fix: replace any types with proper TypeScript types

Replace all `any` types with properly defined TypeScript interfaces and types throughout the codebase to improve type safety and eliminate type-related code quality issues.

Changes:
- Define ElectronSafeStorage interface for Electron's safeStorage API
- Create LegacySettings interface for settings migration in main.ts
- Define JSONValue, JSONRPCParams types for JSON-RPC protocol
- Define JSONSchemaProperty for tool input schemas
- Create YAMLValue type for frontmatter values
- Define FrontmatterValue type for adapter interfaces
- Update middleware to use proper Express NextFunction and JSONRPCResponse types
- Fix tool registry to handle args with proper typing (with eslint-disable for dynamic dispatch)
- Fix notifications to use proper types with eslint-disable where dynamic access is needed
- Add proper null safety assertions where appropriate
- Fix TFolder stat access with proper type extension

All type errors resolved. TypeScript compilation passes with --skipLibCheck.

src/server/mcp-server.ts

@@ -4,6 +4,8 @@ import { Server } from 'http';
 import {
 	JSONRPCRequest,
 	JSONRPCResponse,
+	JSONRPCParams,
+	JSONValue,
 	ErrorCodes,
 	InitializeResult,
 	ListToolsResult,
@@ -36,11 +38,11 @@ export class MCPServer {
 		try {
 			switch (request.method) {
 				case 'initialize':
-					return this.createSuccessResponse(request.id, await this.handleInitialize(request.params));
+					return this.createSuccessResponse(request.id, await this.handleInitialize(request.params ?? {}));
 				case 'tools/list':
 					return this.createSuccessResponse(request.id, await this.handleListTools());
 				case 'tools/call':
-					return this.createSuccessResponse(request.id, await this.handleCallTool(request.params));
+					return this.createSuccessResponse(request.id, await this.handleCallTool(request.params ?? {}));
 				case 'ping':
 					return this.createSuccessResponse(request.id, {});
 				default:
@@ -52,7 +54,7 @@ export class MCPServer {
 		}
 	}
 
-	private async handleInitialize(_params: any): Promise<InitializeResult> {
+	private async handleInitialize(_params: JSONRPCParams): Promise<InitializeResult> {
 		return {
 			protocolVersion: "2024-11-05",
 			capabilities: {
@@ -71,20 +73,20 @@ export class MCPServer {
 		};
 	}
 
-	private async handleCallTool(params: any): Promise<CallToolResult> {
-		const { name, arguments: args } = params;
-		return await this.toolRegistry.callTool(name, args);
+	private async handleCallTool(params: JSONRPCParams): Promise<CallToolResult> {
+		const paramsObj = params as { name: string; arguments: Record<string, unknown> };
+		return await this.toolRegistry.callTool(paramsObj.name, paramsObj.arguments);
 	}
 
-	private createSuccessResponse(id: string | number | undefined, result: any): JSONRPCResponse {
+	private createSuccessResponse(id: string | number | undefined, result: unknown): JSONRPCResponse {
 		return {
 			jsonrpc: "2.0",
 			id: id ?? null,
-			result
+			result: result as JSONValue
 		};
 	}
 
-	private createErrorResponse(id: string | number | undefined | null, code: number, message: string, data?: any): JSONRPCResponse {
+	private createErrorResponse(id: string | number | undefined | null, code: number, message: string, data?: JSONValue): JSONRPCResponse {
 		return {
 			jsonrpc: "2.0",
 			id: id ?? null,
@@ -104,7 +106,7 @@ export class MCPServer {
 					resolve();
 				});
 
-				this.server.on('error', (error: any) => {
+				this.server.on('error', (error: NodeJS.ErrnoException) => {
 					if (error.code === 'EADDRINUSE') {
 						reject(new Error(`Port ${this.settings.port} is already in use`));
 					} else {

src/server/middleware.ts

@@ -1,10 +1,10 @@
-import { Express, Request, Response } from 'express';
+import { Express, Request, Response, NextFunction } from 'express';
 import express from 'express';
 import cors from 'cors';
 import { MCPServerSettings } from '../types/settings-types';
-import { ErrorCodes } from '../types/mcp-types';
+import { ErrorCodes, JSONRPCResponse } from '../types/mcp-types';
 
-export function setupMiddleware(app: Express, settings: MCPServerSettings, createErrorResponse: (id: any, code: number, message: string) => any): void {
+export function setupMiddleware(app: Express, settings: MCPServerSettings, createErrorResponse: (id: string | number | null, code: number, message: string) => JSONRPCResponse): void {
 	// Parse JSON bodies
 	app.use(express.json());
 
@@ -29,7 +29,7 @@ export function setupMiddleware(app: Express, settings: MCPServerSettings, creat
 	app.use(cors(corsOptions));
 
 	// Authentication middleware - Always enabled
-	app.use((req: Request, res: Response, next: any) => {
+	app.use((req: Request, res: Response, next: NextFunction) => {
 		// Defensive check: if no API key is set, reject all requests
 		if (!settings.apiKey || settings.apiKey.trim() === '') {
 			return res.status(500).json(createErrorResponse(null, ErrorCodes.InternalError, 'Server misconfigured: No API key set'));
@@ -45,7 +45,7 @@ export function setupMiddleware(app: Express, settings: MCPServerSettings, creat
 	});
 
 	// Origin validation for security (DNS rebinding protection)
-	app.use((req: Request, res: Response, next: any) => {
+	app.use((req: Request, res: Response, next: NextFunction) => {
 		const host = req.headers.host;
 
 		// Only allow localhost connections

src/server/routes.ts

@@ -2,9 +2,9 @@ import { Express, Request, Response } from 'express';
 import { JSONRPCRequest, JSONRPCResponse, ErrorCodes } from '../types/mcp-types';
 
 export function setupRoutes(
-	app: Express, 
+	app: Express,
 	handleRequest: (request: JSONRPCRequest) => Promise<JSONRPCResponse>,
-	createErrorResponse: (id: any, code: number, message: string) => JSONRPCResponse
+	createErrorResponse: (id: string | number | null, code: number, message: string) => JSONRPCResponse
 ): void {
 	// Main MCP endpoint
 	app.post('/mcp', async (req: Request, res: Response) => {