feat(s1p2): add inotify-based filesystem write detection with external conflict tracking

v2/src-tauri/src/fs_watcher.rs

@@ -0,0 +1,216 @@
+// Filesystem write detection for project directories
+// Uses notify crate (inotify on Linux) to detect file modifications.
+// Emits Tauri events so frontend can detect external writes vs agent-managed writes.
+
+use notify::{Config, Event, EventKind, RecommendedWatcher, RecursiveMode, Watcher};
+use serde::Serialize;
+use std::collections::HashMap;
+use std::path::Path;
+use std::sync::Mutex;
+use std::time::{Duration, Instant};
+use tauri::Emitter;
+
+/// Payload emitted on fs-write-detected events
+#[derive(Clone, Serialize)]
+pub struct FsWritePayload {
+    pub project_id: String,
+    pub file_path: String,
+    pub timestamp_ms: u64,
+}
+
+/// Directories to skip when watching recursively
+const IGNORED_DIRS: &[&str] = &[
+    ".git",
+    "node_modules",
+    "target",
+    ".svelte-kit",
+    "dist",
+    "__pycache__",
+    ".next",
+    ".nuxt",
+    ".cache",
+    "build",
+];
+
+struct ProjectWatch {
+    _watcher: RecommendedWatcher,
+    _cwd: String,
+}
+
+pub struct ProjectFsWatcher {
+    watches: Mutex<HashMap<String, ProjectWatch>>,
+}
+
+impl ProjectFsWatcher {
+    pub fn new() -> Self {
+        Self {
+            watches: Mutex::new(HashMap::new()),
+        }
+    }
+
+    /// Start watching a project's CWD for file writes (Create, Modify, Rename).
+    /// Debounces events per-file (100ms) to avoid flooding on rapid writes.
+    pub fn watch_project(
+        &self,
+        app: &tauri::AppHandle,
+        project_id: &str,
+        cwd: &str,
+    ) -> Result<(), String> {
+        let cwd_path = Path::new(cwd);
+        if !cwd_path.is_dir() {
+            return Err(format!("Not a directory: {cwd}"));
+        }
+
+        let mut watches = self.watches.lock().unwrap();
+
+        // Don't duplicate — unwatch first if already watching
+        if watches.contains_key(project_id) {
+            drop(watches);
+            self.unwatch_project(project_id);
+            watches = self.watches.lock().unwrap();
+        }
+
+        let app_handle = app.clone();
+        let project_id_owned = project_id.to_string();
+        let cwd_owned = cwd.to_string();
+
+        // Per-file debounce state
+        let debounce: std::sync::Arc<Mutex<HashMap<String, Instant>>> =
+            std::sync::Arc::new(Mutex::new(HashMap::new()));
+        let debounce_duration = Duration::from_millis(100);
+
+        let mut watcher = RecommendedWatcher::new(
+            move |res: Result<Event, notify::Error>| {
+                let event = match res {
+                    Ok(e) => e,
+                    Err(_) => return,
+                };
+
+                // Only care about file writes (create, modify, rename-to)
+                let is_write = matches!(
+                    event.kind,
+                    EventKind::Create(_) | EventKind::Modify(_)
+                );
+                if !is_write {
+                    return;
+                }
+
+                for path in &event.paths {
+                    // Skip directories
+                    if path.is_dir() {
+                        continue;
+                    }
+
+                    let path_str = path.to_string_lossy().to_string();
+
+                    // Skip ignored directories
+                    if should_ignore_path(&path_str) {
+                        continue;
+                    }
+
+                    // Debounce: skip if same file was emitted within debounce window
+                    let now = Instant::now();
+                    let mut db = debounce.lock().unwrap();
+                    if let Some(last) = db.get(&path_str) {
+                        if now.duration_since(*last) < debounce_duration {
+                            continue;
+                        }
+                    }
+                    db.insert(path_str.clone(), now);
+                    // Prune old debounce entries (keep map from growing unbounded)
+                    if db.len() > 1000 {
+                        let max_age = debounce_duration * 10;
+                        db.retain(|_, v| now.duration_since(*v) < max_age);
+                    }
+                    drop(db);
+
+                    let timestamp_ms = std::time::SystemTime::now()
+                        .duration_since(std::time::UNIX_EPOCH)
+                        .unwrap_or_default()
+                        .as_millis() as u64;
+
+                    let _ = app_handle.emit(
+                        "fs-write-detected",
+                        FsWritePayload {
+                            project_id: project_id_owned.clone(),
+                            file_path: path_str,
+                            timestamp_ms,
+                        },
+                    );
+                }
+            },
+            Config::default(),
+        )
+        .map_err(|e| format!("Failed to create fs watcher: {e}"))?;
+
+        watcher
+            .watch(cwd_path, RecursiveMode::Recursive)
+            .map_err(|e| format!("Failed to watch directory: {e}"))?;
+
+        log::info!("Started fs watcher for project {project_id} at {cwd}");
+
+        watches.insert(
+            project_id.to_string(),
+            ProjectWatch {
+                _watcher: watcher,
+                _cwd: cwd_owned,
+            },
+        );
+
+        Ok(())
+    }
+
+    /// Stop watching a project's CWD
+    pub fn unwatch_project(&self, project_id: &str) {
+        let mut watches = self.watches.lock().unwrap();
+        if watches.remove(project_id).is_some() {
+            log::info!("Stopped fs watcher for project {project_id}");
+        }
+    }
+
+}
+
+/// Check if a path contains any ignored directory component
+fn should_ignore_path(path: &str) -> bool {
+    for component in Path::new(path).components() {
+        if let std::path::Component::Normal(name) = component {
+            let name_str = name.to_string_lossy();
+            if IGNORED_DIRS.contains(&name_str.as_ref()) {
+                return true;
+            }
+        }
+    }
+    false
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_should_ignore_git() {
+        assert!(should_ignore_path("/home/user/project/.git/objects/abc"));
+        assert!(should_ignore_path("/home/user/project/.git/HEAD"));
+    }
+
+    #[test]
+    fn test_should_ignore_node_modules() {
+        assert!(should_ignore_path("/project/node_modules/pkg/index.js"));
+    }
+
+    #[test]
+    fn test_should_ignore_target() {
+        assert!(should_ignore_path("/project/target/debug/build/foo"));
+    }
+
+    #[test]
+    fn test_should_not_ignore_src() {
+        assert!(!should_ignore_path("/project/src/main.rs"));
+        assert!(!should_ignore_path("/project/src/lib/stores/health.svelte.ts"));
+    }
+
+    #[test]
+    fn test_should_not_ignore_root_file() {
+        assert!(!should_ignore_path("/project/Cargo.toml"));
+    }
+}

v2/src-tauri/src/lib.rs

@@ -1,5 +1,6 @@
 mod ctx;
 mod event_sink;
+mod fs_watcher;
 mod groups;
 mod pty;
 mod remote;
@@ -15,6 +16,7 @@ use pty::{PtyManager, PtyOptions};
 use remote::{RemoteManager, RemoteMachineConfig};
 use session::{Session, SessionDb, LayoutState, SshSession, AgentMessageRecord, ProjectAgentState};
 use sidecar::{AgentQueryOptions, SidecarConfig, SidecarManager};
+use fs_watcher::ProjectFsWatcher;
 use watcher::FileWatcherManager;
 use std::sync::Arc;
 use tauri::{Manager, State};
@@ -24,6 +26,7 @@ struct AppState {
     sidecar_manager: Arc<SidecarManager>,
     session_db: Arc<SessionDb>,
     file_watcher: Arc<FileWatcherManager>,
+    fs_watcher: Arc<ProjectFsWatcher>,
     ctx_db: Arc<CtxDb>,
     remote_manager: Arc<RemoteManager>,
     _telemetry: telemetry::TelemetryGuard,
@@ -111,6 +114,23 @@ fn file_read(state: State<'_, AppState>, path: String) -> Result<String, String>
     state.file_watcher.read_file(&path)
 }
 
+// --- Project filesystem watcher commands (S-1 Phase 2) ---
+
+#[tauri::command]
+fn fs_watch_project(
+    app: tauri::AppHandle,
+    state: State<'_, AppState>,
+    project_id: String,
+    cwd: String,
+) -> Result<(), String> {
+    state.fs_watcher.watch_project(&app, &project_id, &cwd)
+}
+
+#[tauri::command]
+fn fs_unwatch_project(state: State<'_, AppState>, project_id: String) {
+    state.fs_watcher.unwatch_project(&project_id);
+}
+
 // --- Session persistence commands ---
 
 #[tauri::command]
@@ -736,6 +756,8 @@ pub fn run() {
             file_watch,
             file_unwatch,
             file_read,
+            fs_watch_project,
+            fs_unwatch_project,
             session_list,
             session_save,
             session_delete,
@@ -831,6 +853,7 @@ pub fn run() {
             );
 
             let file_watcher = Arc::new(FileWatcherManager::new());
+            let fs_watcher = Arc::new(ProjectFsWatcher::new());
             let ctx_db = Arc::new(CtxDb::new());
             let remote_manager = Arc::new(RemoteManager::new());
 
@@ -845,6 +868,7 @@ pub fn run() {
                 sidecar_manager,
                 session_db,
                 file_watcher,
+                fs_watcher,
                 ctx_db,
                 remote_manager,
                 _telemetry: telemetry_guard,

v2/src/lib/adapters/fs-watcher-bridge.ts

@@ -0,0 +1,28 @@
+// Filesystem watcher bridge — listens for inotify-based write events from Rust
+// Part of S-1 Phase 2: real-time filesystem write detection
+
+import { invoke } from '@tauri-apps/api/core';
+import { listen, type UnlistenFn } from '@tauri-apps/api/event';
+
+export interface FsWriteEvent {
+  project_id: string;
+  file_path: string;
+  timestamp_ms: number;
+}
+
+/** Start watching a project's CWD for filesystem writes */
+export function fsWatchProject(projectId: string, cwd: string): Promise<void> {
+  return invoke('fs_watch_project', { projectId, cwd });
+}
+
+/** Stop watching a project's CWD */
+export function fsUnwatchProject(projectId: string): Promise<void> {
+  return invoke('fs_unwatch_project', { projectId });
+}
+
+/** Listen for filesystem write events from all watched projects */
+export function onFsWriteDetected(
+  callback: (event: FsWriteEvent) => void,
+): Promise<UnlistenFn> {
+  return listen<FsWriteEvent>('fs-write-detected', (e) => callback(e.payload));
+}

v2/src/lib/components/Workspace/ProjectBox.svelte

@@ -1,4 +1,5 @@
 <script lang="ts">
+  import { onDestroy } from 'svelte';
   import type { ProjectConfig } from '../../types/groups';
   import { PROJECT_ACCENTS } from '../../types/groups';
   import ProjectHeader from './ProjectHeader.svelte';
@@ -12,6 +13,9 @@
   import MemoriesTab from './MemoriesTab.svelte';
   import { getTerminalTabs } from '../../stores/workspace.svelte';
   import { getProjectHealth } from '../../stores/health.svelte';
+  import { fsWatchProject, fsUnwatchProject, onFsWriteDetected } from '../../adapters/fs-watcher-bridge';
+  import { recordExternalWrite } from '../../stores/conflicts.svelte';
+  import { notify } from '../../stores/notifications.svelte';
 
   interface Props {
     project: ProjectConfig;
@@ -47,6 +51,35 @@
   function toggleTerminal() {
     terminalExpanded = !terminalExpanded;
   }
+
+  // S-1 Phase 2: start filesystem watcher for this project's CWD
+  $effect(() => {
+    const cwd = project.cwd;
+    const projectId = project.id;
+    if (!cwd) return;
+
+    // Start watching
+    fsWatchProject(projectId, cwd).catch(e =>
+      console.warn(`Failed to start fs watcher for ${projectId}:`, e)
+    );
+
+    // Listen for fs write events (filter to this project)
+    let unlisten: (() => void) | null = null;
+    onFsWriteDetected((event) => {
+      if (event.project_id !== projectId) return;
+      const isNew = recordExternalWrite(projectId, event.file_path, event.timestamp_ms);
+      if (isNew) {
+        const shortName = event.file_path.split('/').pop() ?? event.file_path;
+        notify('warning', `External write: ${shortName} — file also modified by agent`);
+      }
+    }).then(fn => { unlisten = fn; });
+
+    return () => {
+      // Cleanup: stop watching on unmount or project change
+      fsUnwatchProject(projectId).catch(() => {});
+      unlisten?.();
+    };
+  });
 </script>
 
 <div

v2/src/lib/components/Workspace/ProjectHeader.svelte

@@ -81,13 +81,23 @@
     <span class="project-id">({project.identifier})</span>
   </div>
   <div class="header-info">
-    {#if health && health.fileConflictCount > 0}
+    {#if health && health.externalConflictCount > 0}
       <button
-        class="info-conflict"
-        title="{health.fileConflictCount} file conflict{health.fileConflictCount > 1 ? 's' : ''} — click to dismiss"
+        class="info-conflict info-conflict-external"
+        title="{health.externalConflictCount} external write{health.externalConflictCount > 1 ? 's' : ''} — files modified outside agent — click to dismiss"
         onclick={(e: MouseEvent) => { e.stopPropagation(); acknowledgeConflicts(project.id); }}
       >
-        ⚠ {health.fileConflictCount} conflict{health.fileConflictCount > 1 ? 's' : ''} ✕
+        ⚡ {health.externalConflictCount} ext write{health.externalConflictCount > 1 ? 's' : ''} ✕
+      </button>
+      <span class="info-sep">·</span>
+    {/if}
+    {#if health && health.fileConflictCount - (health.externalConflictCount ?? 0) > 0}
+      <button
+        class="info-conflict"
+        title="{health.fileConflictCount - (health.externalConflictCount ?? 0)} agent conflict{health.fileConflictCount - (health.externalConflictCount ?? 0) > 1 ? 's' : ''} — click to dismiss"
+        onclick={(e: MouseEvent) => { e.stopPropagation(); acknowledgeConflicts(project.id); }}
+      >
+        ⚠ {health.fileConflictCount - (health.externalConflictCount ?? 0)} conflict{health.fileConflictCount - (health.externalConflictCount ?? 0) > 1 ? 's' : ''} ✕
       </button>
       <span class="info-sep">·</span>
     {/if}
@@ -253,6 +263,15 @@
     background: color-mix(in srgb, var(--ctp-red) 25%, transparent);
   }
 
+  .info-conflict-external {
+    color: var(--ctp-peach);
+    background: color-mix(in srgb, var(--ctp-peach) 12%, transparent);
+  }
+
+  .info-conflict-external:hover {
+    background: color-mix(in srgb, var(--ctp-peach) 25%, transparent);
+  }
+
   .info-profile {
     font-size: 0.65rem;
     color: var(--ctp-blue);

v2/src/lib/stores/conflicts.svelte.ts

@@ -1,6 +1,10 @@
 // File overlap conflict detection — Svelte 5 runes
 // Tracks which files each agent session writes to per project.
 // Detects when two or more sessions write to the same file (file overlap conflict).
+// Also detects external filesystem writes (S-1 Phase 2) via inotify events.
+
+/** Sentinel session ID for external (non-agent) writes */
+export const EXTERNAL_SESSION_ID = '__external__';
 
 export interface FileConflict {
   /** Absolute file path */
@@ -11,6 +15,8 @@ export interface FileConflict {
   sessionIds: string[];
   /** Timestamp of most recent write */
   lastWriteTs: number;
+  /** True if this conflict involves an external (non-agent) writer */
+  isExternal: boolean;
 }
 
 export interface ProjectConflicts {
@@ -19,6 +25,8 @@ export interface ProjectConflicts {
   conflicts: FileConflict[];
   /** Total conflicting files */
   conflictCount: number;
+  /** Number of files with external write conflicts */
+  externalConflictCount: number;
 }
 
 // --- State ---
@@ -37,6 +45,13 @@ let acknowledgedFiles = $state<Map<string, Set<string>>>(new Map());
 // sessionId -> worktree path (null = main working tree)
 let sessionWorktrees = $state<Map<string, string | null>>(new Map());
 
+// projectId -> filePath -> timestamp of most recent agent write (for external write heuristic)
+let agentWriteTimestamps = $state<Map<string, Map<string, number>>>(new Map());
+
+// Time window: if an fs event arrives within this window after an agent tool_call write,
+// it's attributed to the agent (suppressed). Otherwise it's external.
+const AGENT_WRITE_GRACE_MS = 2000;
+
 // --- Public API ---
 
 /** Register the worktree path for a session (null = main working tree) */
@@ -62,6 +77,16 @@ export function recordFileWrite(projectId: string, sessionId: string, filePath:
     projectFileWrites.set(projectId, projectMap);
   }
 
+  // Track agent write timestamp for external write heuristic
+  if (sessionId !== EXTERNAL_SESSION_ID) {
+    let tsMap = agentWriteTimestamps.get(projectId);
+    if (!tsMap) {
+      tsMap = new Map();
+      agentWriteTimestamps.set(projectId, tsMap);
+    }
+    tsMap.set(filePath, Date.now());
+  }
+
   let entry = projectMap.get(filePath);
   const hadConflict = entry ? countRealConflictSessions(entry, sessionId) >= 2 : false;
 
@@ -88,6 +113,47 @@ export function recordFileWrite(projectId: string, sessionId: string, filePath:
   return isNewConflict;
 }
 
+/**
+ * Record an external filesystem write detected via inotify.
+ * Uses timing heuristic: if an agent wrote this file within AGENT_WRITE_GRACE_MS,
+ * the write is attributed to the agent and suppressed.
+ * Returns true if this creates a new external write conflict.
+ */
+export function recordExternalWrite(projectId: string, filePath: string, timestampMs: number): boolean {
+  // Timing heuristic: check if any agent recently wrote this file
+  const tsMap = agentWriteTimestamps.get(projectId);
+  if (tsMap) {
+    const lastAgentWrite = tsMap.get(filePath);
+    if (lastAgentWrite && (timestampMs - lastAgentWrite) < AGENT_WRITE_GRACE_MS) {
+      // This is likely our agent's write — suppress
+      return false;
+    }
+  }
+
+  // Check if any agent session has written this file (for conflict to be meaningful)
+  const projectMap = projectFileWrites.get(projectId);
+  if (!projectMap) return false; // No agent writes at all — not a conflict
+  const entry = projectMap.get(filePath);
+  if (!entry || entry.sessionIds.size === 0) return false; // No agent wrote this file
+
+  // Record external write as a conflict
+  return recordFileWrite(projectId, EXTERNAL_SESSION_ID, filePath);
+}
+
+/** Get the count of external write conflicts for a project */
+export function getExternalConflictCount(projectId: string): number {
+  const projectMap = projectFileWrites.get(projectId);
+  if (!projectMap) return 0;
+  const ackSet = acknowledgedFiles.get(projectId);
+  let count = 0;
+  for (const [filePath, entry] of projectMap) {
+    if (entry.sessionIds.has(EXTERNAL_SESSION_ID) && !(ackSet?.has(filePath))) {
+      count++;
+    }
+  }
+  return count;
+}
+
 /**
  * Count sessions that are in a real conflict with the given session
  * (same worktree or both in main tree). Returns total including the session itself.
@@ -105,24 +171,28 @@ function countRealConflictSessions(entry: FileWriteEntry, forSessionId: string):
 /** Get all conflicts for a project (excludes acknowledged and worktree-suppressed) */
 export function getProjectConflicts(projectId: string): ProjectConflicts {
   const projectMap = projectFileWrites.get(projectId);
-  if (!projectMap) return { projectId, conflicts: [], conflictCount: 0 };
+  if (!projectMap) return { projectId, conflicts: [], conflictCount: 0, externalConflictCount: 0 };
 
   const ackSet = acknowledgedFiles.get(projectId);
   const conflicts: FileConflict[] = [];
+  let externalConflictCount = 0;
   for (const [filePath, entry] of projectMap) {
     if (hasRealConflict(entry) && !(ackSet?.has(filePath))) {
+      const isExternal = entry.sessionIds.has(EXTERNAL_SESSION_ID);
+      if (isExternal) externalConflictCount++;
       conflicts.push({
         filePath,
         shortName: filePath.split('/').pop() ?? filePath,
         sessionIds: Array.from(entry.sessionIds),
         lastWriteTs: entry.lastWriteTs,
+        isExternal,
       });
     }
   }
 
   // Most recent conflicts first
   conflicts.sort((a, b) => b.lastWriteTs - a.lastWriteTs);
-  return { projectId, conflicts, conflictCount: conflicts.length };
+  return { projectId, conflicts, conflictCount: conflicts.length, externalConflictCount };
 }
 
 /** Check if a project has any unacknowledged real conflicts */
@@ -200,6 +270,7 @@ export function clearSessionWrites(projectId: string, sessionId: string): void {
 export function clearProjectConflicts(projectId: string): void {
   projectFileWrites.delete(projectId);
   acknowledgedFiles.delete(projectId);
+  agentWriteTimestamps.delete(projectId);
 }
 
 /** Clear all conflict state */
@@ -207,4 +278,5 @@ export function clearAllConflicts(): void {
   projectFileWrites = new Map();
   acknowledgedFiles = new Map();
   sessionWorktrees = new Map();
+  agentWriteTimestamps = new Map();
 }

v2/src/lib/stores/conflicts.test.ts

@@ -1,7 +1,9 @@
 import { describe, it, expect, beforeEach, vi, afterEach } from 'vitest';
 import {
   recordFileWrite,
+  recordExternalWrite,
   getProjectConflicts,
+  getExternalConflictCount,
   hasConflicts,
   getTotalConflictCount,
   clearSessionWrites,
@@ -9,6 +11,7 @@ import {
   clearAllConflicts,
   acknowledgeConflicts,
   setSessionWorktree,
+  EXTERNAL_SESSION_ID,
 } from './conflicts.svelte';
 
 beforeEach(() => {
@@ -235,4 +238,98 @@ describe('conflicts store', () => {
       expect(hasConflicts('proj-1')).toBe(true);
     });
   });
+
+  describe('external write detection (S-1 Phase 2)', () => {
+    it('suppresses external write within grace period after agent write', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/main.ts');
+      // External write arrives 500ms later — within 2s grace period
+      vi.setSystemTime(1500);
+      const result = recordExternalWrite('proj-1', '/src/main.ts', 1500);
+      expect(result).toBe(false);
+      expect(getExternalConflictCount('proj-1')).toBe(0);
+      vi.useRealTimers();
+    });
+
+    it('detects external write outside grace period', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/main.ts');
+      // External write arrives 3s later — outside 2s grace period
+      vi.setSystemTime(4000);
+      const result = recordExternalWrite('proj-1', '/src/main.ts', 4000);
+      expect(result).toBe(true);
+      expect(getExternalConflictCount('proj-1')).toBe(1);
+      vi.useRealTimers();
+    });
+
+    it('ignores external write to file no agent has written', () => {
+      recordFileWrite('proj-1', 'sess-a', '/src/other.ts');
+      const result = recordExternalWrite('proj-1', '/src/unrelated.ts', Date.now());
+      expect(result).toBe(false);
+    });
+
+    it('ignores external write for project with no agent writes', () => {
+      const result = recordExternalWrite('proj-1', '/src/main.ts', Date.now());
+      expect(result).toBe(false);
+    });
+
+    it('marks conflict as external in getProjectConflicts', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/main.ts');
+      vi.setSystemTime(4000);
+      recordExternalWrite('proj-1', '/src/main.ts', 4000);
+      const result = getProjectConflicts('proj-1');
+      expect(result.conflictCount).toBe(1);
+      expect(result.externalConflictCount).toBe(1);
+      expect(result.conflicts[0].isExternal).toBe(true);
+      expect(result.conflicts[0].sessionIds).toContain(EXTERNAL_SESSION_ID);
+      vi.useRealTimers();
+    });
+
+    it('external conflicts can be acknowledged', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/main.ts');
+      vi.setSystemTime(4000);
+      recordExternalWrite('proj-1', '/src/main.ts', 4000);
+      expect(hasConflicts('proj-1')).toBe(true);
+      acknowledgeConflicts('proj-1');
+      expect(hasConflicts('proj-1')).toBe(false);
+      expect(getExternalConflictCount('proj-1')).toBe(0);
+      vi.useRealTimers();
+    });
+
+    it('clearAllConflicts clears external write timestamps', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/main.ts');
+      clearAllConflicts();
+      // After clearing, external writes should not create conflicts (no agent writes tracked)
+      vi.setSystemTime(4000);
+      const result = recordExternalWrite('proj-1', '/src/main.ts', 4000);
+      expect(result).toBe(false);
+      vi.useRealTimers();
+    });
+
+    it('external conflict coexists with agent-agent conflict', () => {
+      vi.useFakeTimers();
+      vi.setSystemTime(1000);
+      recordFileWrite('proj-1', 'sess-a', '/src/agent.ts');
+      recordFileWrite('proj-1', 'sess-b', '/src/agent.ts');
+      recordFileWrite('proj-1', 'sess-a', '/src/ext.ts');
+      vi.setSystemTime(4000);
+      recordExternalWrite('proj-1', '/src/ext.ts', 4000);
+      const result = getProjectConflicts('proj-1');
+      expect(result.conflictCount).toBe(2);
+      expect(result.externalConflictCount).toBe(1);
+      const extConflict = result.conflicts.find(c => c.isExternal);
+      const agentConflict = result.conflicts.find(c => !c.isExternal);
+      expect(extConflict?.filePath).toBe('/src/ext.ts');
+      expect(agentConflict?.filePath).toBe('/src/agent.ts');
+      vi.useRealTimers();
+    });
+  });
 });

v2/src/lib/stores/health.svelte.ts

@@ -23,6 +23,8 @@ export interface ProjectHealth {
   contextPressure: number | null;
   /** Number of file conflicts (2+ agents writing same file) */
   fileConflictCount: number;
+  /** Number of external write conflicts (filesystem writes by non-agent processes) */
+  externalConflictCount: number;
   /** Attention urgency score (higher = more urgent, 0 = no attention needed) */
   attentionScore: number;
   /** Human-readable attention reason */
@@ -235,6 +237,7 @@ function computeHealth(tracker: ProjectTracker, now: number): ProjectHealth {
   // File conflicts
   const conflicts = getProjectConflicts(tracker.projectId);
   const fileConflictCount = conflicts.conflictCount;
+  const externalConflictCount = conflicts.externalConflictCount;
 
   // Attention scoring — highest-priority signal wins
   let attentionScore = 0;
@@ -252,7 +255,8 @@ function computeHealth(tracker: ProjectTracker, now: number): ProjectHealth {
     attentionReason = `Context ${Math.round(contextPressure * 100)}% — near limit`;
   } else if (fileConflictCount > 0) {
     attentionScore = SCORE_FILE_CONFLICT;
-    attentionReason = `${fileConflictCount} file conflict${fileConflictCount > 1 ? 's' : ''} — agents writing same file`;
+    const extNote = externalConflictCount > 0 ? ` (${externalConflictCount} external)` : '';
+    attentionReason = `${fileConflictCount} file conflict${fileConflictCount > 1 ? 's' : ''}${extNote}`;
   } else if (contextPressure !== null && contextPressure > 0.75) {
     attentionScore = SCORE_CONTEXT_HIGH;
     attentionReason = `Context ${Math.round(contextPressure * 100)}%`;
@@ -267,6 +271,7 @@ function computeHealth(tracker: ProjectTracker, now: number): ProjectHealth {
     burnRatePerHour,
     contextPressure,
     fileConflictCount,
+    externalConflictCount,
     attentionScore,
     attentionReason,
   };