diff --git a/src/crates/core/src/agentic/tools/registry.rs b/src/crates/core/src/agentic/tools/registry.rs
index ccf81f3c..14a52b26 100644
--- a/src/crates/core/src/agentic/tools/registry.rs
+++ b/src/crates/core/src/agentic/tools/registry.rs
@@ -49,7 +49,7 @@ impl ToolRegistry {
                 );
             }
 
-            self.tools.insert(name.clone(), tool);
+            self.register_tool(tool);
             debug!("MCP tool registered: tool_name={}", name);
         }
 
@@ -146,6 +146,9 @@ impl ToolRegistry {
 
     /// Register a single tool
     pub fn register_tool(&mut self, tool: Arc<dyn Tool>) {
+        // Snapshot-aware wrapping happens once at registration time so every
+        // subsequent lookup returns the same runtime implementation.
+        let tool = crate::service::snapshot::wrap_tool_for_snapshot_tracking(tool);
         let name = tool.name().to_string();
         self.tools.insert(name, tool);
     }
@@ -173,6 +176,7 @@ impl ToolRegistry {
 #[cfg(test)]
 mod tests {
     use super::create_tool_registry;
+    use serde_json::json;
 
     #[test]
     fn registry_includes_webfetch_tool() {
@@ -185,27 +189,32 @@ mod tests {
         let registry = create_tool_registry();
         assert!(registry.get_tool("Cron").is_some());
     }
+
+    #[test]
+    fn registry_wraps_file_modification_tools_for_snapshot_tracking() {
+        let registry = create_tool_registry();
+        let tool = registry
+            .get_tool("Write")
+            .expect("Write tool should be registered");
+
+        let assistant_text = tool.render_result_for_assistant(&json!({
+            "success": true,
+            "file_path": "E:/Projects/demo.txt"
+        }));
+
+        assert!(
+            assistant_text.contains("snapshot system"),
+            "expected snapshot wrapper text, got: {}",
+            assistant_text
+        );
+    }
 }
 
-/// Get all tools
-/// If you need **always include** MCP tools, use [get_all_registered_tools]
+/// Get all tools from the snapshot-aware global registry.
 pub async fn get_all_tools() -> Vec<Arc<dyn Tool>> {
     let registry = get_global_tool_registry();
     let registry_lock = registry.read().await;
-    let all_tools = registry_lock.get_all_tools();
-    let wrapped_tools = crate::service::snapshot::get_snapshot_wrapped_tools();
-    let file_tool_names: std::collections::HashSet<String> = wrapped_tools
-        .iter()
-        .map(|tool| tool.name().to_string())
-        .collect();
-
-    let mut result = wrapped_tools;
-    for tool in all_tools {
-        if !file_tool_names.contains(tool.name()) {
-            result.push(tool);
-        }
-    }
-    result
+    registry_lock.get_all_tools()
 }
 
 /// Get readonly tools
@@ -243,22 +252,9 @@ pub fn get_global_tool_registry() -> Arc<TokioRwLock<ToolRegistry>> {
         .clone()
 }
 
-/// Get all registered tools (**always include** dynamically registered MCP tools)
+/// Backward-compatible alias for callers that expect MCP tools to be included.
 pub async fn get_all_registered_tools() -> Vec<Arc<dyn Tool>> {
-    let registry = get_global_tool_registry();
-    let registry_lock = registry.read().await;
-    let all_tools = registry_lock.get_all_tools();
-    let wrapped_tools = crate::service::snapshot::get_snapshot_wrapped_tools();
-    let file_tool_names: std::collections::HashSet<String> =
-        wrapped_tools.iter().map(|t| t.name().to_string()).collect();
-
-    let mut result = wrapped_tools;
-    for tool in all_tools {
-        if !file_tool_names.contains(tool.name()) {
-            result.push(tool);
-        }
-    }
-    result
+    get_all_tools().await
 }
 
 /// Get all registered tool names
diff --git a/src/crates/core/src/service/snapshot/manager.rs b/src/crates/core/src/service/snapshot/manager.rs
index 208da6e2..b0502e95 100644
--- a/src/crates/core/src/service/snapshot/manager.rs
+++ b/src/crates/core/src/service/snapshot/manager.rs
@@ -7,7 +7,7 @@ use crate::service::snapshot::types::{
 use async_trait::async_trait;
 use log::{debug, error, info, warn};
 use serde_json::Value;
-use std::collections::{HashMap, HashSet};
+use std::collections::HashMap;
 use std::path::{Path, PathBuf};
 use std::sync::{Arc, OnceLock, RwLock as StdRwLock};
 use tokio::sync::RwLock;
@@ -17,9 +17,6 @@ use tokio::sync::RwLock;
 /// Manages all components of the snapshot system.
 pub struct SnapshotManager {
     snapshot_service: Arc<RwLock<SnapshotService>>,
-    original_tools: Vec<Arc<dyn Tool>>,
-    file_modification_tools: HashSet<String>,
-    initialized: bool,
 }
 
 impl SnapshotManager {
@@ -36,56 +33,7 @@ impl SnapshotManager {
         let mut snapshot_service = SnapshotService::new(workspace_dir, config);
         snapshot_service.initialize().await?;
         let snapshot_service = Arc::new(RwLock::new(snapshot_service));
-
-        let original_tools = ToolRegistry::new().get_all_tools();
-
-        let file_modification_tools = [
-            "Write",
-            "Edit",
-            "Delete",
-            "write_file",
-            "edit_file",
-            "create_file",
-            "delete_file",
-            "rename_file",
-            "move_file",
-        ]
-        .iter()
-        .map(|s| s.to_string())
-        .collect();
-
-        Ok(Self {
-            snapshot_service,
-            original_tools,
-            file_modification_tools,
-            initialized: true,
-        })
-    }
-
-    /// Returns whether the tool modifies files.
-    fn is_file_modification_tool(&self, tool_name: &str) -> bool {
-        self.file_modification_tools.contains(tool_name)
-    }
-
-    /// Returns wrapped tool list.
-    pub fn get_wrapped_tools(&self) -> Vec<Arc<dyn Tool>> {
-        if !self.initialized {
-            error!("Snapshot manager not initialized");
-            return vec![];
-        }
-
-        let mut wrapped_tools: Vec<Arc<dyn Tool>> = Vec::new();
-
-        for tool in &self.original_tools {
-            if self.is_file_modification_tool(tool.name()) {
-                let wrapped_tool: Arc<dyn Tool> = Arc::new(WrappedTool::new(tool.clone()));
-                wrapped_tools.push(wrapped_tool);
-            } else {
-                wrapped_tools.push(tool.clone());
-            }
-        }
-
-        wrapped_tools
+        Ok(Self { snapshot_service })
     }
 
     /// Records a file change.
@@ -340,18 +288,20 @@ fn snapshot_managers() -> &'static StdRwLock<HashMap<PathBuf, Arc<SnapshotManage
     SNAPSHOT_MANAGERS.get_or_init(|| StdRwLock::new(HashMap::new()))
 }
 
+/// Ensures the registry always exposes the same tool implementation that will be
+/// executed at runtime. File-modifying tools are wrapped once at registration time
+/// so tool definitions, permission checks, and execution all share one source of truth.
+pub fn wrap_tool_for_snapshot_tracking(tool: Arc<dyn Tool>) -> Arc<dyn Tool> {
+    if WrappedTool::is_file_modification_tool_name(tool.name()) {
+        Arc::new(WrappedTool::new(tool))
+    } else {
+        tool
+    }
+}
+
+/// Compatibility helper that returns a fresh snapshot-aware tool list.
 pub fn get_snapshot_wrapped_tools() -> Vec<Arc<dyn Tool>> {
-    ToolRegistry::new()
-        .get_all_tools()
-        .into_iter()
-        .map(|tool| {
-            if WrappedTool::is_file_modification_tool_name(tool.name()) {
-                Arc::new(WrappedTool::new(tool)) as Arc<dyn Tool>
-            } else {
-                tool
-            }
-        })
-        .collect()
+    ToolRegistry::new().get_all_tools()
 }
 
 /// Wrapped tool
diff --git a/src/crates/core/src/service/snapshot/mod.rs b/src/crates/core/src/service/snapshot/mod.rs
index 5fa50ca5..64dd4b38 100644
--- a/src/crates/core/src/service/snapshot/mod.rs
+++ b/src/crates/core/src/service/snapshot/mod.rs
@@ -14,7 +14,7 @@ pub use events::{
 pub use manager::{
     ensure_snapshot_manager_for_workspace, get_or_create_snapshot_manager,
     get_snapshot_manager_for_workspace, get_snapshot_wrapped_tools,
-    initialize_snapshot_manager_for_workspace, SnapshotManager,
+    initialize_snapshot_manager_for_workspace, wrap_tool_for_snapshot_tracking, SnapshotManager,
 };
 pub use service::{SnapshotService, SystemStats};
 pub use snapshot_core::{FileChangeEntry, FileChangeQueue, SessionStats, SnapshotCore};
diff --git a/src/web-ui/src/flow_chat/tool-cards/FileOperationToolCard.tsx b/src/web-ui/src/flow_chat/tool-cards/FileOperationToolCard.tsx
index b774cfb2..ee35ff2a 100644
--- a/src/web-ui/src/flow_chat/tool-cards/FileOperationToolCard.tsx
+++ b/src/web-ui/src/flow_chat/tool-cards/FileOperationToolCard.tsx
@@ -42,6 +42,8 @@ export const FileOperationToolCard: React.FC<FileOperationToolCardProps> = ({
   
   const prevIsParamsStreamingRef = useRef(isParamsStreaming);
   const userCollapsedRef = useRef(false);
+  const hasInitializedCompletionEffectRef = useRef(false);
+  const previousCompletionEndTimeRef = useRef<number | null>(toolItem.endTime ?? null);
   
   useEffect(() => {
     const prevIsParamsStreaming = prevIsParamsStreamingRef.current;
@@ -108,13 +110,33 @@ export const FileOperationToolCard: React.FC<FileOperationToolCardProps> = ({
   const currentFile = files.find(f => f.filePath === currentFilePath);
 
   useEffect(() => {
-    if (status === 'completed' && toolResult?.success && sessionId && currentFilePath) {
-      eventBus.emit(SNAPSHOT_EVENTS.FILE_OPERATION_COMPLETED, {
-        toolName: toolItem.toolName,
-        toolResult
-      }, sessionId, currentFilePath);
+    const completionEndTime = toolItem.endTime ?? null;
+    const isCompletedSuccess = status === 'completed' && Boolean(toolResult?.success);
+
+    if (!hasInitializedCompletionEffectRef.current) {
+      hasInitializedCompletionEffectRef.current = true;
+      previousCompletionEndTimeRef.current = completionEndTime;
+      return;
+    }
+
+    const shouldEmitCompletionEvent =
+      isCompletedSuccess &&
+      completionEndTime !== null &&
+      previousCompletionEndTimeRef.current !== completionEndTime &&
+      Boolean(sessionId) &&
+      Boolean(currentFilePath);
+
+    previousCompletionEndTimeRef.current = completionEndTime;
+
+    if (!shouldEmitCompletionEvent || !sessionId || !currentFilePath) {
+      return;
     }
-  }, [status, toolResult, sessionId, currentFilePath, toolItem.toolName, eventBus]);
+
+    eventBus.emit(SNAPSHOT_EVENTS.FILE_OPERATION_COMPLETED, {
+      toolName: toolItem.toolName,
+      toolResult
+    }, sessionId, currentFilePath);
+  }, [status, toolResult, sessionId, currentFilePath, toolItem.toolName, toolItem.endTime, eventBus]);
 
   const getToolDisplayInfo = () => {
     const toolMap: Record<string, { icon: string; name: string }> = {