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/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