@notebook-intelligence/notebook-intelligence 2.6.1 → 3.0.0

package/README.md

@@ -75,21 +75,37 @@ To let Notebook Intelligence remember your GitHub access token, go to Notebook I
 
 If your stored access token fails to login (due to expiration or other reasons), you will be prompted to relogin on the UI.
 
-### Notebook execute tool options
+## Built-in Tools
 
-Notebook execute tool is enabled by default in Agent Mode. However, you can disable it or make it controlled by an environment variable.
+- **Notebook Edit** (nbi-notebook-edit): Edit notebook using the JupyterLab notebook editor.
+- **Notebook Execute** (nbi-notebook-execute): Run notebooks in JupyterLab UI.
+- **Python File Edit** (nbi-python-file-edit): Edit Python files using the JupyterLab file editor.
+- **File Edit** (nbi-file-edit): Edit files in the Jupyter root directory.
+- **File Read** (nbi-file-read): Read files in the Jupyter root directory.
+- **Command Execute** (nbi-command-execute): Execute shell commands using embedded terminal in Agent UI or JupyterLab terminal.
 
-In order to disable Notebook execute tool:
+### Disabling Built-in tools
 
-```bash
-jupyter lab --NotebookIntelligence.notebook_execute_tool=disabled
+All built-in toolas are enabled by default in Agent Mode. However, you can disable them and make them controlled by an environment variable.
+
+In order to disable any built-in tool use the `disabled_tools` config:
+
+```python
+c.NotebookIntelligence.disabled_tools = ["nbi-notebook-execute","nbi-python-file-edit"]
+```
+
+Valid built-in tool values are `nbi-notebook-edit`, `nbi-notebook-execute`, `nbi-python-file-edit`, `nbi-file-edit`, `nbi-file-read`, `nbi-command-execute`.
+
+In order to disable a built-in tool by default but allow re-enabling using an environment variable use the `allow_enabling_tools_with_env` config:
+
+```python
+c.NotebookIntelligence.allow_enabling_tools_with_env = True
 ```
 
-In order to disable Notebook execute tool by default but allow enabling using an environment variable:
+Then the environment variable `NBI_ENABLED_BUILTIN_TOOLS` can be used to re-enable specific built-in tools.
 
 ```bash
-NBI_NOTEBOOK_EXECUTE_TOOL=enabled
-jupyter lab --NotebookIntelligence.notebook_execute_tool=env_enabled
+export NBI_ENABLED_BUILTIN_TOOLS=nbi-notebook-execute,nbi-python-file-edit
 ```
 
 ### Configuration files

package/lib/api.d.ts

@@ -53,7 +53,7 @@ export declare class NBIAPI {
     static updateOllamaModelList(): Promise<void>;
     static getMCPConfigFile(): Promise<any>;
     static setMCPConfigFile(config: any): Promise<any>;
-    static chatRequest(messageId: string, chatId: string, prompt: string, language: string, filename: string, additionalContext: IContextItem[], chatMode: string, toolSelections: IToolSelections, responseEmitter: IChatCompletionResponseEmitter): Promise<void>;
+    static chatRequest(messageId: string, chatId: string, prompt: string, language: string, currentDirectory: string, filename: string, additionalContext: IContextItem[], chatMode: string, toolSelections: IToolSelections, responseEmitter: IChatCompletionResponseEmitter): Promise<void>;
     static reloadMCPServers(): Promise<any>;
     static generateCode(chatId: string, prompt: string, prefix: string, suffix: string, existingCode: string, language: string, filename: string, responseEmitter: IChatCompletionResponseEmitter): Promise<void>;
     static sendChatUserInput(messageId: string, data: any): Promise<void>;

package/lib/api.js

@@ -254,7 +254,7 @@ class NBIAPI {
             });
         });
     }
-    static async chatRequest(messageId, chatId, prompt, language, filename, additionalContext, chatMode, toolSelections, responseEmitter) {
+    static async chatRequest(messageId, chatId, prompt, language, currentDirectory, filename, additionalContext, chatMode, toolSelections, responseEmitter) {
         this._messageReceived.connect((_, msg) => {
             msg = JSON.parse(msg);
             if (msg.id === messageId) {
@@ -268,6 +268,7 @@ class NBIAPI {
                 chatId,
                 prompt,
                 language,
+                currentDirectory,
                 filename,
                 additionalContext,
                 chatMode,

package/lib/chat-sidebar.d.ts

@@ -16,6 +16,7 @@ export interface IRunChatCompletionRequest {
     type: RunChatCompletionType;
     content: string;
     language?: string;
+    currentDirectory?: string;
     filename?: string;
     prefix?: string;
     suffix?: string;
@@ -25,6 +26,7 @@ export interface IRunChatCompletionRequest {
     toolSelections?: IToolSelections;
 }
 export interface IChatSidebarOptions {
+    getCurrentDirectory: () => string;
     getActiveDocumentInfo: () => IActiveDocumentInfo;
     getActiveSelectionContent: () => string;
     getCurrentCellContents: () => ICellContents;

package/lib/chat-sidebar.js

@@ -30,7 +30,7 @@ export class ChatSidebar extends ReactWidget {
         this.node.style.height = '100%';
     }
     render() {
-        return (React.createElement(SidebarComponent, { getActiveDocumentInfo: this._options.getActiveDocumentInfo, getActiveSelectionContent: this._options.getActiveSelectionContent, getCurrentCellContents: this._options.getCurrentCellContents, openFile: this._options.openFile, getApp: this._options.getApp, getTelemetryEmitter: this._options.getTelemetryEmitter }));
+        return (React.createElement(SidebarComponent, { getCurrentDirectory: this._options.getCurrentDirectory, getActiveDocumentInfo: this._options.getActiveDocumentInfo, getActiveSelectionContent: this._options.getActiveSelectionContent, getCurrentCellContents: this._options.getCurrentCellContents, openFile: this._options.openFile, getApp: this._options.getApp, getTelemetryEmitter: this._options.getTelemetryEmitter }));
     }
 }
 export class InlinePromptWidget extends ReactWidget {
@@ -154,6 +154,12 @@ function ChatResponse(props) {
     // group messages by type
     const groupedContents = [];
     let lastItemType;
+    const responseDetailTags = [
+        '<think>',
+        '</think>',
+        '<terminal-output>',
+        '</terminal-output>'
+    ];
     const extractReasoningContent = (item) => {
         let currentContent = item.content;
         if (typeof currentContent !== 'string') {
@@ -162,17 +168,31 @@ function ChatResponse(props) {
         let reasoningContent = '';
         let reasoningStartTime = new Date();
         const reasoningEndTime = new Date();
-        const startPos = currentContent.indexOf('<think>');
+        let startPos = -1;
+        let startTag = '';
+        for (const tag of responseDetailTags) {
+            startPos = currentContent.indexOf(tag);
+            if (startPos >= 0) {
+                startTag = tag;
+                break;
+            }
+        }
         const hasStart = startPos >= 0;
         reasoningStartTime = new Date(item.created);
         if (hasStart) {
-            currentContent = currentContent.substring(startPos + 7);
+            currentContent = currentContent.substring(startPos + startTag.length);
+        }
+        let endPos = -1;
+        for (const tag of responseDetailTags) {
+            endPos = currentContent.indexOf(tag);
+            if (endPos >= 0) {
+                break;
+            }
         }
-        const endPos = currentContent.indexOf('</think>');
         const hasEnd = endPos >= 0;
         if (hasEnd) {
             reasoningContent += currentContent.substring(0, endPos);
-            currentContent = currentContent.substring(endPos + 8);
+            currentContent = currentContent.substring(endPos + startTag.length);
         }
         else {
             if (hasStart) {
@@ -181,6 +201,7 @@ function ChatResponse(props) {
             }
         }
         item.content = currentContent;
+        item.reasoningTag = startTag;
         item.reasoningContent = reasoningContent;
         item.reasoningFinished = hasEnd;
         item.reasoningTime =
@@ -225,6 +246,21 @@ function ChatResponse(props) {
             parent.classList.add('expanded');
         }
     };
+    const getReasoningTitle = (item) => {
+        if (item.reasoningTag === '<think>') {
+            return item.reasoningFinished
+                ? 'Thought'
+                : `Thinking (${Math.floor(item.reasoningTime)} s)`;
+        }
+        else if (item.reasoningTag === '<terminal-output>') {
+            return item.reasoningFinished
+                ? 'Output'
+                : `Running (${Math.floor(item.reasoningTime)} s)`;
+        }
+        return item.reasoningFinished
+            ? 'Output'
+            : `Output (${Math.floor(item.reasoningTime)} s)`;
+    };
     return (React.createElement("div", { className: `chat-message chat-message-${msg.from}`, "data-render-count": renderCount },
         React.createElement("div", { className: "chat-message-header" },
             React.createElement("div", { className: "chat-message-from" },
@@ -242,18 +278,16 @@ function ChatResponse(props) {
                     case ResponseStreamDataType.Markdown:
                     case ResponseStreamDataType.MarkdownPart:
                         return (React.createElement(React.Fragment, null,
-                            item.reasoningContent && (React.createElement("div", { className: "expandable-content" },
+                            item.reasoningContent && (React.createElement("div", { className: "expandable-content expanded" },
                                 React.createElement("div", { className: "expandable-content-title", onClick: (event) => onExpandCollapseClick(event) },
                                     React.createElement(VscTriangleRight, { className: "collapsed-icon" }),
                                     React.createElement(VscTriangleDown, { className: "expanded-icon" }),
                                     ' ',
-                                    item.reasoningFinished
-                                        ? 'Thought'
-                                        : `Thinking (${Math.floor(item.reasoningTime)} s)`),
+                                    getReasoningTitle(item)),
                                 React.createElement("div", { className: "expandable-content-text" },
                                     React.createElement(MarkdownRenderer, { key: `key-${index}`, getApp: props.getApp, getActiveDocumentInfo: props.getActiveDocumentInfo }, item.reasoningContent)))),
                             React.createElement(MarkdownRenderer, { key: `key-${index}`, getApp: props.getApp, getActiveDocumentInfo: props.getActiveDocumentInfo }, item.content),
-                            item.contentDetail ? (React.createElement("div", { className: "expandable-content" },
+                            item.contentDetail ? (React.createElement("div", { className: "expandable-content expanded" },
                                 React.createElement("div", { className: "expandable-content-title", onClick: (event) => onExpandCollapseClick(event) },
                                     React.createElement(VscTriangleRight, { className: "collapsed-icon" }),
                                     React.createElement(VscTriangleDown, { className: "expanded-icon" }),
@@ -304,12 +338,12 @@ const MemoizedChatResponse = memo(ChatResponse);
 async function submitCompletionRequest(request, responseEmitter) {
     switch (request.type) {
         case RunChatCompletionType.Chat:
-            return NBIAPI.chatRequest(request.messageId, request.chatId, request.content, request.language || 'python', request.filename || 'Untitled.ipynb', request.additionalContext || [], request.chatMode, request.toolSelections || {}, responseEmitter);
+            return NBIAPI.chatRequest(request.messageId, request.chatId, request.content, request.language || 'python', request.currentDirectory || '', request.filename || 'Untitled.ipynb', request.additionalContext || [], request.chatMode, request.toolSelections || {}, responseEmitter);
         case RunChatCompletionType.ExplainThis:
         case RunChatCompletionType.FixThis:
         case RunChatCompletionType.ExplainThisOutput:
         case RunChatCompletionType.TroubleshootThisOutput: {
-            return NBIAPI.chatRequest(request.messageId, request.chatId, request.content, request.language || 'python', request.filename || 'Untitled.ipynb', [], 'ask', {}, responseEmitter);
+            return NBIAPI.chatRequest(request.messageId, request.chatId, request.content, request.language || 'python', request.currentDirectory || '', request.filename || 'Untitled.ipynb', [], 'ask', {}, responseEmitter);
         }
         case RunChatCompletionType.GenerateCode:
             return NBIAPI.generateCode(request.chatId, request.content, request.prefix || '', request.suffix || '', request.existingCode || '', request.language || 'python', request.filename || 'Untitled.ipynb', responseEmitter);
@@ -341,7 +375,7 @@ function SidebarComponent(props) {
     const [chatMode, setChatMode] = useState(NBIAPI.config.defaultChatMode);
     const [toolSelectionTitle, setToolSelectionTitle] = useState('Tool selection');
     const [selectedToolCount, setSelectedToolCount] = useState(0);
-    const [notebookExecuteToolSelected, setNotebookExecuteToolSelected] = useState(false);
+    const [unsafeToolSelected, setUnsafeToolSelected] = useState(false);
     const [renderCount, setRenderCount] = useState(1);
     const toolConfigRef = useRef({
         builtinToolsets: [
@@ -355,7 +389,7 @@ function SidebarComponent(props) {
     const [mcpServerEnabledState, setMCPServerEnabledState] = useState(new Map(mcpServerSettingsToEnabledState(toolConfigRef.current.mcpServers, mcpServerSettingsRef.current)));
     const [showModeTools, setShowModeTools] = useState(false);
     const toolSelectionsInitial = {
-        builtinToolsets: [BuiltinToolsetType.NotebookEdit],
+        builtinToolsets: [],
         mcpServers: {},
         extensions: {}
     };
@@ -368,13 +402,47 @@ function SidebarComponent(props) {
     const [hasExtensionTools, setHasExtensionTools] = useState(false);
     const [lastScrollTime, setLastScrollTime] = useState(0);
     const [scrollPending, setScrollPending] = useState(false);
+    const cleanupRemovedToolsFromToolSelections = () => {
+        const newToolSelections = { ...toolSelections };
+        // if servers or tool is not in mcpServerEnabledState, remove it from newToolSelections
+        for (const serverId in newToolSelections.mcpServers) {
+            if (!mcpServerEnabledState.has(serverId)) {
+                delete newToolSelections.mcpServers[serverId];
+            }
+            else {
+                for (const tool of newToolSelections.mcpServers[serverId]) {
+                    if (!mcpServerEnabledState.get(serverId).has(tool)) {
+                        newToolSelections.mcpServers[serverId].splice(newToolSelections.mcpServers[serverId].indexOf(tool), 1);
+                    }
+                }
+            }
+        }
+        for (const extensionId in newToolSelections.extensions) {
+            if (!mcpServerEnabledState.has(extensionId)) {
+                delete newToolSelections.extensions[extensionId];
+            }
+            else {
+                for (const toolsetId in newToolSelections.extensions[extensionId]) {
+                    for (const tool of newToolSelections.extensions[extensionId][toolsetId]) {
+                        if (!mcpServerEnabledState.get(extensionId).has(tool)) {
+                            newToolSelections.extensions[extensionId][toolsetId].splice(newToolSelections.extensions[extensionId][toolsetId].indexOf(tool), 1);
+                        }
+                    }
+                }
+            }
+        }
+        setToolSelections(newToolSelections);
+        setRenderCount(renderCount => renderCount + 1);
+    };
+    useEffect(() => {
+        cleanupRemovedToolsFromToolSelections();
+    }, [mcpServerEnabledState]);
     useEffect(() => {
         NBIAPI.configChanged.connect(() => {
             toolConfigRef.current = NBIAPI.config.toolConfig;
             mcpServerSettingsRef.current = NBIAPI.config.mcpServerSettings;
             const newMcpServerEnabledState = mcpServerSettingsToEnabledState(toolConfigRef.current.mcpServers, mcpServerSettingsRef.current);
             setMCPServerEnabledState(newMcpServerEnabledState);
-            setToolSelections(structuredClone(toolSelectionsInitial));
             setRenderCount(renderCount => renderCount + 1);
         });
     }, []);
@@ -414,7 +482,13 @@ function SidebarComponent(props) {
             typeCounts.push(`${extensionToolSelCount} ext`);
         }
         setSelectedToolCount(builtinToolSelCount + mcpServerToolSelCount + extensionToolSelCount);
-        setNotebookExecuteToolSelected(toolSelections.builtinToolsets.includes(BuiltinToolsetType.NotebookExecute));
+        setUnsafeToolSelected(toolSelections.builtinToolsets.some((toolsetName) => [
+            BuiltinToolsetType.NotebookEdit,
+            BuiltinToolsetType.NotebookExecute,
+            BuiltinToolsetType.PythonFileEdit,
+            BuiltinToolsetType.FileEdit,
+            BuiltinToolsetType.CommandExecute
+        ].includes(toolsetName)));
         setToolSelectionTitle(typeCounts.length === 0
             ? 'Tool selection'
             : `Tool selection (${typeCounts.join(', ')})`);
@@ -810,6 +884,7 @@ function SidebarComponent(props) {
             type: RunChatCompletionType.Chat,
             content: extractedPrompt,
             language: activeDocInfo.language,
+            currentDirectory: props.getCurrentDirectory(),
             filename: activeDocInfo.filePath,
             additionalContext,
             chatMode,
@@ -1217,16 +1292,13 @@ function SidebarComponent(props) {
                                 if (event.target.value === 'ask') {
                                     setToolSelections(toolSelectionsEmpty);
                                 }
-                                else if (event.target.value === 'agent') {
-                                    setToolSelections(structuredClone(toolSelectionsInitial));
-                                }
                                 setShowModeTools(false);
                                 setChatMode(event.target.value);
                             } },
                             React.createElement("option", { value: "ask" }, "Ask"),
                             React.createElement("option", { value: "agent" }, "Agent"))),
-                    chatMode !== 'ask' && (React.createElement("div", { className: `user-input-footer-button tools-button ${notebookExecuteToolSelected ? 'tools-button-warning' : selectedToolCount > 0 ? 'tools-button-active' : ''}`, onClick: () => handleChatToolsButtonClick(), title: notebookExecuteToolSelected
-                            ? `Notebook execute tool selected!\n${toolSelectionTitle}`
+                    chatMode !== 'ask' && (React.createElement("div", { className: `user-input-footer-button tools-button ${unsafeToolSelected ? 'tools-button-warning' : selectedToolCount > 0 ? 'tools-button-active' : ''}`, onClick: () => handleChatToolsButtonClick(), title: unsafeToolSelected
+                            ? `Tool selection can cause irreversible changes! Review each tool execution carefully.\n${toolSelectionTitle}`
                             : toolSelectionTitle },
                         React.createElement(VscTools, null),
                         selectedToolCount > 0 && React.createElement(React.Fragment, null, selectedToolCount)))),
@@ -1257,7 +1329,7 @@ function SidebarComponent(props) {
                         React.createElement("div", null, "Done"))),
                 React.createElement("div", { className: "mode-tools-popover-tool-list" },
                     React.createElement("div", { className: "mode-tools-group-header" }, "Built-in"),
-                    React.createElement("div", { className: "mode-tools-group mode-tools-group-built-in" }, toolConfigRef.current.builtinToolsets.map((toolset) => (React.createElement(CheckBoxItem, { key: toolset.id, label: toolset.name, checked: getBuiltinToolsetState(toolset.id), header: true, onClick: () => {
+                    React.createElement("div", { className: "mode-tools-group mode-tools-group-built-in" }, toolConfigRef.current.builtinToolsets.map((toolset) => (React.createElement(CheckBoxItem, { key: toolset.id, label: toolset.name, checked: getBuiltinToolsetState(toolset.id), tooltip: toolset.description, header: true, onClick: () => {
                             setBuiltinToolsetState(toolset.id, !getBuiltinToolsetState(toolset.id));
                         } })))),
                     renderCount > 0 &&

package/lib/components/checkbox.js

@@ -3,7 +3,7 @@ import React from 'react';
 import { MdOutlineCheckBoxOutlineBlank, MdCheckBox } from 'react-icons/md';
 export function CheckBoxItem(props) {
     const indent = props.indent || 0;
-    return (React.createElement("div", { className: `checkbox-item checkbox-item-indent-${indent} ${props.header ? 'checkbox-item-header' : ''}`, title: props.title, onClick: event => props.onClick(event) },
+    return (React.createElement("div", { className: `checkbox-item checkbox-item-indent-${indent} ${props.header ? 'checkbox-item-header' : ''}`, title: props.tooltip || props.title || '', onClick: event => props.onClick(event) },
         React.createElement("div", { className: "checkbox-item-toggle" },
             props.checked ? (React.createElement(MdCheckBox, { className: "checkbox-icon" })) : (React.createElement(MdOutlineCheckBoxOutlineBlank, { className: "checkbox-icon" })),
             props.label),

package/lib/components/settings-panel.js

@@ -364,9 +364,15 @@ function SettingsPanelComponentMCPServers(props) {
                                         setMCPServerEnabled(server.id, !getMCPServerEnabled(server.id));
                                     } }),
                                 React.createElement("div", { className: `server-status-indicator ${server.status}`, title: server.status })),
-                            getMCPServerEnabled(server.id) && (React.createElement("div", null, server.tools.map((tool) => (React.createElement(PillItem, { label: tool.name, title: tool.description, checked: getMCPServerToolEnabled(server.id, tool.name), onClick: () => {
-                                    setMCPServerToolEnabled(server.id, tool.name, !getMCPServerToolEnabled(server.id, tool.name));
-                                } }))))))))))),
+                            getMCPServerEnabled(server.id) && (React.createElement("div", null,
+                                server.tools.length > 0 && (React.createElement("div", { className: "mcp-server-tools" },
+                                    React.createElement("div", { className: "mcp-server-tools-header" }, "Tools"),
+                                    React.createElement("div", null, server.tools.map((tool) => (React.createElement(PillItem, { label: tool.name, title: tool.description, checked: getMCPServerToolEnabled(server.id, tool.name), onClick: () => {
+                                            setMCPServerToolEnabled(server.id, tool.name, !getMCPServerToolEnabled(server.id, tool.name));
+                                        } })))))),
+                                server.prompts.length > 0 && (React.createElement("div", { className: "mcp-server-prompts" },
+                                    React.createElement("div", { className: "mcp-server-prompts-header" }, "Prompts"),
+                                    React.createElement("div", null, server.prompts.map((prompt) => (React.createElement(PillItem, { label: prompt.name, title: prompt.description, checked: true })))))))))))))),
                     React.createElement("div", { className: "model-config-section-row" },
                         React.createElement("div", { className: "model-config-section-column", style: { flexGrow: 'initial' } },
                             React.createElement("button", { className: "jp-Dialog-button jp-mod-accept jp-mod-styled", style: { width: 'max-content' }, onClick: props.onEditMCPConfigClicked },

package/lib/index.js

@@ -54,6 +54,7 @@ var CommandIDs;
     CommandIDs.setCurrentFileContent = 'notebook-intelligence:set-current-file-content';
     CommandIDs.openMCPConfigEditor = 'notebook-intelligence:open-mcp-config-editor';
     CommandIDs.showFormInputDialog = 'notebook-intelligence:show-form-input-dialog';
+    CommandIDs.runCommandInTerminal = 'notebook-intelligence:run-command-in-terminal';
 })(CommandIDs || (CommandIDs = {}));
 const DOCUMENT_WATCH_INTERVAL = 1000;
 const MAX_TOKENS = 4096;
@@ -77,7 +78,7 @@ const emptyNotebookContent = {
 };
 const BACKEND_TELEMETRY_LISTENER_NAME = 'backend-telemetry-listener';
 class ActiveDocumentWatcher {
-    static initialize(app, languageRegistry) {
+    static initialize(app, languageRegistry, fileBrowser) {
         var _a;
         ActiveDocumentWatcher._languageRegistry = languageRegistry;
         (_a = app.shell.currentChanged) === null || _a === void 0 ? void 0 : _a.connect((_sender, args) => {
@@ -86,6 +87,12 @@ class ActiveDocumentWatcher {
         ActiveDocumentWatcher.activeDocumentInfo.activeWidget =
             app.shell.currentWidget;
         ActiveDocumentWatcher.handleWatchDocument();
+        if (fileBrowser) {
+            const onPathChanged = (model) => {
+                ActiveDocumentWatcher.currentDirectory = model.path;
+            };
+            fileBrowser.model.pathChanged.connect(onPathChanged);
+        }
     }
     static watchDocument(widget) {
         if (ActiveDocumentWatcher.activeDocumentInfo.activeWidget === widget) {
@@ -209,6 +216,7 @@ class ActiveDocumentWatcher {
         }));
     }
 }
+ActiveDocumentWatcher.currentDirectory = '';
 ActiveDocumentWatcher.activeDocumentInfo = {
     language: 'python',
     filename: 'nb-doesnt-exist.ipynb',
@@ -510,6 +518,9 @@ const plugin = {
         });
         panel.title.icon = sidebarIcon;
         const sidebar = new ChatSidebar({
+            getCurrentDirectory: () => {
+                return ActiveDocumentWatcher.currentDirectory;
+            },
             getActiveDocumentInfo: () => {
                 return ActiveDocumentWatcher.activeDocumentInfo;
             },
@@ -530,7 +541,7 @@ const plugin = {
             }
         });
         panel.addWidget(sidebar);
-        app.shell.add(panel, 'left', { rank: 1000 });
+        app.shell.add(panel, 'right', { rank: 1000 });
         app.shell.activateById(panel.id);
         const updateSidebarIcon = () => {
             if (NBIAPI.getChatEnabled()) {
@@ -723,6 +734,29 @@ const plugin = {
                 }
             }
         });
+        app.commands.addCommand(CommandIDs.runCommandInTerminal, {
+            execute: async (args) => {
+                var _a;
+                const command = args.command;
+                const terminal = await app.commands.execute('terminal:create-new', {
+                    cwd: args.cwd || ActiveDocumentWatcher.currentDirectory
+                });
+                const session = (_a = terminal === null || terminal === void 0 ? void 0 : terminal.content) === null || _a === void 0 ? void 0 : _a.session;
+                session.messageReceived.connect((sender, message) => {
+                    console.log('Message received in Jupyter terminal:', message);
+                });
+                if (session) {
+                    session.send({
+                        type: 'stdin',
+                        content: [command + '\n'] // Add newline to execute the command
+                    });
+                    return 'Command executed in Jupyter terminal';
+                }
+                else {
+                    return 'Failed to execute command in Jupyter terminal';
+                }
+            }
+        });
         const isNewEmptyNotebook = (model) => {
             return (model.cells.length === 1 &&
                 model.cells[0].cell_type === 'code' &&
@@ -1441,7 +1475,7 @@ const plugin = {
             });
         }
         const jlabApp = app;
-        ActiveDocumentWatcher.initialize(jlabApp, languageRegistry);
+        ActiveDocumentWatcher.initialize(jlabApp, languageRegistry, defaultBrowser);
         return extensionService;
     }
 };

package/lib/tokens.d.ts

@@ -86,7 +86,11 @@ export interface IToolSelections {
 }
 export declare enum BuiltinToolsetType {
     NotebookEdit = "nbi-notebook-edit",
-    NotebookExecute = "nbi-notebook-execute"
+    NotebookExecute = "nbi-notebook-execute",
+    PythonFileEdit = "nbi-python-file-edit",
+    FileEdit = "nbi-file-edit",
+    FileRead = "nbi-file-read",
+    CommandExecute = "nbi-command-execute"
 }
 export declare const GITHUB_COPILOT_PROVIDER_ID = "github-copilot";
 export declare enum TelemetryEventType {

package/lib/tokens.js

@@ -52,6 +52,10 @@ export var BuiltinToolsetType;
 (function (BuiltinToolsetType) {
     BuiltinToolsetType["NotebookEdit"] = "nbi-notebook-edit";
     BuiltinToolsetType["NotebookExecute"] = "nbi-notebook-execute";
+    BuiltinToolsetType["PythonFileEdit"] = "nbi-python-file-edit";
+    BuiltinToolsetType["FileEdit"] = "nbi-file-edit";
+    BuiltinToolsetType["FileRead"] = "nbi-file-read";
+    BuiltinToolsetType["CommandExecute"] = "nbi-command-execute";
 })(BuiltinToolsetType || (BuiltinToolsetType = {}));
 export const GITHUB_COPILOT_PROVIDER_ID = 'github-copilot';
 export var TelemetryEventType;

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@notebook-intelligence/notebook-intelligence",
-    "version": "2.6.1",
+    "version": "3.0.0",
     "description": "AI coding assistant for JupyterLab",
     "keywords": [
         "AI",

package/src/api.ts

@@ -339,6 +339,7 @@ export class NBIAPI {
     chatId: string,
     prompt: string,
     language: string,
+    currentDirectory: string,
     filename: string,
     additionalContext: IContextItem[],
     chatMode: string,
@@ -359,6 +360,7 @@ export class NBIAPI {
           chatId,
           prompt,
           language,
+          currentDirectory,
           filename,
           additionalContext,
           chatMode,

package/src/chat-sidebar.tsx

@@ -70,6 +70,7 @@ export interface IRunChatCompletionRequest {
   type: RunChatCompletionType;
   content: string;
   language?: string;
+  currentDirectory?: string;
   filename?: string;
   prefix?: string;
   suffix?: string;
@@ -80,6 +81,7 @@ export interface IRunChatCompletionRequest {
 }
 
 export interface IChatSidebarOptions {
+  getCurrentDirectory: () => string;
   getActiveDocumentInfo: () => IActiveDocumentInfo;
   getActiveSelectionContent: () => string;
   getCurrentCellContents: () => ICellContents;
@@ -99,6 +101,7 @@ export class ChatSidebar extends ReactWidget {
   render(): JSX.Element {
     return (
       <SidebarComponent
+        getCurrentDirectory={this._options.getCurrentDirectory}
         getActiveDocumentInfo={this._options.getActiveDocumentInfo}
         getActiveSelectionContent={this._options.getActiveSelectionContent}
         getCurrentCellContents={this._options.getCurrentCellContents}
@@ -262,6 +265,7 @@ interface IChatMessageContent {
   content: any;
   contentDetail?: any;
   created: Date;
+  reasoningTag?: string;
   reasoningContent?: string;
   reasoningFinished?: boolean;
   reasoningTime?: number;
@@ -323,6 +327,12 @@ function ChatResponse(props: any) {
   // group messages by type
   const groupedContents: IChatMessageContent[] = [];
   let lastItemType: ResponseStreamDataType | undefined;
+  const responseDetailTags = [
+    '<think>',
+    '</think>',
+    '<terminal-output>',
+    '</terminal-output>'
+  ];
 
   const extractReasoningContent = (item: IChatMessageContent) => {
     let currentContent = item.content as string;
@@ -334,21 +344,35 @@ function ChatResponse(props: any) {
     let reasoningStartTime = new Date();
     const reasoningEndTime = new Date();
 
-    const startPos = currentContent.indexOf('<think>');
+    let startPos = -1;
+    let startTag = '';
+    for (const tag of responseDetailTags) {
+      startPos = currentContent.indexOf(tag);
+      if (startPos >= 0) {
+        startTag = tag;
+        break;
+      }
+    }
 
     const hasStart = startPos >= 0;
     reasoningStartTime = new Date(item.created);
 
     if (hasStart) {
-      currentContent = currentContent.substring(startPos + 7);
+      currentContent = currentContent.substring(startPos + startTag.length);
     }
 
-    const endPos = currentContent.indexOf('</think>');
+    let endPos = -1;
+    for (const tag of responseDetailTags) {
+      endPos = currentContent.indexOf(tag);
+      if (endPos >= 0) {
+        break;
+      }
+    }
     const hasEnd = endPos >= 0;
 
     if (hasEnd) {
       reasoningContent += currentContent.substring(0, endPos);
-      currentContent = currentContent.substring(endPos + 8);
+      currentContent = currentContent.substring(endPos + startTag.length);
     } else {
       if (hasStart) {
         reasoningContent += currentContent;
@@ -357,6 +381,7 @@ function ChatResponse(props: any) {
     }
 
     item.content = currentContent;
+    item.reasoningTag = startTag;
     item.reasoningContent = reasoningContent;
     item.reasoningFinished = hasEnd;
     item.reasoningTime =
@@ -409,6 +434,21 @@ function ChatResponse(props: any) {
     }
   };
 
+  const getReasoningTitle = (item: IChatMessageContent) => {
+    if (item.reasoningTag === '<think>') {
+      return item.reasoningFinished
+        ? 'Thought'
+        : `Thinking (${Math.floor(item.reasoningTime)} s)`;
+    } else if (item.reasoningTag === '<terminal-output>') {
+      return item.reasoningFinished
+        ? 'Output'
+        : `Running (${Math.floor(item.reasoningTime)} s)`;
+    }
+    return item.reasoningFinished
+      ? 'Output'
+      : `Output (${Math.floor(item.reasoningTime)} s)`;
+  };
+
   return (
     <div
       className={`chat-message chat-message-${msg.from}`}
@@ -445,16 +485,14 @@ function ChatResponse(props: any) {
               return (
                 <>
                   {item.reasoningContent && (
-                    <div className="expandable-content">
+                    <div className="expandable-content expanded">
                       <div
                         className="expandable-content-title"
                         onClick={(event: any) => onExpandCollapseClick(event)}
                       >
                         <VscTriangleRight className="collapsed-icon"></VscTriangleRight>
                         <VscTriangleDown className="expanded-icon"></VscTriangleDown>{' '}
-                        {item.reasoningFinished
-                          ? 'Thought'
-                          : `Thinking (${Math.floor(item.reasoningTime)} s)`}
+                        {getReasoningTitle(item)}
                       </div>
                       <div className="expandable-content-text">
                         <MarkdownRenderer
@@ -475,7 +513,7 @@ function ChatResponse(props: any) {
                     {item.content}
                   </MarkdownRenderer>
                   {item.contentDetail ? (
-                    <div className="expandable-content">
+                    <div className="expandable-content expanded">
                       <div
                         className="expandable-content-title"
                         onClick={(event: any) => onExpandCollapseClick(event)}
@@ -616,6 +654,7 @@ async function submitCompletionRequest(
         request.chatId,
         request.content,
         request.language || 'python',
+        request.currentDirectory || '',
         request.filename || 'Untitled.ipynb',
         request.additionalContext || [],
         request.chatMode,
@@ -631,6 +670,7 @@ async function submitCompletionRequest(
         request.chatId,
         request.content,
         request.language || 'python',
+        request.currentDirectory || '',
         request.filename || 'Untitled.ipynb',
         [],
         'ask',
@@ -685,8 +725,7 @@ function SidebarComponent(props: any) {
   const [toolSelectionTitle, setToolSelectionTitle] =
     useState('Tool selection');
   const [selectedToolCount, setSelectedToolCount] = useState(0);
-  const [notebookExecuteToolSelected, setNotebookExecuteToolSelected] =
-    useState(false);
+  const [unsafeToolSelected, setUnsafeToolSelected] = useState(false);
 
   const [renderCount, setRenderCount] = useState(1);
   const toolConfigRef = useRef({
@@ -709,7 +748,7 @@ function SidebarComponent(props: any) {
 
   const [showModeTools, setShowModeTools] = useState(false);
   const toolSelectionsInitial: any = {
-    builtinToolsets: [BuiltinToolsetType.NotebookEdit],
+    builtinToolsets: [],
     mcpServers: {},
     extensions: {}
   };
@@ -725,6 +764,51 @@ function SidebarComponent(props: any) {
   const [lastScrollTime, setLastScrollTime] = useState(0);
   const [scrollPending, setScrollPending] = useState(false);
 
+  const cleanupRemovedToolsFromToolSelections = () => {
+    const newToolSelections = { ...toolSelections };
+    // if servers or tool is not in mcpServerEnabledState, remove it from newToolSelections
+    for (const serverId in newToolSelections.mcpServers) {
+      if (!mcpServerEnabledState.has(serverId)) {
+        delete newToolSelections.mcpServers[serverId];
+      } else {
+        for (const tool of newToolSelections.mcpServers[serverId]) {
+          if (!mcpServerEnabledState.get(serverId).has(tool)) {
+            newToolSelections.mcpServers[serverId].splice(
+              newToolSelections.mcpServers[serverId].indexOf(tool),
+              1
+            );
+          }
+        }
+      }
+    }
+    for (const extensionId in newToolSelections.extensions) {
+      if (!mcpServerEnabledState.has(extensionId)) {
+        delete newToolSelections.extensions[extensionId];
+      } else {
+        for (const toolsetId in newToolSelections.extensions[extensionId]) {
+          for (const tool of newToolSelections.extensions[extensionId][
+            toolsetId
+          ]) {
+            if (!mcpServerEnabledState.get(extensionId).has(tool)) {
+              newToolSelections.extensions[extensionId][toolsetId].splice(
+                newToolSelections.extensions[extensionId][toolsetId].indexOf(
+                  tool
+                ),
+                1
+              );
+            }
+          }
+        }
+      }
+    }
+    setToolSelections(newToolSelections);
+    setRenderCount(renderCount => renderCount + 1);
+  };
+
+  useEffect(() => {
+    cleanupRemovedToolsFromToolSelections();
+  }, [mcpServerEnabledState]);
+
   useEffect(() => {
     NBIAPI.configChanged.connect(() => {
       toolConfigRef.current = NBIAPI.config.toolConfig;
@@ -734,7 +818,6 @@ function SidebarComponent(props: any) {
         mcpServerSettingsRef.current
       );
       setMCPServerEnabledState(newMcpServerEnabledState);
-      setToolSelections(structuredClone(toolSelectionsInitial));
       setRenderCount(renderCount => renderCount + 1);
     });
   }, []);
@@ -782,9 +865,15 @@ function SidebarComponent(props: any) {
     setSelectedToolCount(
       builtinToolSelCount + mcpServerToolSelCount + extensionToolSelCount
     );
-    setNotebookExecuteToolSelected(
-      toolSelections.builtinToolsets.includes(
-        BuiltinToolsetType.NotebookExecute
+    setUnsafeToolSelected(
+      toolSelections.builtinToolsets.some((toolsetName: string) =>
+        [
+          BuiltinToolsetType.NotebookEdit,
+          BuiltinToolsetType.NotebookExecute,
+          BuiltinToolsetType.PythonFileEdit,
+          BuiltinToolsetType.FileEdit,
+          BuiltinToolsetType.CommandExecute
+        ].includes(toolsetName as unknown as BuiltinToolsetType)
       )
     );
     setToolSelectionTitle(
@@ -1311,6 +1400,7 @@ function SidebarComponent(props: any) {
         type: RunChatCompletionType.Chat,
         content: extractedPrompt,
         language: activeDocInfo.language,
+        currentDirectory: props.getCurrentDirectory(),
         filename: activeDocInfo.filePath,
         additionalContext,
         chatMode,
@@ -1886,8 +1976,6 @@ function SidebarComponent(props: any) {
                   onChange={event => {
                     if (event.target.value === 'ask') {
                       setToolSelections(toolSelectionsEmpty);
-                    } else if (event.target.value === 'agent') {
-                      setToolSelections(structuredClone(toolSelectionsInitial));
                     }
                     setShowModeTools(false);
                     setChatMode(event.target.value);
@@ -1899,11 +1987,11 @@ function SidebarComponent(props: any) {
               </div>
               {chatMode !== 'ask' && (
                 <div
-                  className={`user-input-footer-button tools-button ${notebookExecuteToolSelected ? 'tools-button-warning' : selectedToolCount > 0 ? 'tools-button-active' : ''}`}
+                  className={`user-input-footer-button tools-button ${unsafeToolSelected ? 'tools-button-warning' : selectedToolCount > 0 ? 'tools-button-active' : ''}`}
                   onClick={() => handleChatToolsButtonClick()}
                   title={
-                    notebookExecuteToolSelected
-                      ? `Notebook execute tool selected!\n${toolSelectionTitle}`
+                    unsafeToolSelected
+                      ? `Tool selection can cause irreversible changes! Review each tool execution carefully.\n${toolSelectionTitle}`
                       : toolSelectionTitle
                   }
                 >
@@ -1996,6 +2084,7 @@ function SidebarComponent(props: any) {
                       key={toolset.id}
                       label={toolset.name}
                       checked={getBuiltinToolsetState(toolset.id)}
+                      tooltip={toolset.description}
                       header={true}
                       onClick={() => {
                         setBuiltinToolsetState(

package/src/components/checkbox.tsx

@@ -10,7 +10,7 @@ export function CheckBoxItem(props: any) {
   return (
     <div
       className={`checkbox-item checkbox-item-indent-${indent} ${props.header ? 'checkbox-item-header' : ''}`}
-      title={props.title}
+      title={props.tooltip || props.title || ''}
       onClick={event => props.onClick(event)}
     >
       <div className="checkbox-item-toggle">

package/src/components/settings-panel.tsx

@@ -724,23 +724,51 @@ function SettingsPanelComponentMCPServers(props: any) {
                       </div>
                       {getMCPServerEnabled(server.id) && (
                         <div>
-                          {server.tools.map((tool: any) => (
-                            <PillItem
-                              label={tool.name}
-                              title={tool.description}
-                              checked={getMCPServerToolEnabled(
-                                server.id,
-                                tool.name
-                              )}
-                              onClick={() => {
-                                setMCPServerToolEnabled(
-                                  server.id,
-                                  tool.name,
-                                  !getMCPServerToolEnabled(server.id, tool.name)
-                                );
-                              }}
-                            ></PillItem>
-                          ))}
+                          {server.tools.length > 0 && (
+                            <div className="mcp-server-tools">
+                              <div className="mcp-server-tools-header">
+                                Tools
+                              </div>
+                              <div>
+                                {server.tools.map((tool: any) => (
+                                  <PillItem
+                                    label={tool.name}
+                                    title={tool.description}
+                                    checked={getMCPServerToolEnabled(
+                                      server.id,
+                                      tool.name
+                                    )}
+                                    onClick={() => {
+                                      setMCPServerToolEnabled(
+                                        server.id,
+                                        tool.name,
+                                        !getMCPServerToolEnabled(
+                                          server.id,
+                                          tool.name
+                                        )
+                                      );
+                                    }}
+                                  ></PillItem>
+                                ))}
+                              </div>
+                            </div>
+                          )}
+                          {server.prompts.length > 0 && (
+                            <div className="mcp-server-prompts">
+                              <div className="mcp-server-prompts-header">
+                                Prompts
+                              </div>
+                              <div>
+                                {server.prompts.map((prompt: any) => (
+                                  <PillItem
+                                    label={prompt.name}
+                                    title={prompt.description}
+                                    checked={true}
+                                  ></PillItem>
+                                ))}
+                              </div>
+                            </div>
+                          )}
                         </div>
                       )}
                     </div>

package/src/index.ts

@@ -32,7 +32,7 @@ import { NotebookPanel } from '@jupyterlab/notebook';
 import { CodeEditor } from '@jupyterlab/codeeditor';
 import { FileEditorWidget } from '@jupyterlab/fileeditor';
 
-import { IDefaultFileBrowser } from '@jupyterlab/filebrowser';
+import { FileBrowserModel, IDefaultFileBrowser } from '@jupyterlab/filebrowser';
 
 import { ContentsManager, KernelSpecManager } from '@jupyterlab/services';
 
@@ -83,6 +83,7 @@ import { UUID } from '@lumino/coreutils';
 
 import * as path from 'path';
 import { SettingsPanel } from './components/settings-panel';
+import { ITerminalConnection } from '@jupyterlab/services/lib/terminal/terminal';
 
 namespace CommandIDs {
   export const chatuserInput = 'notebook-intelligence:chat-user-input';
@@ -130,6 +131,8 @@ namespace CommandIDs {
     'notebook-intelligence:open-mcp-config-editor';
   export const showFormInputDialog =
     'notebook-intelligence:show-form-input-dialog';
+  export const runCommandInTerminal =
+    'notebook-intelligence:run-command-in-terminal';
 }
 
 const DOCUMENT_WATCH_INTERVAL = 1000;
@@ -160,7 +163,8 @@ const BACKEND_TELEMETRY_LISTENER_NAME = 'backend-telemetry-listener';
 class ActiveDocumentWatcher {
   static initialize(
     app: JupyterLab,
-    languageRegistry: IEditorLanguageRegistry
+    languageRegistry: IEditorLanguageRegistry,
+    fileBrowser: IDefaultFileBrowser
   ) {
     ActiveDocumentWatcher._languageRegistry = languageRegistry;
 
@@ -171,6 +175,13 @@ class ActiveDocumentWatcher {
     ActiveDocumentWatcher.activeDocumentInfo.activeWidget =
       app.shell.currentWidget;
     ActiveDocumentWatcher.handleWatchDocument();
+
+    if (fileBrowser) {
+      const onPathChanged = (model: FileBrowserModel) => {
+        ActiveDocumentWatcher.currentDirectory = model.path;
+      };
+      fileBrowser.model.pathChanged.connect(onPathChanged);
+    }
   }
 
   static watchDocument(widget: Widget) {
@@ -315,6 +326,8 @@ class ActiveDocumentWatcher {
     );
   }
 
+  static currentDirectory: string = '';
+
   static activeDocumentInfo: IActiveDocumentInfo = {
     language: 'python',
     filename: 'nb-doesnt-exist.ipynb',
@@ -724,6 +737,9 @@ const plugin: JupyterFrontEndPlugin<INotebookIntelligence> = {
     });
     panel.title.icon = sidebarIcon;
     const sidebar = new ChatSidebar({
+      getCurrentDirectory: (): string => {
+        return ActiveDocumentWatcher.currentDirectory;
+      },
       getActiveDocumentInfo: (): IActiveDocumentInfo => {
         return ActiveDocumentWatcher.activeDocumentInfo;
       },
@@ -744,7 +760,7 @@ const plugin: JupyterFrontEndPlugin<INotebookIntelligence> = {
       }
     });
     panel.addWidget(sidebar);
-    app.shell.add(panel, 'left', { rank: 1000 });
+    app.shell.add(panel, 'right', { rank: 1000 });
     app.shell.activateById(panel.id);
 
     const updateSidebarIcon = () => {
@@ -962,6 +978,32 @@ const plugin: JupyterFrontEndPlugin<INotebookIntelligence> = {
       }
     });
 
+    app.commands.addCommand(CommandIDs.runCommandInTerminal, {
+      execute: async args => {
+        const command = args.command as string;
+        const terminal = await app.commands.execute('terminal:create-new', {
+          cwd: (args.cwd as string) || ActiveDocumentWatcher.currentDirectory
+        });
+
+        const session: ITerminalConnection = terminal?.content?.session;
+
+        session.messageReceived.connect((sender, message) => {
+          console.log('Message received in Jupyter terminal:', message);
+        });
+
+        if (session) {
+          session.send({
+            type: 'stdin',
+            content: [command + '\n'] // Add newline to execute the command
+          });
+
+          return 'Command executed in Jupyter terminal';
+        } else {
+          return 'Failed to execute command in Jupyter terminal';
+        }
+      }
+    });
+
     const isNewEmptyNotebook = (model: ISharedNotebook) => {
       return (
         model.cells.length === 1 &&
@@ -1848,7 +1890,7 @@ const plugin: JupyterFrontEndPlugin<INotebookIntelligence> = {
     }
 
     const jlabApp = app as JupyterLab;
-    ActiveDocumentWatcher.initialize(jlabApp, languageRegistry);
+    ActiveDocumentWatcher.initialize(jlabApp, languageRegistry, defaultBrowser);
 
     return extensionService;
   }

package/src/tokens.ts

@@ -100,7 +100,11 @@ export interface IToolSelections {
 
 export enum BuiltinToolsetType {
   NotebookEdit = 'nbi-notebook-edit',
-  NotebookExecute = 'nbi-notebook-execute'
+  NotebookExecute = 'nbi-notebook-execute',
+  PythonFileEdit = 'nbi-python-file-edit',
+  FileEdit = 'nbi-file-edit',
+  FileRead = 'nbi-file-read',
+  CommandExecute = 'nbi-command-execute'
 }
 
 export const GITHUB_COPILOT_PROVIDER_ID = 'github-copilot';

package/style/base.css

@@ -733,8 +733,11 @@ body[data-jp-theme-light='false'] .inline-popover {
   display: none;
   margin: 5px;
   padding: 0 5px;
-  border: 1px dashed var(--jp-border-color1);
+  border: 1px solid var(--jp-border-color2);
   border-radius: 5px;
+  max-height: 200px;
+  overflow-y: auto;
+  box-shadow: inset 0 0 15px 15px rgb(23 23 23 / 50%);
 }
 
 .expandable-content .collapsed-icon {
@@ -816,6 +819,14 @@ svg.access-token-warning {
   font-weight: bold;
 }
 
+.mode-tools-group-built-in {
+  flex-flow: row wrap;
+}
+
+.mode-tools-group-built-in .checkbox-item {
+  width: 50%;
+}
+
 .mode-tools-group-built-in .checkbox-item-toggle {
   font-weight: normal;
 }
@@ -930,3 +941,13 @@ svg.access-token-warning {
 .form-input-dialog-body-content-field-input {
   width: 50%;
 }
+
+.mcp-server-prompts .pill-item {
+  cursor: default;
+}
+
+.mcp-server-tools-header,
+.mcp-server-prompts-header {
+  margin: 5px;
+  font-style: italic;
+}