feat: implement Obsidian MCP Bundle MVP (Phase 1-3)

- Complete project setup with TypeScript, Jest, MCPB manifest
- Implement foundational infrastructure (CLI executor, logger, error handler)
- Add 9 file operation tools for User Story 1
- Full MCP protocol compliance with stdio transport
- Input validation and sanitization for security
- Comprehensive error handling with actionable messages
- Constitutional compliance: all 6 principles satisfied

MVP includes:
- obsidian_create_note, read, append, prepend, delete, move, rename, open, file_info
- Zod validation schemas for all parameters
- 30s timeout configuration with per-command overrides
- Stderr-only logging with sanitized output
- Graceful shutdown handling

Build: ✅ 0 errors, 0 vulnerabilities
Tasks: 48/167 complete (MVP milestone)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/config/timeouts.ts

@@ -0,0 +1,61 @@
+/**
+ * Timeout configuration for CLI commands
+ * Constitutional Principle IV: Defensive Programming
+ * FR-018: 30-second default timeout with per-command overrides
+ */
+
+import { TimeoutConfig } from '../utils/types.js';
+
+/**
+ * Default timeout configuration
+ */
+export const timeoutConfig: TimeoutConfig = {
+  // Default timeout for all commands (30 seconds)
+  default: 30000,
+
+  // Per-command overrides (in milliseconds)
+  perCommand: {
+    // Search operations may take longer on large vaults
+    search: 45000,
+    'search-tags': 45000,
+    'search-properties': 45000,
+
+    // Sync operations may take longer
+    'sync-start': 60000,
+    'sync-status': 10000,
+
+    // Quick operations can have shorter timeouts
+    'vault-list': 5000,
+    'note-read': 10000,
+    open: 5000,
+
+    // File operations are typically fast
+    'create-note': 10000,
+    'delete-note': 10000,
+    'move-note': 10000,
+    'rename-note': 10000,
+  },
+};
+
+/**
+ * Get timeout for a specific command
+ */
+export function getCommandTimeout(command: string): number {
+  // Extract base command name (remove subcommands and flags)
+  const baseCommand = command.split(' ')[0];
+
+  return timeoutConfig.perCommand[baseCommand] || timeoutConfig.default;
+}
+
+/**
+ * Set custom timeout for a command
+ */
+export function setCommandTimeout(command: string, timeout: number): void {
+  if (timeout < 1000) {
+    throw new Error('Timeout must be at least 1000ms (1 second)');
+  }
+  if (timeout > 300000) {
+    throw new Error('Timeout must not exceed 300000ms (5 minutes)');
+  }
+  timeoutConfig.perCommand[command] = timeout;
+}