Restructure src/ modules with consistent internal organization

Reorganize major src/ directories to follow a consistent pattern with
core/, menu/, submenu/, inputs/, logs/, layout/, feedback/ subdirectories.

Changes by module:

- stores/: Move 5 store files to stores/core/
- utils/: Create core/ (terminal, tools, etc.) and menu/ (progress-bar)
- api/: Create copilot/core/, copilot/auth/, ollama/core/
- providers/: Create core/, copilot/core/, copilot/auth/, ollama/core/, login/core/
- ui/: Create core/, banner/core/, banner/menu/, spinner/core/,
       input-editor/core/, components/core/, components/menu/
- tools/: Create core/ for registry.ts and types.ts
- tui-solid/: Reorganize components/ into menu/, submenu/, inputs/,
              logs/, modals/, panels/, layout/, feedback/
- commands/: Create core/ for runner.ts and handlers.ts
- services/: Create core/ for agent.ts, permissions.ts, session.ts,
             executor.ts, config.ts

All imports updated to use new paths. TypeScript compilation verified.

src/tools/apply-patch/execute.ts

@@ -21,7 +21,7 @@ import type {
   PatchRollback,
   ParsedFilePatch,
 } from "@/types/apply-patch";
-import type { ToolContext, ToolResult } from "@tools/types";
+import type { ToolContext, ToolResult } from "@tools/core/types";
 
 // Rollback storage (in-memory for session)
 const rollbackStore: Map<string, PatchRollback> = new Map();

src/tools/apply-patch/index.ts

@@ -4,7 +4,7 @@
  * Applies unified diff patches to files with fuzzy matching support.
  */
 
-import type { ToolDefinition } from "@tools/types";
+import type { ToolDefinition } from "@tools/core/types";
 import { applyPatchParams } from "@tools/apply-patch/params";
 import { executeApplyPatch } from "@tools/apply-patch/execute";
 

src/tools/bash/execute.ts

@@ -9,7 +9,7 @@ import {
   BASH_MESSAGES,
   BASH_DESCRIPTION,
 } from "@constants/bash";
-import { promptPermission } from "@services/permissions";
+import { promptPermission } from "@services/core/permissions";
 import { bashParams } from "@tools/bash/params";
 import {
   truncateOutput,

src/tools/core/index.ts

@@ -0,0 +1,6 @@
+/**
+ * Tools Core - Registry and Types
+ */
+
+export * from "./registry";
+export * from "./types";

src/tools/core/registry.ts

@@ -0,0 +1,219 @@
+/**
+ * Tool Registry
+ *
+ * Central registry for all available tools with support for
+ * built-in tools, MCP tools, and plugin tools.
+ */
+
+import type { ToolDefinition, FunctionDefinition } from "@tools/core/types";
+import { toolToFunction } from "@tools/core/types";
+import { bashTool } from "@/tools/bash";
+import { readTool } from "@/tools/read";
+import { writeTool } from "@/tools/write";
+import { editTool } from "@/tools/edit";
+import { todoWriteTool } from "@/tools/todo-write";
+import { todoReadTool } from "@/tools/todo-read";
+import { globToolDefinition } from "@/tools/glob/definition";
+import { grepToolDefinition } from "@/tools/grep/definition";
+import { webSearchTool } from "@/tools/web-search";
+import { webFetchTool } from "@/tools/web-fetch";
+import { multiEditTool } from "@/tools/multi-edit";
+import { lspTool } from "@/tools/lsp";
+import { applyPatchTool } from "@/tools/apply-patch";
+import {
+  isMCPTool,
+  executeMCPTool,
+  getMCPToolsForApi,
+} from "@/services/mcp/tools";
+import {
+  isPluginTool,
+  getPluginTool,
+  getPluginToolsForApi,
+} from "@/services/plugin-service";
+import { z } from "zod";
+
+/**
+ * All built-in tools
+ */
+export const tools: ToolDefinition[] = [
+  bashTool,
+  readTool,
+  writeTool,
+  editTool,
+  multiEditTool,
+  globToolDefinition,
+  grepToolDefinition,
+  todoWriteTool,
+  todoReadTool,
+  webSearchTool,
+  webFetchTool,
+  lspTool,
+  applyPatchTool,
+];
+
+/**
+ * Tools that are read-only (allowed in chat mode)
+ */
+const READ_ONLY_TOOLS = new Set([
+  "read",
+  "glob",
+  "grep",
+  "todo_read",
+  "web_search",
+  "web_fetch",
+  "lsp",
+]);
+
+/**
+ * Map of tools by name for fast lookup
+ */
+export const toolMap: Map<string, ToolDefinition> = new Map(
+  tools.map((t) => [t.name, t]),
+);
+
+/**
+ * Cached MCP tools
+ */
+let mcpToolsCache: Awaited<ReturnType<typeof getMCPToolsForApi>> | null = null;
+
+/**
+ * Get tool by name (including MCP tools and plugin tools)
+ */
+export const getTool = (name: string): ToolDefinition | undefined => {
+  const builtInTool = toolMap.get(name);
+  if (builtInTool) {
+    return builtInTool;
+  }
+
+  if (isPluginTool(name)) {
+    return getPluginTool(name);
+  }
+
+  if (isMCPTool(name)) {
+    return {
+      name,
+      description: `MCP tool: ${name}`,
+      parameters: z.object({}).passthrough(),
+      execute: async (args) => {
+        const result = await executeMCPTool(
+          name,
+          args as Record<string, unknown>,
+        );
+        return {
+          success: result.success,
+          title: name,
+          output: result.output,
+          error: result.error,
+        };
+      },
+    };
+  }
+
+  return undefined;
+};
+
+/**
+ * Get all tools as OpenAI function definitions
+ */
+export const getToolFunctions = (): FunctionDefinition[] => {
+  return tools.map(toolToFunction);
+};
+
+/**
+ * Filter tools based on chat mode (read-only vs full access)
+ */
+const filterToolsForMode = (
+  toolList: ToolDefinition[],
+  chatMode: boolean,
+): ToolDefinition[] => {
+  if (!chatMode) return toolList;
+  return toolList.filter((t) => READ_ONLY_TOOLS.has(t.name));
+};
+
+/**
+ * Get tools as format expected by Copilot/OpenAI API
+ * This includes both built-in tools and MCP tools
+ * @param chatMode - If true, only return read-only tools (no file modifications)
+ */
+export const getToolsForApiAsync = async (
+  chatMode = false,
+): Promise<
+  {
+    type: "function";
+    function: FunctionDefinition;
+  }[]
+> => {
+  const filteredTools = filterToolsForMode(tools, chatMode);
+  const builtInTools = filteredTools.map((t) => ({
+    type: "function" as const,
+    function: toolToFunction(t),
+  }));
+
+  if (chatMode) {
+    return builtInTools;
+  }
+
+  try {
+    mcpToolsCache = await getMCPToolsForApi();
+    const pluginTools = getPluginToolsForApi();
+    return [...builtInTools, ...pluginTools, ...mcpToolsCache];
+  } catch {
+    const pluginTools = getPluginToolsForApi();
+    return [...builtInTools, ...pluginTools];
+  }
+};
+
+/**
+ * Get tools synchronously (uses cached MCP tools if available)
+ * @param chatMode - If true, only return read-only tools (no file modifications)
+ */
+export const getToolsForApi = (
+  chatMode = false,
+): {
+  type: "function";
+  function: FunctionDefinition;
+}[] => {
+  const filteredTools = filterToolsForMode(tools, chatMode);
+  const builtInTools = filteredTools.map((t) => ({
+    type: "function" as const,
+    function: toolToFunction(t),
+  }));
+
+  if (chatMode) {
+    return builtInTools;
+  }
+
+  const pluginTools = getPluginToolsForApi();
+
+  if (mcpToolsCache) {
+    return [...builtInTools, ...pluginTools, ...mcpToolsCache];
+  }
+
+  return [...builtInTools, ...pluginTools];
+};
+
+/**
+ * Refresh MCP tools cache
+ * Returns information about the refresh result for logging
+ */
+export const refreshMCPTools = async (): Promise<{
+  success: boolean;
+  toolCount: number;
+  error?: string;
+}> => {
+  try {
+    mcpToolsCache = await getMCPToolsForApi();
+    return {
+      success: true,
+      toolCount: mcpToolsCache.length,
+    };
+  } catch (err) {
+    mcpToolsCache = null;
+    const errorMessage = err instanceof Error ? err.message : String(err);
+    return {
+      success: false,
+      toolCount: 0,
+      error: errorMessage,
+    };
+  }
+};

src/tools/edit/execute.ts

@@ -6,7 +6,7 @@ import fs from "fs/promises";
 import path from "path";
 
 import { EDIT_MESSAGES, EDIT_TITLES, EDIT_DESCRIPTION } from "@constants/edit";
-import { isFileOpAllowed, promptFilePermission } from "@services/permissions";
+import { isFileOpAllowed, promptFilePermission } from "@services/core/permissions";
 import { formatDiff } from "@utils/diff/format";
 import { generateDiff } from "@utils/diff/generate";
 import { editParams } from "@tools/edit/params";

src/tools/index.ts

@@ -2,7 +2,7 @@
  * Tool registry - exports all available tools
  */
 
-export * from "@tools/types";
+export * from "@tools/core/types";
 export { bashTool } from "@tools/bash";
 export { readTool } from "@tools/read";
 export { writeTool } from "@tools/write";
@@ -17,8 +17,8 @@ export { multiEditTool } from "@tools/multi-edit";
 export { lspTool } from "@tools/lsp";
 export { applyPatchTool } from "@tools/apply-patch";
 
-import type { ToolDefinition, FunctionDefinition } from "@tools/types";
-import { toolToFunction } from "@tools/types";
+import type { ToolDefinition, FunctionDefinition } from "@tools/core/types";
+import { toolToFunction } from "@tools/core/types";
 import { bashTool } from "@tools/bash";
 import { readTool } from "@tools/read";
 import { writeTool } from "@tools/write";

src/tools/lsp.ts

@@ -17,7 +17,7 @@ import {
   type DocumentSymbol,
   type Hover,
 } from "@services/lsp/index";
-import type { ToolDefinition } from "@tools/types";
+import type { ToolDefinition } from "@tools/core/types";
 import fs from "fs/promises";
 
 const PositionSchema = z.object({

src/tools/multi-edit/execute.ts

@@ -13,7 +13,7 @@ import {
   MULTI_EDIT_TITLES,
   MULTI_EDIT_DESCRIPTION,
 } from "@constants/multi-edit";
-import { isFileOpAllowed, promptFilePermission } from "@services/permissions";
+import { isFileOpAllowed, promptFilePermission } from "@services/core/permissions";
 import { formatDiff } from "@utils/diff/format";
 import { generateDiff } from "@utils/diff/generate";
 import { multiEditParams } from "@tools/multi-edit/params";

src/tools/read/execute.ts

@@ -11,7 +11,7 @@ import {
   READ_TITLES,
   READ_DESCRIPTION,
 } from "@constants/read";
-import { isFileOpAllowed, promptFilePermission } from "@services/permissions";
+import { isFileOpAllowed, promptFilePermission } from "@services/core/permissions";
 import { readParams } from "@tools/read/params";
 import { processLines } from "@tools/read/format";
 import type {

src/tools/todo-read.ts

@@ -5,8 +5,8 @@
  */
 
 import { z } from "zod";
-import { todoStore } from "@stores/todo-store";
-import type { ToolDefinition } from "@tools/types";
+import { todoStore } from "@stores/core/todo-store";
+import type { ToolDefinition } from "@tools/core/types";
 
 const parametersSchema = z.object({});
 

src/tools/todo-write.ts

@@ -5,8 +5,8 @@
  */
 
 import { z } from "zod";
-import { todoStore } from "@stores/todo-store";
-import type { ToolDefinition } from "@tools/types";
+import { todoStore } from "@stores/core/todo-store";
+import type { ToolDefinition } from "@tools/core/types";
 import type { TodoStatus } from "@/types/todo";
 
 const TodoItemSchema = z.object({

src/tools/write/execute.ts

@@ -10,7 +10,7 @@ import {
   WRITE_TITLES,
   WRITE_DESCRIPTION,
 } from "@constants/write";
-import { isFileOpAllowed, promptFilePermission } from "@services/permissions";
+import { isFileOpAllowed, promptFilePermission } from "@services/core/permissions";
 import { formatDiff } from "@utils/diff/format";
 import { generateDiff } from "@utils/diff/generate";
 import { writeParams } from "@tools/write/params";