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/tools/index.ts

@@ -474,6 +474,7 @@ export class ToolRegistry {
 		];
 	}
 
+	// eslint-disable-next-line @typescript-eslint/no-explicit-any
 	async callTool(name: string, args: any): Promise<CallToolResult> {
 		const startTime = Date.now();
 		

src/tools/note-tools.ts

@@ -13,7 +13,7 @@ import {
 } from '../types/mcp-types';
 import { PathUtils } from '../utils/path-utils';
 import { ErrorMessages } from '../utils/error-messages';
-import { FrontmatterUtils } from '../utils/frontmatter-utils';
+import { FrontmatterUtils, YAMLValue } from '../utils/frontmatter-utils';
 import { WaypointUtils } from '../utils/waypoint-utils';
 import { VersionUtils } from '../utils/version-utils';
 import { ContentUtils } from '../utils/content-utils';
@@ -364,16 +364,28 @@ export class NoteTools {
 			await this.vault.modify(file, content);
 
 			// Build response with word count and link validation
-			const result: any = {
+			interface UpdateNoteResult {
+				success: boolean;
+				path: string;
+				versionId: string;
+				modified: number;
+				wordCount?: number;
+				linkValidation?: {
+					valid: string[];
+					brokenNotes: Array<{ link: string; line: number; context: string }>;
+					brokenHeadings: Array<{ link: string; line: number; context: string; note: string }>;
+					summary: string;
+				};
+			}
+
+			const result: UpdateNoteResult = {
 				success: true,
 				path: file.path,
 				versionId: VersionUtils.generateVersionId(file),
-				modified: file.stat.mtime
+				modified: file.stat.mtime,
+				wordCount: ContentUtils.countWords(content)
 			};
 
-			// Add word count
-			result.wordCount = ContentUtils.countWords(content);
-
 			// Add link validation if requested
 			if (validateLinks) {
 				result.linkValidation = await LinkUtils.validateLinks(
@@ -731,7 +743,7 @@ export class NoteTools {
 	 */
 	async updateFrontmatter(
 		path: string,
-		patch?: Record<string, any>,
+		patch?: Record<string, YAMLValue>,
 		remove: string[] = [],
 		ifMatch?: string
 	): Promise<CallToolResult> {

src/tools/vault-tools.ts

@@ -385,8 +385,10 @@ export class VaultTools {
 		// In most cases, this will be 0 for directories
 		let modified = 0;
 		try {
-			if ((folder as any).stat && typeof (folder as any).stat.mtime === 'number') {
-				modified = (folder as any).stat.mtime;
+			// TFolder doesn't officially have stat, but it may exist in practice
+			const folderWithStat = folder as TFolder & { stat?: { mtime?: number } };
+			if (folderWithStat.stat && typeof folderWithStat.stat.mtime === 'number') {
+				modified = folderWithStat.stat.mtime;
 			}
 		} catch (error) {
 			// Silently fail - modified will remain 0