refactor(vscode-ide-companion/qwenAgentManager): remove saveCheckpointViaCommand method

refactor(vscode-ide-companion/webview): improve message handling during checkpoint saves
feat(vscode-ide-companion/markdown): enhance file path link handling with line numbers support
feat(vscode-ide-companion/message): add enableFileLinks prop to MessageContent component
feat(vscode-ide-companion/user-message): disable file links in user messages

packages/vscode-ide-companion/src/services/qwenAgentManager.ts

@@ -900,50 +900,6 @@ export class QwenAgentManager {
     return this.saveSessionViaCommand(sessionId, tag);
   }
 
-  /**
-   * Save session via /chat save command (CLI way)
-   * Calls CLI's native save function to ensure complete content is saved
-   *
-   * @param tag - Checkpoint tag
-   * @returns Save result
-   */
-  async saveCheckpointViaCommand(
-    tag: string,
-  ): Promise<{ success: boolean; tag?: string; message?: string }> {
-    try {
-      console.log(
-        '[QwenAgentManager] ===== SAVING VIA /chat save COMMAND =====',
-      );
-      console.log('[QwenAgentManager] Tag:', tag);
-
-      // Send /chat save command as a prompt
-      // The CLI will handle this as a special command and save the checkpoint
-      const command = `/chat save "${tag}"`;
-      console.log('[QwenAgentManager] Sending command:', command);
-
-      await this.connection.sendPrompt(command);
-
-      console.log(
-        '[QwenAgentManager] Command sent, checkpoint should be saved by CLI',
-      );
-
-      // Wait a bit for CLI to process the command
-      await new Promise((resolve) => setTimeout(resolve, 500));
-
-      return {
-        success: true,
-        tag,
-        message: `Checkpoint saved via CLI: ${tag}`,
-      };
-    } catch (error) {
-      console.error('[QwenAgentManager] /chat save command failed:', error);
-      return {
-        success: false,
-        message: error instanceof Error ? error.message : String(error),
-      };
-    }
-  }
-
   /**
    * Save session as checkpoint (using CLI format)
    * Saves to ~/.qwen/tmp/{projectHash}/checkpoint-{tag}.json

packages/vscode-ide-companion/src/webview/WebViewProvider.ts

@@ -58,13 +58,12 @@ export class WebViewProvider {
 
     // Setup agent callbacks
     this.agentManager.onMessage((message) => {
-      // Ignore history replay while background /chat save is running
+      // Do not suppress messages during checkpoint saves.
-      if (this.messageHandler.getIsSavingCheckpoint()) {
+      // Checkpoint persistence now writes directly to disk and should not
-        console.log(
+      // generate ACP session/update traffic. Suppressing here could drop
-          '[WebViewProvider] Ignoring message during checkpoint save',
+      // legitimate history replay messages (e.g., session/load) or
-        );
+      // assistant replies when a new prompt starts while an async save is
-        return;
+      // still finishing.
-      }
       this.sendMessageToWebView({
         type: 'message',
         data: message,
@@ -72,14 +71,8 @@ export class WebViewProvider {
     });
 
     this.agentManager.onStreamChunk((chunk: string) => {
-      // Ignore stream chunks from background /chat save commands
+      // Always forward stream chunks; do not gate on checkpoint saves.
-      if (this.messageHandler.getIsSavingCheckpoint()) {
+      // See note in onMessage() above.
-        console.log(
-          '[WebViewProvider] Ignoring stream chunk from /chat save command',
-        );
-        return;
-      }
-
       this.messageHandler.appendStreamContent(chunk);
       this.sendMessageToWebView({
         type: 'streamChunk',
@@ -89,14 +82,7 @@ export class WebViewProvider {
 
     // Setup thought chunk handler
     this.agentManager.onThoughtChunk((chunk: string) => {
-      // Ignore thought chunks from background /chat save commands
+      // Always forward thought chunks; do not gate on checkpoint saves.
-      if (this.messageHandler.getIsSavingCheckpoint()) {
-        console.log(
-          '[WebViewProvider] Ignoring thought chunk from /chat save command',
-        );
-        return;
-      }
-
       this.messageHandler.appendStreamContent(chunk);
       this.sendMessageToWebView({
         type: 'thoughtChunk',
@@ -148,14 +134,7 @@ export class WebViewProvider {
     // Note: Tool call updates are handled in handleSessionUpdate within QwenAgentManager
     // and sent via onStreamChunk callback
     this.agentManager.onToolCall((update) => {
-      // Ignore tool calls from background /chat save commands
+      // Always surface tool calls; they are part of the live assistant flow.
-      if (this.messageHandler.getIsSavingCheckpoint()) {
-        console.log(
-          '[WebViewProvider] Ignoring tool call from /chat save command',
-        );
-        return;
-      }
-
       // Cast update to access sessionUpdate property
       const updateData = update as unknown as Record<string, unknown>;
 

packages/vscode-ide-companion/src/webview/components/messages/MarkdownRenderer/MarkdownRenderer.tsx

@@ -14,6 +14,8 @@ import './MarkdownRenderer.css';
 interface MarkdownRendererProps {
   content: string;
   onFileClick?: (filePath: string) => void;
+  /** When false, do not convert file paths into clickable links. Default: true */
+  enableFileLinks?: boolean;
 }
 
 /**
@@ -32,6 +34,7 @@ const FILE_PATH_WITH_LINES_REGEX =
 export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
   content,
   onFileClick,
+  enableFileLinks = true,
 }) => {
   /**
    * Initialize markdown-it with plugins
@@ -59,8 +62,10 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
       // Process the markdown content
       let html = md.render(content);
 
-      // Post-process to add file path click handlers
+      // Post-process to add file path click handlers unless disabled
-      html = processFilePaths(html);
+      if (enableFileLinks) {
+        html = processFilePaths(html);
+      }
 
       return html;
     } catch (error) {
@@ -108,20 +113,41 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
     container.innerHTML = html;
 
     const union = new RegExp(
-      `${FILE_PATH_WITH_LINES_REGEX.source}|${FILE_PATH_REGEX.source}`,
+      `${FILE_PATH_WITH_LINES_REGEX.source}|${FILE_PATH_REGEX.source}|${BARE_FILE_REGEX.source}`,
       'gi',
     );
 
+    // Convert a "path#fragment" into VS Code friendly "path:line" (we only keep the start line)
+    const normalizePathAndLine = (
+      raw: string,
+    ): { displayText: string; dataPath: string } => {
+      const displayText = raw;
+      let base = raw;
+      // Extract hash fragment like #12, #L12 or #12-34 and keep only the first number
+      const hashIndex = raw.indexOf('#');
+      if (hashIndex >= 0) {
+        const frag = raw.slice(hashIndex + 1);
+        // Accept L12, 12 or 12-34
+        const m = frag.match(/^L?(\d+)(?:-\d+)?$/i);
+        if (m) {
+          const line = parseInt(m[1], 10);
+          base = raw.slice(0, hashIndex);
+          return { displayText, dataPath: `${base}:${line}` };
+        }
+      }
+      return { displayText, dataPath: base };
+    };
+
     const makeLink = (text: string) => {
       const link = document.createElement('a');
-      // Pass base path to the handler; keep the full text as label
+      // Pass base path (with optional :line) to the handler; keep the full text as label
-      const filePath = text.split('#')[0];
+      const { dataPath } = normalizePathAndLine(text);
       link.className = 'file-path-link';
       link.textContent = text;
       link.setAttribute('href', '#');
       link.setAttribute('title', `Open ${text}`);
       // Carry file path via data attribute; click handled by event delegation
-      link.setAttribute('data-file-path', filePath);
+      link.setAttribute('data-file-path', dataPath);
       return link;
     };
 
@@ -129,29 +155,54 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
       const href = a.getAttribute('href') || '';
       const text = (a.textContent || '').trim();
 
-      // Helper function to check if a string looks like a code reference
+      // Helper: identify dot-chained code refs (e.g. vscode.commands.register)
+      // but DO NOT treat filenames/paths as code refs.
       const isCodeReference = (str: string): boolean => {
-        // Check if it looks like a code reference (e.g., module.property)
+        if (BARE_FILE_REGEX.test(str)) {
-        // Patterns like "vscode.contribution", "module.submodule.function"
+          return false; // looks like a filename
+        }
+        if (/[/\\]/.test(str)) {
+          return false; // contains a path separator
+        }
         const codeRefPattern = /^[a-zA-Z_$][\w$]*(\.[a-zA-Z_$][\w$]*)+$/;
         return codeRefPattern.test(str);
       };
 
-      // If linkify turned a bare filename into http://<filename>, convert it back
+      // If linkify turned a bare filename (e.g. README.md) into http://<filename>, convert it back
       const httpMatch = href.match(/^https?:\/\/(.+)$/i);
-      if (httpMatch && BARE_FILE_REGEX.test(text) && httpMatch[1] === text) {
+      if (httpMatch) {
-        // Skip if it looks like a code reference
+        try {
-        if (isCodeReference(text)) {
+          const url = new URL(href);
-          return;
+          const host = url.hostname || '';
-        }
+          const pathname = url.pathname || '';
+          const noPath = pathname === '' || pathname === '/';
 
-        // Treat as a file link instead of external URL
+          // Case 1: anchor text itself is a bare filename and equals the host (e.g. README.md)
-        const filePath = text; // no leading slash
+          if (
-        a.classList.add('file-path-link');
+            noPath &&
-        a.setAttribute('href', '#');
+            BARE_FILE_REGEX.test(text) &&
-        a.setAttribute('title', `Open ${text}`);
+            host.toLowerCase() === text.toLowerCase()
-        a.setAttribute('data-file-path', filePath);
+          ) {
-        return;
+            const { dataPath } = normalizePathAndLine(text);
+            a.classList.add('file-path-link');
+            a.setAttribute('href', '#');
+            a.setAttribute('title', `Open ${text}`);
+            a.setAttribute('data-file-path', dataPath);
+            return;
+          }
+
+          // Case 2: host itself looks like a filename (rare but happens), use it
+          if (noPath && BARE_FILE_REGEX.test(host)) {
+            const { dataPath } = normalizePathAndLine(host);
+            a.classList.add('file-path-link');
+            a.setAttribute('href', '#');
+            a.setAttribute('title', `Open ${text || host}`);
+            a.setAttribute('data-file-path', dataPath);
+            return;
+          }
+        } catch {
+          // fall through; unparseable URL
+        }
       }
 
       // Ignore other external protocols
@@ -170,18 +221,33 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
         FILE_PATH_WITH_LINES_NO_G.test(candidate) ||
         FILE_PATH_NO_G.test(candidate)
       ) {
-        const filePath = candidate.split('#')[0];
+        const { dataPath } = normalizePathAndLine(candidate);
         a.classList.add('file-path-link');
         a.setAttribute('href', '#');
         a.setAttribute('title', `Open ${text || href}`);
-        a.setAttribute('data-file-path', filePath);
+        a.setAttribute('data-file-path', dataPath);
+        return;
+      }
+
+      // Bare file name or relative path (e.g. README.md or docs/README.md)
+      if (BARE_FILE_REGEX.test(candidate)) {
+        const { dataPath } = normalizePathAndLine(candidate);
+        a.classList.add('file-path-link');
+        a.setAttribute('href', '#');
+        a.setAttribute('title', `Open ${text || href}`);
+        a.setAttribute('data-file-path', dataPath);
       }
     };
 
-    // Helper function to check if a string looks like a code reference
+    // Helper: identify dot-chained code refs (e.g. vscode.commands.register)
+    // but DO NOT treat filenames/paths as code refs.
     const isCodeReference = (str: string): boolean => {
-      // Check if it looks like a code reference (e.g., module.property)
+      if (BARE_FILE_REGEX.test(str)) {
-      // Patterns like "vscode.contribution", "module.submodule.function"
+        return false; // looks like a filename
+      }
+      if (/[/\\]/.test(str)) {
+        return false; // contains a path separator
+      }
       const codeRefPattern = /^[a-zA-Z_$][\w$]*(\.[a-zA-Z_$][\w$]*)+$/;
       return codeRefPattern.test(str);
     };
@@ -194,6 +260,11 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
           upgradeAnchorIfFilePath(el as HTMLAnchorElement);
           return; // Don't descend into <a>
         }
+        // Avoid transforming inside code/pre blocks
+        const tag = el.tagName.toLowerCase();
+        if (tag === 'code' || tag === 'pre') {
+          return;
+        }
       }
 
       for (let child = node.firstChild; child; ) {
@@ -252,6 +323,10 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
   const handleContainerClick = (
     e: React.MouseEvent<HTMLDivElement, MouseEvent>,
   ) => {
+    // If file links disabled, do nothing
+    if (!enableFileLinks) {
+      return;
+    }
     const target = e.target as HTMLElement | null;
     if (!target) {
       return;
@@ -260,18 +335,46 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({
     // Find nearest anchor with our marker class
     const anchor = (target.closest &&
       target.closest('a.file-path-link')) as HTMLAnchorElement | null;
-    if (!anchor) {
+    if (anchor) {
+      const filePath = anchor.getAttribute('data-file-path');
+      if (!filePath) {
+        return;
+      }
+      e.preventDefault();
+      e.stopPropagation();
+      onFileClick?.(filePath);
       return;
     }
 
-    const filePath = anchor.getAttribute('data-file-path');
+    // Fallback: intercept "http://README.md" style links that slipped through
-    if (!filePath) {
+    const anyAnchor = (target.closest &&
+      target.closest('a')) as HTMLAnchorElement | null;
+    if (!anyAnchor) {
       return;
     }
 
-    e.preventDefault();
+    const href = anyAnchor.getAttribute('href') || '';
-    e.stopPropagation();
+    if (!/^https?:\/\//i.test(href)) {
-    onFileClick?.(filePath);
+      return;
+    }
+    try {
+      const url = new URL(href);
+      const host = url.hostname || '';
+      const path = url.pathname || '';
+      const noPath = path === '' || path === '/';
+
+      // Basic bare filename heuristic on the host part (e.g. README.md)
+      if (noPath && /\.[a-z0-9]+$/i.test(host)) {
+        // Prefer the readable text content if it looks like a file
+        const text = (anyAnchor.textContent || '').trim();
+        const candidate = /\.[a-z0-9]+$/i.test(text) ? text : host;
+        e.preventDefault();
+        e.stopPropagation();
+        onFileClick?.(candidate);
+      }
+    } catch {
+      // ignore
+    }
   };
 
   return (

packages/vscode-ide-companion/src/webview/components/messages/MessageContent.tsx

@@ -10,9 +10,17 @@ import { MarkdownRenderer } from './MarkdownRenderer/MarkdownRenderer.js';
 interface MessageContentProps {
   content: string;
   onFileClick?: (filePath: string) => void;
+  enableFileLinks?: boolean;
 }
 
 export const MessageContent: React.FC<MessageContentProps> = ({
   content,
   onFileClick,
-}) => <MarkdownRenderer content={content} onFileClick={onFileClick} />;
+  enableFileLinks,
+}) => (
+  <MarkdownRenderer
+    content={content}
+    onFileClick={onFileClick}
+    enableFileLinks={enableFileLinks}
+  />
+);

packages/vscode-ide-companion/src/webview/components/messages/UserMessage.tsx

@@ -58,7 +58,12 @@ export const UserMessage: React.FC<UserMessageProps> = ({
           color: 'var(--app-primary-foreground)',
         }}
       >
-        <MessageContent content={content} onFileClick={onFileClick} />
+        {/* For user messages, do NOT convert filenames to clickable links */}
+        <MessageContent
+          content={content}
+          onFileClick={onFileClick}
+          enableFileLinks={false}
+        />
       </div>
 
       {/* File context indicator */}