggerSync()
+    },
+    onToast: (msg) => setToastMessage(msg),
+    onOpenFile: (relativePath) => openConflictFileRef.current(relativePath),
+  })
+
+  const handleOpenConflictResolver = useCallback(() => {
+    if (autoSync.conflictFiles.length === 0) return
+    autoSync.pausePull()
+    conflictResolver.initFiles(autoSync.conflictFiles)
+    dialogs.openConflictResolver()
+  }, [autoSync, conflictResolver, dialogs])
+
+  const handleCloseConflictResolver = useCallback(() => {
+    autoSync.resumePull()
+    dialogs.closeConflictResolver()
+  }, [autoSync, dialogs])
+
   // Ref bridges handleContentChange (created after notes) into useNoteActions.
   // Read at callback time, so it's always current when user presses Cmd+N.
   const contentChangeRef = useRef<(path: string, content: string) => void>(() => {})
@@ -185,53 +189,33 @@ function App() {
     }
   }, [navHistory, isEntryExists, vault.entries, notes])
 
-  // Mouse button 3/4 (back/forward) and macOS trackpad two-finger swipe
-  useEffect(() => {
-    const handleMouseBack = (e: MouseEvent) => {
-      if (e.button === 3) { e.preventDefault(); handleGoBack() }
-      if (e.button === 4) { e.preventDefault(); handleGoForward() }
-    }
-    window.addEventListener('mouseup', handleMouseBack)
+  useNavigationGestures({ onGoBack: handleGoBack, onGoForward: handleGoForward })
 
-    // Trackpad swipe: accumulate horizontal wheel delta and trigger on threshold
-    let accumulatedDeltaX = 0
-    let resetTimer: ReturnType<typeof setTimeout> | null = null
-    const SWIPE_THRESHOLD = 120
-
-    const handleWheel = (e: WheelEvent) => {
-      // Only handle horizontal-dominant gestures (trackpad swipe)
-      if (Math.abs(e.deltaX) <= Math.abs(e.deltaY)) return
-      if (e.ctrlKey || e.metaKey) return // ignore pinch-zoom
-
-      accumulatedDeltaX += e.deltaX
-
-      if (resetTimer) clearTimeout(resetTimer)
-      resetTimer = setTimeout(() => { accumulatedDeltaX = 0 }, 300)
-
-      if (accumulatedDeltaX > SWIPE_THRESHOLD) {
-        accumulatedDeltaX = 0
-        handleGoForward()
-      } else if (accumulatedDeltaX < -SWIPE_THRESHOLD) {
-        accumulatedDeltaX = 0
-        handleGoBack()
-      }
-    }
-    window.addEventListener('wheel', handleWheel, { passive: true })
-
-    return () => {
-      window.removeEventListener('mouseup', handleMouseBack)
-      window.removeEventListener('wheel', handleWheel)
-      if (resetTimer) clearTimeout(resetTimer)
-    }
-  }, [handleGoBack, handleGoForward])
+  const { triggerIncrementalIndex } = indexing
+  const onAfterSave = useCallback(() => {
+    vault.loadModifiedFiles()
+    triggerIncrementalIndex()
+  }, [vault, triggerIncrementalIndex])
 
   const { handleSave: handleSaveRaw, handleContentChange, savePendingForPath, savePending } = useEditorSaveWithLinks({
     updateContent: vault.updateContent, updateEntry: vault.updateEntry,
-    setTabs: notes.setTabs, setToastMessage, onAfterSave: vault.loadModifiedFiles,
+    setTabs: notes.setTabs, setToastMessage, onAfterSave,
     onNotePersisted: vault.clearUnsaved,
   })
   useEffect(() => { contentChangeRef.current = handleContentChange }, [handleContentChange])
 
+  // Wire conflict file opener now that notes is available
+  useEffect(() => {
+    openConflictFileRef.current = (relativePath: string) => {
+      const fullPath = `${resolvedPath}/${relativePath}`
+      const entry = vault.entries.find(e => e.path === fullPath)
+      if (entry) {
+        notes.handleSelectNote(entry)
+        dialogs.closeConflictResolver()
+      }
+    }
+  }, [resolvedPath, vault.entries, notes, dialogs])
+
   // Wrap handleSave to also persist unsaved notes that have no pending edits (user pressed Cmd+S without typing)
   const handleSave = useCallback(async () => {
     const activeTab = notes.tabs.find(t => t.entry.path === notes.activeTabPath)
@@ -321,7 +305,10 @@ function App() {
     onOpenSettings: dialogs.openSettings,
     onTrashNote: entryActions.handleTrashNote, onRestoreNote: entryActions.handleRestoreNote,
     onArchiveNote: entryActions.handleArchiveNote, onUnarchiveNote: entryActions.handleUnarchiveNote,
-    onCommitPush: commitFlow.openCommitDialog, onSetViewMode: setViewMode,
+    onCommitPush: commitFlow.openCommitDialog,
+    onResolveConflicts: handleOpenConflictResolver,
+    conflictCount: autoSync.conflictFiles.length,
+    onSetViewMode: setViewMode,
     onToggleInspector: () => layout.setInspectorCollapsed(c => !c),
     onToggleDiff: () => diffToggleRef.current(),
     onToggleRawEditor: () => rawToggleRef.current(),
@@ -452,13 +439,24 @@ function App() {
         </div>
       </div>
       <UpdateBanner status={updateStatus} actions={updateActions} />
-      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onRemoveVault={vaultSwitcher.removeVault} />
+      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} indexingProgress={indexing.progress} onRemoveVault={vaultSwitcher.removeVault} />
       <Toast message={toastMessage} onDismiss={() => setToastMessage(null)} />
       <QuickOpenPalette open={dialogs.showQuickOpen} entries={vault.entries} onSelect={notes.handleSelectNote} onClose={dialogs.closeQuickOpen} />
       <CommandPalette open={dialogs.showCommandPalette} commands={commands} onClose={dialogs.closeCommandPalette} />
       <SearchPanel open={dialogs.showSearch} vaultPath={resolvedPath} entries={vault.entries} onSelectNote={notes.handleSelectNote} onClose={dialogs.closeSearch} />
       <CreateTypeDialog open={dialogs.showCreateTypeDialog} onClose={dialogs.closeCreateType} onCreate={handleCreateType} />
       <CommitDialog open={commitFlow.showCommitDialog} modifiedCount={vault.modifiedFiles.length} onCommit={commitFlow.handleCommitPush} onClose={commitFlow.closeCommitDialog} />
+      <ConflictResolverModal
+        open={dialogs.showConflictResolver}
+        fileStates={conflictResolver.fileStates}
+        allResolved={conflictResolver.allResolved}
+        committing={conflictResolver.committing}
+        error={conflictResolver.error}
+        onResolveFile={conflictResolver.resolveFile}
+        onOpenInEditor={conflictResolver.openInEditor}
+        onCommit={conflictResolver.commitResolution}
+        onClose={handleCloseConflictResolver}
+      />
       <SettingsPanel open={dialogs.showSettings} settings={settings} onSave={saveSettings} onClose={dialogs.closeSettings} themeManager={themeManager} />
       <GitHubVaultModal
         open={dialogs.showGitHubVault}

src/components/ConflictResolverModal.tsx

@@ -0,0 +1,246 @@
+import { useState, useEffect, useRef, useCallback } from 'react'
+import { Dialog, DialogContent, DialogHeader, DialogTitle, DialogFooter, DialogDescription } from '@/components/ui/dialog'
+import { Button } from '@/components/ui/button'
+import { AlertTriangle, FileText, Check, Loader2 } from 'lucide-react'
+import type { ConflictFileState } from '../hooks/useConflictResolver'
+
+interface ConflictResolverModalProps {
+  open: boolean
+  fileStates: ConflictFileState[]
+  allResolved: boolean
+  committing: boolean
+  error: string | null
+  onResolveFile: (file: string, strategy: 'ours' | 'theirs') => void
+  onOpenInEditor: (file: string) => void
+  onCommit: () => void
+  onClose: () => void
+}
+
+function isBinaryFile(file: string): boolean {
+  const binaryExts = ['.png', '.jpg', '.jpeg', '.gif', '.webp', '.ico', '.pdf', '.zip', '.tar', '.gz', '.mp3', '.mp4', '.wav', '.ogg', '.woff', '.woff2', '.ttf', '.otf', '.eot']
+  return binaryExts.some(ext => file.toLowerCase().endsWith(ext))
+}
+
+function fileName(path: string): string {
+  return path.split('/').pop() ?? path
+}
+
+function ResolutionLabel({ resolution }: { resolution: ConflictFileState['resolution'] }) {
+  if (!resolution) return null
+  const labels = { ours: 'Keeping mine', theirs: 'Keeping theirs', manual: 'Edited manually' }
+  return (
+    <span className="flex items-center gap-1 text-xs text-green-600">
+      <Check size={12} />{labels[resolution]}
+    </span>
+  )
+}
+
+function ConflictFileRow({
+  state,
+  focused,
+  onResolve,
+  onOpenInEditor,
+  onFocus,
+}: {
+  state: ConflictFileState
+  focused: boolean
+  onResolve: (strategy: 'ours' | 'theirs') => void
+  onOpenInEditor: () => void
+  onFocus: () => void
+}) {
+  const rowRef = useRef<HTMLDivElement>(null)
+  const binary = isBinaryFile(state.file)
+  const resolved = state.resolution !== null
+
+  useEffect(() => {
+    if (focused) rowRef.current?.scrollIntoView({ block: 'nearest' })
+  }, [focused])
+
+  return (
+    <div
+      ref={rowRef}
+      role="row"
+      tabIndex={0}
+      onFocus={onFocus}
+      className={`flex items-center justify-between gap-2 rounded-md border px-3 py-2 transition-colors ${
+        focused ? 'border-ring bg-accent/50' : 'border-border bg-background'
+      } ${resolved ? 'opacity-70' : ''}`}
+      data-testid={`conflict-file-${state.file}`}
+    >
+      <div className="flex items-center gap-2 min-w-0 flex-1">
+        <FileText size={14} className="shrink-0 text-muted-foreground" />
+        <span className="text-sm truncate" title={state.file}>{fileName(state.file)}</span>
+        <ResolutionLabel resolution={state.resolution} />
+      </div>
+      <div className="flex items-center gap-1 shrink-0">
+        {state.resolving ? (
+          <Loader2 size={14} className="animate-spin text-muted-foreground" />
+        ) : (
+          <>
+            <Button
+              variant="outline"
+              size="sm"
+              className="text-xs h-7 px-2"
+              onClick={() => onResolve('ours')}
+              disabled={state.resolving}
+              title="Keep my local version (K)"
+              data-testid={`resolve-ours-${state.file}`}
+            >
+              Keep mine
+            </Button>
+            <Button
+              variant="outline"
+              size="sm"
+              className="text-xs h-7 px-2"
+              onClick={() => onResolve('theirs')}
+              disabled={state.resolving}
+              title="Keep remote version (T)"
+              data-testid={`resolve-theirs-${state.file}`}
+            >
+              Keep theirs
+            </Button>
+            {!binary && (
+              <Button
+                variant="ghost"
+                size="sm"
+                className="text-xs h-7 px-2"
+                onClick={onOpenInEditor}
+                title="Open file in editor (O)"
+                data-testid={`resolve-open-${state.file}`}
+              >
+                Open in editor
+              </Button>
+            )}
+          </>
+        )}
+      </div>
+    </div>
+  )
+}
+
+export function ConflictResolverModal({
+  open,
+  fileStates,
+  allResolved,
+  committing,
+  error,
+  onResolveFile,
+  onOpenInEditor,
+  onCommit,
+  onClose,
+}: ConflictResolverModalProps) {
+  const [focusIdx, setFocusIdx] = useState(0)
+  const focusIdxRef = useRef(0)
+  const listRef = useRef<HTMLDivElement>(null)
+
+  useEffect(() => {
+    if (open) {
+      setFocusIdx(0) // eslint-disable-line react-hooks/set-state-in-effect -- reset on dialog open
+      focusIdxRef.current = 0
+    }
+  }, [open])
+
+  const handleKeyDown = useCallback((e: React.KeyboardEvent) => {
+    if (e.key === 'Escape') {
+      onClose()
+      return
+    }
+
+    const idx = focusIdxRef.current
+    const file = fileStates[idx]
+
+    if (e.key === 'ArrowDown' || (e.key === 'Tab' && !e.shiftKey)) {
+      e.preventDefault()
+      const next = Math.min(idx + 1, fileStates.length - 1)
+      setFocusIdx(next)
+      focusIdxRef.current = next
+      return
+    }
+    if (e.key === 'ArrowUp' || (e.key === 'Tab' && e.shiftKey)) {
+      e.preventDefault()
+      const prev = Math.max(idx - 1, 0)
+      setFocusIdx(prev)
+      focusIdxRef.current = prev
+      return
+    }
+
+    if ((e.key === 'k' || e.key === 'K') && file && !file.resolving && !e.metaKey && !e.ctrlKey) {
+      e.preventDefault()
+      onResolveFile(file.file, 'ours')
+    } else if ((e.key === 't' || e.key === 'T') && file && !file.resolving && !e.metaKey && !e.ctrlKey) {
+      e.preventDefault()
+      onResolveFile(file.file, 'theirs')
+    } else if ((e.key === 'o' || e.key === 'O') && file && !isBinaryFile(file.file) && !e.metaKey && !e.ctrlKey) {
+      e.preventDefault()
+      onOpenInEditor(file.file)
+    } else if (e.key === 'Enter' && allResolved && !committing) {
+      e.preventDefault()
+      onCommit()
+    }
+  }, [fileStates, allResolved, committing, onResolveFile, onOpenInEditor, onCommit, onClose])
+
+  return (
+    <Dialog open={open} onOpenChange={(isOpen) => { if (!isOpen) onClose() }}>
+      <DialogContent
+        showCloseButton={false}
+        className="sm:max-w-[520px]"
+        onKeyDown={handleKeyDown}
+      >
+        <DialogHeader>
+          <div className="flex items-center gap-2">
+            <AlertTriangle size={18} className="text-orange-500" />
+            <DialogTitle>Resolve Merge Conflicts</DialogTitle>
+          </div>
+          <DialogDescription>
+            {fileStates.length} file{fileStates.length !== 1 ? 's have' : ' has'} merge conflicts. Choose how to resolve each file.
+          </DialogDescription>
+        </DialogHeader>
+
+        <div
+          ref={listRef}
+          className="flex flex-col gap-2 max-h-[300px] overflow-y-auto"
+          role="grid"
+          data-testid="conflict-file-list"
+        >
+          {fileStates.map((state, i) => (
+            <ConflictFileRow
+              key={state.file}
+              state={state}
+              focused={i === focusIdx}
+              onResolve={(strategy) => onResolveFile(state.file, strategy)}
+              onOpenInEditor={() => onOpenInEditor(state.file)}
+              onFocus={() => {
+                setFocusIdx(i)
+                focusIdxRef.current = i
+              }}
+            />
+          ))}
+        </div>
+
+        {error && (
+          <p className="text-xs text-destructive" data-testid="conflict-error">{error}</p>
+        )}
+
+        <DialogFooter className="flex-row items-center justify-between sm:justify-between">
+          <span className="text-[11px] text-muted-foreground">
+            K = keep mine · T = keep theirs · O = open · Enter = commit
+          </span>
+          <div className="flex gap-2">
+            <Button variant="outline" onClick={onClose}>Cancel</Button>
+            <Button
+              onClick={onCommit}
+              disabled={!allResolved || committing}
+              data-testid="conflict-commit-btn"
+            >
+              {committing ? (
+                <><Loader2 size={14} className="animate-spin mr-1" />Committing…</>
+              ) : (
+                'Commit & continue'
+              )}
+            </Button>
+          </div>
+        </DialogFooter>
+      </DialogContent>
+    </Dialog>
+  )
+}

src/components/StatusBar.test.tsx

@@ -213,58 +213,89 @@ describe('StatusBar', () => {
     expect(screen.getByTitle('View pending changes')).toBeInTheDocument()
   })
 
-  describe('vault removal', () => {
-    it('shows remove button for each vault when onRemoveVault is provided and multiple vaults exist', () => {
-      render(
-        <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} onRemoveVault={vi.fn()} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      expect(screen.getByTestId('vault-menu-remove-Main Vault')).toBeInTheDocument()
-      expect(screen.getByTestId('vault-menu-remove-Work Vault')).toBeInTheDocument()
-    })
+  it('shows indexing badge when indexing is in progress', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'scanning', current: 342, total: 1057, done: false, error: null }}
+      />
+    )
+    expect(screen.getByTestId('status-indexing')).toBeInTheDocument()
+    expect(screen.getByText(/Indexing… 342\/1,057/)).toBeInTheDocument()
+  })
 
-    it('does not show remove button when only one vault exists', () => {
-      const singleVault: VaultOption[] = [{ label: 'Only Vault', path: '/only/vault' }]
-      render(
-        <StatusBar noteCount={100} vaultPath="/only/vault" vaults={singleVault} onSwitchVault={vi.fn()} onRemoveVault={vi.fn()} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      expect(screen.queryByTestId('vault-menu-remove-Only Vault')).not.toBeInTheDocument()
-    })
+  it('shows embedding phase in indexing badge', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'embedding', current: 50, total: 200, done: false, error: null }}
+      />
+    )
+    expect(screen.getByText(/Embedding… 50\/200/)).toBeInTheDocument()
+  })
 
-    it('calls onRemoveVault with vault path when remove button is clicked', () => {
-      const onRemoveVault = vi.fn()
-      render(
-        <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} onRemoveVault={onRemoveVault} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      fireEvent.click(screen.getByTestId('vault-menu-remove-Work Vault'))
-      expect(onRemoveVault).toHaveBeenCalledWith('/Users/luca/Work')
-    })
+  it('shows index ready when indexing is complete', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'complete', current: 1057, total: 1057, done: true, error: null }}
+      />
+    )
+    expect(screen.getByText('Index ready')).toBeInTheDocument()
+  })
 
-    it('closes menu after removing a vault', () => {
-      render(
-        <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} onRemoveVault={vi.fn()} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      fireEvent.click(screen.getByTestId('vault-menu-remove-Work Vault'))
-      expect(screen.queryByTestId('vault-menu-remove-Work Vault')).not.toBeInTheDocument()
-    })
+  it('shows error state in indexing badge', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'error', current: 0, total: 0, done: true, error: 'qmd not available' }}
+      />
+    )
+    expect(screen.getByText('Index error')).toBeInTheDocument()
+  })
 
-    it('remove button has "Remove from list" title for accessibility', () => {
-      render(
-        <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} onRemoveVault={vi.fn()} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      expect(screen.getAllByTitle('Remove from list')).toHaveLength(2)
-    })
+  it('hides indexing badge when phase is idle', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'idle', current: 0, total: 0, done: false, error: null }}
+      />
+    )
+    expect(screen.queryByTestId('status-indexing')).not.toBeInTheDocument()
+  })
 
-    it('does not show remove button when onRemoveVault is not provided', () => {
-      render(
-        <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} />
-      )
-      fireEvent.click(screen.getByTitle('Switch vault'))
-      expect(screen.queryByTestId('vault-menu-remove-Main Vault')).not.toBeInTheDocument()
-    })
+  it('hides indexing badge when no progress prop provided', () => {
+    render(
+      <StatusBar noteCount={100} vaultPath="/Users/luca/Laputa" vaults={vaults} onSwitchVault={vi.fn()} />
+    )
+    expect(screen.queryByTestId('status-indexing')).not.toBeInTheDocument()
+  })
+
+  it('shows installing phase in indexing badge', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'installing', current: 0, total: 0, done: false, error: null }}
+      />
+    )
+    expect(screen.getByText('Installing search…')).toBeInTheDocument()
   })
 })

src/components/StatusBar.tsx

@@ -1,6 +1,7 @@
 import { useState, useRef, useEffect } from 'react'
-import { Package, RefreshCw, Sparkles, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, X } from 'lucide-react'
+import { Package, RefreshCw, Sparkles, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, Search, X } from 'lucide-react'
 import type { LastCommitInfo, SyncStatus } from '../types'
+import type { IndexingProgress } from '../hooks/useIndexing'
 import { openExternalUrl } from '../utils/url'
 
 export interface VaultOption {
@@ -25,9 +26,11 @@ interface StatusBarProps {
   conflictCount?: number
   lastCommitInfo?: LastCommitInfo | null
   onTriggerSync?: () => void
+  onOpenConflictResolver?: () => void
   zoomLevel?: number
   onZoomReset?: () => void
   buildNumber?: string
+  indexingProgress?: IndexingProgress
   onRemoveVault?: (path: string) => void
 }
 
@@ -190,15 +193,17 @@ function CommitBadge({ info }: { info: LastCommitInfo }) {
   )
 }
 
-function SyncBadge({ status, lastSyncTime, onTriggerSync }: { status: SyncStatus; lastSyncTime: number | null; onTriggerSync?: () => void }) {
+function SyncBadge({ status, lastSyncTime, onTriggerSync, onOpenConflictResolver }: { status: SyncStatus; lastSyncTime: number | null; onTriggerSync?: () => void; onOpenConflictResolver?: () => void }) {
   const SyncIcon = SYNC_ICON_MAP[status] ?? RefreshCw
   const isSyncing = status === 'syncing'
+  const isConflict = status === 'conflict'
+  const handleClick = isConflict ? onOpenConflictResolver : onTriggerSync
   return (
     <span
       role="button"
-      onClick={onTriggerSync}
-      style={{ ...ICON_STYLE, cursor: onTriggerSync ? 'pointer' : 'default', padding: '2px 4px', borderRadius: 3 }}
-      title={isSyncing ? 'Syncing…' : 'Click to sync now'}
+      onClick={handleClick}
+      style={{ ...ICON_STYLE, cursor: handleClick ? 'pointer' : 'default', padding: '2px 4px', borderRadius: 3 }}
+      title={isConflict ? 'Click to resolve conflicts' : isSyncing ? 'Syncing…' : 'Click to sync now'}
       data-testid="status-sync"
     >
       <SyncIcon size={13} style={{ color: syncIconColor(status) }} className={isSyncing ? 'animate-spin' : ''} />{formatSyncLabel(status, lastSyncTime)}
@@ -206,18 +211,58 @@ function SyncBadge({ status, lastSyncTime, onTriggerSync }: { status: SyncStatus
   )
 }
 
-function ConflictBadge({ count }: { count: number }) {
+function ConflictBadge({ count, onClick }: { count: number; onClick?: () => void }) {
   if (count <= 0) return null
   return (
     <>
       <span style={SEP_STYLE}>|</span>
-      <span style={{ ...ICON_STYLE, color: 'var(--destructive, #e03e3e)' }} data-testid="status-conflict-count">
+      <span
+        role="button"
+        onClick={onClick}
+        style={{ ...ICON_STYLE, color: 'var(--destructive, #e03e3e)', cursor: onClick ? 'pointer' : 'default', padding: '2px 4px', borderRadius: 3, background: 'transparent' }}
+        title="Resolve merge conflicts"
+        onMouseEnter={onClick ? (e) => { e.currentTarget.style.background = 'var(--hover)' } : undefined}
+        onMouseLeave={onClick ? (e) => { e.currentTarget.style.background = 'transparent' } : undefined}
+        data-testid="status-conflict-count"
+      >
         <AlertTriangle size={13} />{count} conflict{count > 1 ? 's' : ''}
       </span>
     </>
   )
 }
 
+const INDEXING_LABELS: Record<string, string> = {
+  installing: 'Installing search…',
+  scanning: 'Indexing…',
+  embedding: 'Embedding…',
+  complete: 'Index ready',
+  error: 'Index error',
+}
+
+function IndexingBadge({ progress }: { progress: IndexingProgress }) {
+  if (progress.phase === 'idle') return null
+  const label = INDEXING_LABELS[progress.phase] ?? progress.phase
+  const isActive = !progress.done
+  const showCount = progress.total > 0 && isActive
+  const displayText = showCount
+    ? `${label} ${progress.current.toLocaleString()}/${progress.total.toLocaleString()}`
+    : label
+  const color = progress.phase === 'error' ? 'var(--accent-orange)' : 'var(--accent-blue, #3b82f6)'
+
+  return (
+    <>
+      <span style={SEP_STYLE}>|</span>
+      <span style={{ ...ICON_STYLE, color }} data-testid="status-indexing">
+        {isActive
+          ? <Loader2 size={13} className="animate-spin" />
+          : <Search size={13} />
+        }
+        {displayText}
+      </span>
+    </>
+  )
+}
+
 function PendingBadge({ count, onClick }: { count: number; onClick?: () => void }) {
   if (count <= 0) return null
   return (
@@ -236,7 +281,7 @@ function PendingBadge({ count, onClick }: { count: number; onClick?: () => void
   )
 }
 
-export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, zoomLevel = 100, onZoomReset, buildNumber, onRemoveVault }: StatusBarProps) {
+export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, onOpenConflictResolver, zoomLevel = 100, onZoomReset, buildNumber, indexingProgress, onRemoveVault }: StatusBarProps) {
   const [, setTick] = useState(0)
   useEffect(() => {
     const id = setInterval(() => setTick((t) => t + 1), 30_000)
@@ -250,10 +295,11 @@ export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onS
         <span style={SEP_STYLE}>|</span>
         <span style={ICON_STYLE} data-testid="status-build-number"><Package size={13} />{buildNumber ?? 'b?'}</span>
         <span style={SEP_STYLE}>|</span>
-        <SyncBadge status={syncStatus} lastSyncTime={lastSyncTime} onTriggerSync={onTriggerSync} />
+        <SyncBadge status={syncStatus} lastSyncTime={lastSyncTime} onTriggerSync={onTriggerSync} onOpenConflictResolver={onOpenConflictResolver} />
         {lastCommitInfo && <CommitBadge info={lastCommitInfo} />}
-        <ConflictBadge count={conflictCount} />
+        <ConflictBadge count={conflictCount} onClick={onOpenConflictResolver} />
         <PendingBadge count={modifiedCount} onClick={onClickPending} />
+        {indexingProgress && <IndexingBadge progress={indexingProgress} />}
       </div>
       <div style={{ display: 'flex', alignItems: 'center', gap: 12 }}>
         <span style={ICON_STYLE}><Sparkles size={13} style={{ color: 'var(--accent-purple)' }} />Claude Sonnet 4</span>

src/hooks/useAppCommands.ts

@@ -31,6 +31,8 @@ interface AppCommandsConfig {
   onArchiveNote: (path: string) => void
   onUnarchiveNote: (path: string) => void
   onCommitPush: () => void
+  onResolveConflicts?: () => void
+  conflictCount?: number
   onSetViewMode: (mode: ViewMode) => void
   onToggleInspector: () => void
   onToggleDiff?: () => void
@@ -139,6 +141,8 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
     onArchiveNote: config.onArchiveNote,
     onUnarchiveNote: config.onUnarchiveNote,
     onCommitPush: config.onCommitPush,
+    onResolveConflicts: config.onResolveConflicts,
+    conflictCount: config.conflictCount,
     onSetViewMode: config.onSetViewMode,
     onToggleInspector: config.onToggleInspector,
     onToggleDiff: config.onToggleDiff,

src/hooks/useAutoSync.test.ts

@@ -194,6 +194,28 @@ describe('useAutoSync', () => {
     })
   })
 
+  it('skips pull when paused via pausePull', async () => {
+    const { result } = renderSync()
+
+    await waitFor(() => {
+      expect(result.current.syncStatus).toBe('idle')
+    })
+
+    // Pause and clear mocks
+    act(() => { result.current.pausePull() })
+    mockInvokeFn.mockClear()
+
+    // Trigger sync while paused
+    act(() => { result.current.triggerSync() })
+
+    // Should not have called git_pull
+    const pullCalls = mockInvokeFn.mock.calls.filter((c: unknown[]) => c[0] === 'git_pull').length
+    expect(pullCalls).toBe(0)
+
+    // Resume
+    act(() => { result.current.resumePull() })
+  })
+
   it('handles error status from git_pull result', async () => {
     mockInvokeFn.mockImplementation((cmd: string) => {
       if (cmd === 'get_last_commit_info') return Promise.resolve(null)

src/hooks/useAutoSync.ts

@@ -23,6 +23,10 @@ export interface AutoSyncState {
   conflictFiles: string[]
   lastCommitInfo: LastCommitInfo | null
   triggerSync: () => void
+  /** Pause auto-pull (e.g. while conflict resolver modal is open). */
+  pausePull: () => void
+  /** Resume auto-pull after pausing. */
+  resumePull: () => void
 }
 
 export function useAutoSync({
@@ -37,11 +41,12 @@ export function useAutoSync({
   const [conflictFiles, setConflictFiles] = useState<string[]>([])
   const [lastCommitInfo, setLastCommitInfo] = useState<LastCommitInfo | null>(null)
   const syncingRef = useRef(false)
+  const pauseRef = useRef(false)
   const callbacksRef = useRef({ onVaultUpdated, onConflict, onToast })
   callbacksRef.current = { onVaultUpdated, onConflict, onToast }
 
   const performPull = useCallback(async () => {
-    if (syncingRef.current) return
+    if (syncingRef.current || pauseRef.current) return
     syncingRef.current = true
     setSyncStatus('syncing')
 
@@ -95,5 +100,8 @@ export function useAutoSync({
     return () => clearInterval(id)
   }, [performPull, intervalMinutes])
 
-  return { syncStatus, lastSyncTime, conflictFiles, lastCommitInfo, triggerSync: performPull }
+  const pausePull = useCallback(() => { pauseRef.current = true }, [])
+  const resumePull = useCallback(() => { pauseRef.current = false }, [])
+
+  return { syncStatus, lastSyncTime, conflictFiles, lastCommitInfo, triggerSync: performPull, pausePull, resumePull }
 }

src/hooks/useCommandRegistry.ts

@@ -18,6 +18,7 @@ interface CommandRegistryConfig {
   activeTabPath: string | null
   entries: VaultEntry[]
   modifiedCount: number
+  conflictCount?: number
 
   onQuickOpen: () => void
   onCreateNote: () => void
@@ -31,6 +32,7 @@ interface CommandRegistryConfig {
   onArchiveNote: (path: string) => void
   onUnarchiveNote: (path: string) => void
   onCommitPush: () => void
+  onResolveConflicts?: () => void
   onSetViewMode: (mode: ViewMode) => void
   onToggleInspector: () => void
   onToggleDiff?: () => void
@@ -180,10 +182,10 @@ export function buildThemeCommands(
 
 export function useCommandRegistry(config: CommandRegistryConfig): CommandAction[] {
   const {
-    activeTabPath, entries, modifiedCount,
+    activeTabPath, entries, modifiedCount, conflictCount,
     onQuickOpen, onCreateNote, onCreateNoteOfType, onSave, onOpenSettings,
     onTrashNote, onRestoreNote, onArchiveNote, onUnarchiveNote,
-    onCommitPush, onSetViewMode, onToggleInspector, onToggleDiff, onToggleRawEditor, onToggleAIChat, onOpenVault,
+    onCommitPush, onResolveConflicts, onSetViewMode, onToggleInspector, onToggleDiff, onToggleRawEditor, onToggleAIChat, onOpenVault,
     activeNoteModified,
     onZoomIn, onZoomOut, onZoomReset, zoomLevel,
     onSelect, onOpenDailyNote, onCloseTab,
@@ -236,6 +238,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
 
       // Git
       { id: 'commit-push', label: 'Commit & Push', group: 'Git', keywords: ['git', 'save', 'sync'], enabled: modifiedCount > 0, execute: onCommitPush },
+      { id: 'resolve-conflicts', label: 'Resolve Conflicts', group: 'Git', keywords: ['conflict', 'merge', 'git', 'sync'], enabled: (conflictCount ?? 0) > 0, execute: () => onResolveConflicts?.() },
       { id: 'view-changes', label: 'View Pending Changes', group: 'Git', keywords: ['modified', 'diff'], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'changes' }) },
 
       // View
@@ -257,15 +260,15 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
 
     return cmds
   }, [
-    hasActiveNote, activeTabPath, isArchived, isTrashed, modifiedCount, activeNoteModified,
+    hasActiveNote, activeTabPath, isArchived, isTrashed, modifiedCount, conflictCount, activeNoteModified,
     onQuickOpen, onCreateNote, onCreateNoteOfType, onCreateType, onSave, onOpenSettings,
     onTrashNote, onRestoreNote, onArchiveNote, onUnarchiveNote,
-    onCommitPush, onSetViewMode, onToggleInspector, onToggleDiff, onToggleRawEditor, onToggleAIChat, onOpenVault,
-    onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
+    onCommitPush, onResolveConflicts, onSetViewMode, onToggleInspector, onToggleDiff, onToggleRawEditor, onToggleAIChat, onOpenVault,
     onCheckForUpdates, isUpdating,
     onZoomIn, onZoomOut, onZoomReset, zoomLevel,
     onSelect, onOpenDailyNote, onCloseTab,
     onGoBack, onGoForward, canGoBack, canGoForward,
     vaultTypes, themes, activeThemeId, onSwitchTheme, onCreateTheme, onOpenTheme,
+    onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
   ])
 }

src/hooks/useConflictResolver.test.ts

@@ -0,0 +1,173 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest'
+import { renderHook, act } from '@testing-library/react'
+import { useConflictResolver } from './useConflictResolver'
+
+const mockInvokeFn = vi.fn()
+vi.mock('@tauri-apps/api/core', () => ({
+  invoke: (...args: unknown[]) => mockInvokeFn(...args),
+}))
+vi.mock('../mock-tauri', () => ({
+  isTauri: () => false,
+  mockInvoke: (...args: unknown[]) => mockInvokeFn(...args),
+}))
+
+describe('useConflictResolver', () => {
+  const onResolved = vi.fn()
+  const onToast = vi.fn()
+  const onOpenFile = vi.fn()
+
+  beforeEach(() => {
+    vi.clearAllMocks()
+    mockInvokeFn.mockResolvedValue(undefined)
+  })
+
+  function renderResolver(files: string[] = ['note.md', 'plan.md']) {
+    const hook = renderHook(() =>
+      useConflictResolver({
+        vaultPath: '/vault',
+        onResolved,
+        onToast,
+        onOpenFile,
+      }),
+    )
+    // Initialize files
+    act(() => { hook.result.current.initFiles(files) })
+    return hook
+  }
+
+  it('initializes file states from conflict files', () => {
+    const { result } = renderResolver()
+    expect(result.current.fileStates).toHaveLength(2)
+    expect(result.current.fileStates[0]).toEqual({ file: 'note.md', resolution: null, resolving: false })
+    expect(result.current.fileStates[1]).toEqual({ file: 'plan.md', resolution: null, resolving: false })
+    expect(result.current.allResolved).toBe(false)
+  })
+
+  it('resolves a file with ours strategy', async () => {
+    const { result } = renderResolver()
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+
+    expect(mockInvokeFn).toHaveBeenCalledWith('git_resolve_conflict', {
+      vaultPath: '/vault', file: 'note.md', strategy: 'ours',
+    })
+    expect(result.current.fileStates[0].resolution).toBe('ours')
+    expect(result.current.allResolved).toBe(false) // plan.md still unresolved
+  })
+
+  it('resolves a file with theirs strategy', async () => {
+    const { result } = renderResolver()
+
+    await act(async () => {
+      await result.current.resolveFile('plan.md', 'theirs')
+    })
+
+    expect(mockInvokeFn).toHaveBeenCalledWith('git_resolve_conflict', {
+      vaultPath: '/vault', file: 'plan.md', strategy: 'theirs',
+    })
+    expect(result.current.fileStates[1].resolution).toBe('theirs')
+  })
+
+  it('marks allResolved when all files are resolved', async () => {
+    const { result } = renderResolver()
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+    expect(result.current.allResolved).toBe(false)
+
+    await act(async () => {
+      await result.current.resolveFile('plan.md', 'theirs')
+    })
+    expect(result.current.allResolved).toBe(true)
+  })
+
+  it('sets manual resolution when opening in editor', () => {
+    const { result } = renderResolver()
+
+    act(() => { result.current.openInEditor('note.md') })
+
+    expect(onOpenFile).toHaveBeenCalledWith('note.md')
+    expect(result.current.fileStates[0].resolution).toBe('manual')
+  })
+
+  it('commits resolution and calls onResolved', async () => {
+    mockInvokeFn.mockImplementation((cmd: string) => {
+      if (cmd === 'git_commit_conflict_resolution') return Promise.resolve('Committed')
+      return Promise.resolve(undefined)
+    })
+
+    const { result } = renderResolver(['note.md'])
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+
+    await act(async () => {
+      await result.current.commitResolution()
+    })
+
+    expect(mockInvokeFn).toHaveBeenCalledWith('git_commit_conflict_resolution', { vaultPath: '/vault' })
+    expect(onResolved).toHaveBeenCalled()
+    expect(onToast).toHaveBeenCalledWith('Conflicts resolved — sync resumed')
+  })
+
+  it('does not commit when not all files are resolved', async () => {
+    const { result } = renderResolver()
+
+    await act(async () => {
+      await result.current.commitResolution()
+    })
+
+    expect(mockInvokeFn).not.toHaveBeenCalledWith('git_commit_conflict_resolution', expect.anything())
+  })
+
+  it('shows error when resolve fails', async () => {
+    mockInvokeFn.mockRejectedValueOnce(new Error('git checkout failed'))
+
+    const { result } = renderResolver()
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+
+    expect(result.current.error).toContain('Failed to resolve note.md')
+    expect(result.current.fileStates[0].resolution).toBeNull()
+  })
+
+  it('shows error when commit fails', async () => {
+    mockInvokeFn.mockImplementation((cmd: string) => {
+      if (cmd === 'git_commit_conflict_resolution') return Promise.reject(new Error('user.email not set'))
+      return Promise.resolve(undefined)
+    })
+
+    const { result } = renderResolver(['note.md'])
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+    await act(async () => {
+      await result.current.commitResolution()
+    })
+
+    expect(result.current.error).toContain('Commit failed')
+    expect(onResolved).not.toHaveBeenCalled()
+  })
+
+  it('resets state on initFiles', async () => {
+    const { result } = renderResolver(['note.md'])
+
+    await act(async () => {
+      await result.current.resolveFile('note.md', 'ours')
+    })
+    expect(result.current.fileStates[0].resolution).toBe('ours')
+
+    act(() => { result.current.initFiles(['other.md']) })
+
+    expect(result.current.fileStates).toHaveLength(1)
+    expect(result.current.fileStates[0]).toEqual({ file: 'other.md', resolution: null, resolving: false })
+    expect(result.current.error).toBeNull()
+  })
+})

src/hooks/useConflictResolver.ts

@@ -0,0 +1,96 @@
+import { useCallback, useState } from 'react'
+import { invoke } from '@tauri-apps/api/core'
+import { isTauri, mockInvoke } from '../mock-tauri'
+
+function tauriCall<T>(cmd: string, args: Record<string, unknown>): Promise<T> {
+  return isTauri() ? invoke<T>(cmd, args) : mockInvoke<T>(cmd, args)
+}
+
+export type FileResolution = 'ours' | 'theirs' | 'manual' | null
+
+export interface ConflictFileState {
+  file: string
+  resolution: FileResolution
+  resolving: boolean
+}
+
+interface UseConflictResolverConfig {
+  vaultPath: string
+  onResolved: () => void
+  onToast: (msg: string) => void
+  onOpenFile: (relativePath: string) => void
+}
+
+export function useConflictResolver({
+  vaultPath,
+  onResolved,
+  onToast,
+  onOpenFile,
+}: UseConflictResolverConfig) {
+  const [fileStates, setFileStates] = useState<ConflictFileState[]>([])
+  const [committing, setCommitting] = useState(false)
+  const [error, setError] = useState<string | null>(null)
+
+  const initFiles = useCallback((files: string[]) => {
+    setFileStates(files.map(file => ({ file, resolution: null, resolving: false })))
+    setError(null)
+    setCommitting(false)
+  }, [])
+
+  const resolveFile = useCallback(async (file: string, strategy: 'ours' | 'theirs') => {
+    setFileStates(prev => prev.map(f =>
+      f.file === file ? { ...f, resolving: true } : f
+    ))
+    setError(null)
+
+    try {
+      await tauriCall<void>('git_resolve_conflict', { vaultPath, file, strategy })
+      setFileStates(prev => prev.map(f =>
+        f.file === file ? { ...f, resolution: strategy, resolving: false } : f
+      ))
+    } catch (err) {
+      setFileStates(prev => prev.map(f =>
+        f.file === file ? { ...f, resolving: false } : f
+      ))
+      setError(`Failed to resolve ${file}: ${err}`)
+    }
+  }, [vaultPath])
+
+  const openInEditor = useCallback((file: string) => {
+    onOpenFile(file)
+    setFileStates(prev => prev.map(f =>
+      f.file === file ? { ...f, resolution: 'manual' } : f
+    ))
+  }, [onOpenFile])
+
+  const allResolved = fileStates.length > 0 && fileStates.every(f => f.resolution !== null)
+  const anyResolving = fileStates.some(f => f.resolving)
+
+  const commitResolution = useCallback(async () => {
+    if (!allResolved || committing) return
+    setCommitting(true)
+    setError(null)
+
+    try {
+      await tauriCall<string>('git_commit_conflict_resolution', { vaultPath })
+      onResolved()
+      onToast('Conflicts resolved — sync resumed')
+    } catch (err) {
+      setError(`Commit failed: ${err}`)
+    } finally {
+      setCommitting(false)
+    }
+  }, [vaultPath, allResolved, committing, onResolved, onToast])
+
+  return {
+    fileStates,
+    committing,
+    error,
+    allResolved,
+    anyResolving,
+    initFiles,
+    resolveFile,
+    openInEditor,
+    commitResolution,
+  }
+}

src/hooks/useDialogs.ts

@@ -8,6 +8,7 @@ export function useDialogs() {
   const [showSettings, setShowSettings] = useState(false)
   const [showGitHubVault, setShowGitHubVault] = useState(false)
   const [showSearch, setShowSearch] = useState(false)
+  const [showConflictResolver, setShowConflictResolver] = useState(false)
 
   const openCreateType = useCallback(() => setShowCreateTypeDialog(true), [])
   const closeCreateType = useCallback(() => setShowCreateTypeDialog(false), [])
@@ -22,6 +23,8 @@ export function useDialogs() {
   const toggleAIChat = useCallback(() => setShowAIChat((c) => !c), [])
   const openSearch = useCallback(() => setShowSearch(true), [])
   const closeSearch = useCallback(() => setShowSearch(false), [])
+  const openConflictResolver = useCallback(() => setShowConflictResolver(true), [])
+  const closeConflictResolver = useCallback(() => setShowConflictResolver(false), [])
 
   return {
     showCreateTypeDialog, openCreateType, closeCreateType,
@@ -31,5 +34,6 @@ export function useDialogs() {
     showSettings, openSettings, closeSettings,
     showGitHubVault, openGitHubVault, closeGitHubVault,
     showSearch, openSearch, closeSearch,
+    showConflictResolver, openConflictResolver, closeConflictResolver,
   }
 }

src/hooks/useEditorSaveWithLinks.ts

@@ -0,0 +1,32 @@
+import { useCallback, useRef } from 'react'
+import { useEditorSave } from './useEditorSave'
+import { extractOutgoingLinks } from '../utils/wikilinks'
+import type { VaultEntry } from '../types'
+
+export function useEditorSaveWithLinks(config: {
+  updateContent: (path: string, content: string) => void
+  updateEntry: (path: string, patch: Partial<VaultEntry>) => void
+  setTabs: Parameters<typeof useEditorSave>[0]['setTabs']
+  setToastMessage: (msg: string | null) => void
+  onAfterSave: () => void
+  onNotePersisted?: (path: string) => void
+}) {
+  const { updateContent, updateEntry } = config
+  const saveContent = useCallback((path: string, content: string) => {
+    updateContent(path, content)
+    updateEntry(path, { outgoingLinks: extractOutgoingLinks(content) })
+  }, [updateContent, updateEntry])
+  const editor = useEditorSave({ updateVaultContent: saveContent, setTabs: config.setTabs, setToastMessage: config.setToastMessage, onAfterSave: config.onAfterSave, onNotePersisted: config.onNotePersisted })
+  const { handleContentChange: rawOnChange } = editor
+  const prevLinksKeyRef = useRef('')
+  const handleContentChange = useCallback((path: string, content: string) => {
+    rawOnChange(path, content)
+    const links = extractOutgoingLinks(content)
+    const key = links.join('\0')
+    if (key !== prevLinksKeyRef.current) {
+      prevLinksKeyRef.current = key
+      updateEntry(path, { outgoingLinks: links })
+    }
+  }, [rawOnChange, updateEntry])
+  return { ...editor, handleContentChange }
+}

src/hooks/useIndexing.test.ts

@@ -0,0 +1,159 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest'
+import { renderHook, act, waitFor } from '@testing-library/react'
+import { useIndexing } from './useIndexing'
+
+vi.mock('../mock-tauri', () => ({
+  isTauri: () => false,
+  mockInvoke: vi.fn().mockImplementation((cmd: string) => {
+    if (cmd === 'get_index_status') {
+      return Promise.resolve({
+        available: true,
+        qmd_installed: true,
+        collection_exists: true,
+        indexed_count: 100,
+        embedded_count: 80,
+        pending_embed: 0,
+      })
+    }
+    if (cmd === 'start_indexing') return Promise.resolve(null)
+    if (cmd === 'trigger_incremental_index') return Promise.resolve(null)
+    return Promise.resolve(null)
+  }),
+}))
+
+const { mockInvoke } = await import('../mock-tauri') as { mockInvoke: ReturnType<typeof vi.fn> }
+
+describe('useIndexing', () => {
+  beforeEach(() => {
+    vi.clearAllMocks()
+  })
+
+  it('starts with idle progress', () => {
+    const { result } = renderHook(() => useIndexing('/vault'))
+    expect(result.current.progress.phase).toBe('idle')
+    expect(result.current.progress.done).toBe(false)
+  })
+
+  it('checks index status on mount', async () => {
+    renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('get_index_status', { vaultPath: '/vault' })
+    })
+  })
+
+  it('does not start indexing when collection exists and no pending embeds', async () => {
+    renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('get_index_status', { vaultPath: '/vault' })
+    })
+    expect(mockInvoke).not.toHaveBeenCalledWith('start_indexing', expect.anything())
+  })
+
+  it('starts indexing when collection is missing', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'get_index_status') {
+        return Promise.resolve({
+          available: true,
+          qmd_installed: true,
+          collection_exists: false,
+          indexed_count: 0,
+          embedded_count: 0,
+          pending_embed: 0,
+        })
+      }
+      return Promise.resolve(null)
+    })
+
+    const { result } = renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
+    })
+    expect(result.current.progress.phase).not.toBe('idle')
+  })
+
+  it('starts indexing when qmd is not installed', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'get_index_status') {
+        return Promise.resolve({
+          available: false,
+          qmd_installed: false,
+          collection_exists: false,
+          indexed_count: 0,
+          embedded_count: 0,
+          pending_embed: 0,
+        })
+      }
+      return Promise.resolve(null)
+    })
+
+    renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
+    })
+  })
+
+  it('starts indexing when pending embeds exist', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'get_index_status') {
+        return Promise.resolve({
+          available: true,
+          qmd_installed: true,
+          collection_exists: true,
+          indexed_count: 100,
+          embedded_count: 80,
+          pending_embed: 20,
+        })
+      }
+      return Promise.resolve(null)
+    })
+
+    renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(mockInvoke).toHaveBeenCalledWith('start_indexing', { vaultPath: '/vault' })
+    })
+  })
+
+  it('triggerIncrementalIndex calls the command', async () => {
+    const { result } = renderHook(() => useIndexing('/vault'))
+    await act(async () => {
+      await result.current.triggerIncrementalIndex()
+    })
+    expect(mockInvoke).toHaveBeenCalledWith('trigger_incremental_index', { vaultPath: '/vault' })
+  })
+
+  it('handles index status check failure gracefully', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'get_index_status') return Promise.reject(new Error('network error'))
+      return Promise.resolve(null)
+    })
+
+    const { result } = renderHook(() => useIndexing('/vault'))
+    // Should remain idle — not crash
+    await waitFor(() => {
+      expect(result.current.progress.phase).toBe('idle')
+    })
+  })
+
+  it('sets error phase when start_indexing fails', async () => {
+    mockInvoke.mockImplementation((cmd: string) => {
+      if (cmd === 'get_index_status') {
+        return Promise.resolve({
+          available: false,
+          qmd_installed: false,
+          collection_exists: false,
+          indexed_count: 0,
+          embedded_count: 0,
+          pending_embed: 0,
+        })
+      }
+      if (cmd === 'start_indexing') return Promise.reject(new Error('install failed'))
+      return Promise.resolve(null)
+    })
+
+    const { result } = renderHook(() => useIndexing('/vault'))
+    await waitFor(() => {
+      expect(result.current.progress.phase).toBe('error')
+    })
+    expect(result.current.progress.error).toContain('install failed')
+  })
+})

src/hooks/useIndexing.ts

@@ -0,0 +1,116 @@
+import { useState, useEffect, useCallback, useRef } from 'react'
+import { invoke } from '@tauri-apps/api/core'
+import { isTauri, mockInvoke } from '../mock-tauri'
+
+export interface IndexingProgress {
+  phase: 'idle' | 'installing' | 'scanning' | 'embedding' | 'complete' | 'error'
+  current: number
+  total: number
+  done: boolean
+  error: string | null
+}
+
+interface IndexStatus {
+  available: boolean
+  qmd_installed: boolean
+  collection_exists: boolean
+  indexed_count: number
+  embedded_count: number
+  pending_embed: number
+}
+
+const IDLE: IndexingProgress = { phase: 'idle', current: 0, total: 0, done: false, error: null }
+
+function invokeCmd<T>(cmd: string, args?: Record<string, unknown>): Promise<T> {
+  return isTauri() ? invoke<T>(cmd, args) : mockInvoke<T>(cmd, args)
+}
+
+export function useIndexing(vaultPath: string) {
+  const [progress, setProgress] = useState<IndexingProgress>(IDLE)
+  const indexingRef = useRef(false)
+  const vaultPathRef = useRef(vaultPath)
+
+  useEffect(() => { vaultPathRef.current = vaultPath }, [vaultPath])
+
+  // Listen for progress events from Rust
+  useEffect(() => {
+    if (!isTauri()) return
+
+    let cleanup: (() => void) | null = null
+
+    import('@tauri-apps/api/event').then(({ listen }) => {
+      const unlisten = listen<IndexingProgress>('indexing-progress', (event) => {
+        setProgress(event.payload)
+        if (event.payload.done) {
+          indexingRef.current = false
+        }
+      })
+      cleanup = () => { unlisten.then(fn => fn()) }
+    })
+
+    return () => { cleanup?.() }
+  }, [])
+
+  // Check index status and auto-trigger indexing on vault open
+  useEffect(() => {
+    if (!vaultPath) return
+    let cancelled = false
+
+    async function checkAndIndex() {
+      try {
+        const status = await invokeCmd<IndexStatus>('get_index_status', { vaultPath })
+        if (cancelled) return
+
+        // If qmd not installed or no collection or pending embeds, trigger indexing
+        const needsIndexing = !status.qmd_installed || !status.collection_exists || status.pending_embed > 0
+        if (needsIndexing && !indexingRef.current) {
+          indexingRef.current = true
+          setProgress({
+            phase: 'scanning',
+            current: 0,
+            total: status.indexed_count,
+            done: false,
+            error: null,
+          })
+          // Fire and forget — progress updates come via events
+          invokeCmd('start_indexing', { vaultPath }).catch((err) => {
+            if (!cancelled) {
+              setProgress({
+                phase: 'error',
+                current: 0,
+                total: 0,
+                done: true,
+                error: String(err),
+              })
+              indexingRef.current = false
+            }
+          })
+        }
+      } catch {
+        // get_index_status failed — likely qmd not available, non-fatal
+      }
+    }
+
+    checkAndIndex()
+    return () => { cancelled = true }
+  }, [vaultPath])
+
+  // Auto-dismiss the "complete" status after 5 seconds
+  useEffect(() => {
+    if (progress.phase === 'complete') {
+      const timer = setTimeout(() => setProgress(IDLE), 5000)
+      return () => clearTimeout(timer)
+    }
+  }, [progress.phase])
+
+  const triggerIncrementalIndex = useCallback(async () => {
+    if (indexingRef.current) return
+    try {
+      await invokeCmd('trigger_incremental_index', { vaultPath: vaultPathRef.current })
+    } catch {
+      // Incremental update failure is non-fatal
+    }
+  }, [])
+
+  return { progress, triggerIncrementalIndex }
+}

src/hooks/useNavigationGestures.ts

@@ -0,0 +1,52 @@
+import { useEffect } from 'react'
+
+/**
+ * Registers mouse button 3/4 (back/forward) and macOS trackpad two-finger
+ * horizontal swipe gestures for navigation.
+ */
+export function useNavigationGestures({
+  onGoBack,
+  onGoForward,
+}: {
+  onGoBack: () => void
+  onGoForward: () => void
+}) {
+  useEffect(() => {
+    const handleMouseBack = (e: MouseEvent) => {
+      if (e.button === 3) { e.preventDefault(); onGoBack() }
+      if (e.button === 4) { e.preventDefault(); onGoForward() }
+    }
+    window.addEventListener('mouseup', handleMouseBack)
+
+    // Trackpad swipe: accumulate horizontal wheel delta and trigger on threshold
+    let accumulatedDeltaX = 0
+    let resetTimer: ReturnType<typeof setTimeout> | null = null
+    const SWIPE_THRESHOLD = 120
+
+    const handleWheel = (e: WheelEvent) => {
+      // Only handle horizontal-dominant gestures (trackpad swipe)
+      if (Math.abs(e.deltaX) <= Math.abs(e.deltaY)) return
+      if (e.ctrlKey || e.metaKey) return // ignore pinch-zoom
+
+      accumulatedDeltaX += e.deltaX
+
+      if (resetTimer) clearTimeout(resetTimer)
+      resetTimer = setTimeout(() => { accumulatedDeltaX = 0 }, 300)
+
+      if (accumulatedDeltaX > SWIPE_THRESHOLD) {
+        accumulatedDeltaX = 0
+        onGoForward()
+      } else if (accumulatedDeltaX < -SWIPE_THRESHOLD) {
+        accumulatedDeltaX = 0
+        onGoBack()
+      }
+    }
+    window.addEventListener('wheel', handleWheel, { passive: true })
+
+    return () => {
+      window.removeEventListener('mouseup', handleMouseBack)
+      window.removeEventListener('wheel', handleWheel)
+      if (resetTimer) clearTimeout(resetTimer)
+    }
+  }, [onGoBack, onGoForward])
+}

src/mock-tauri/mock-handlers.ts

@@ -264,6 +264,9 @@ export const mockHandlers: Record<string, (args: any) => any> = {
   },
   create_getting_started_vault: () => '/Users/mock/Documents/Getting Started',
   register_mcp_tools: () => 'registered',
+  get_index_status: () => ({ available: true, qmd_installed: true, collection_exists: true, indexed_count: 100, embedded_count: 80, pending_embed: 0 }),
+  start_indexing: () => null,
+  trigger_incremental_index: () => null,
   list_themes: (): ThemeFile[] => [...mockThemes],
   get_theme: (args: { themeId: string }): ThemeFile => {
     const t = mockThemes.find(t => t.id === args.themeId)