feat: Implement repositories for authentication, certificates, metrics, and platform services

- Added AuthRepository for user and settings management with CRUD operations.
- Introduced CertificateRepository to handle domains, certificates, and requirements.
- Created MetricsRepository for managing metrics and logs.
- Developed PlatformRepository for platform services and resources management.
- Established RegistryRepository for registry and token operations.
- Implemented ServiceRepository for CRUD operations on services.
- Defined types and interfaces in types.ts for database interactions.

ts/classes/cert-requirement-manager.ts

@@ -152,9 +152,9 @@ export class CertRequirementManager {
         domainId: domain.id!,
         certDomain: domain.domain,
         isWildcard: useWildcard,
-        certPath: certData.certPath,
-        keyPath: certData.keyPath,
-        fullChainPath: certData.fullChainPath,
+        certPem: certData.certPem,
+        keyPem: certData.keyPem,
+        fullchainPem: certData.fullchainPem,
         expiryDate: certData.expiryDate,
         issuer: certData.issuer,
         isValid: true,
@@ -239,9 +239,9 @@ export class CertRequirementManager {
 
       // Update certificate in database
       this.database.updateCertificate(cert.id!, {
-        certPath: certData.certPath,
-        keyPath: certData.keyPath,
-        fullChainPath: certData.fullChainPath,
+        certPem: certData.certPem,
+        keyPem: certData.keyPem,
+        fullchainPem: certData.fullchainPem,
         expiryDate: certData.expiryDate,
         issuer: certData.issuer,
       });
@@ -260,7 +260,7 @@ export class CertRequirementManager {
   /**
    * Clean up old invalid certificates (90+ days old)
    */
-  async cleanupOldCertificates(): Promise<void> {
+  cleanupOldCertificates(): void {
     try {
       const allCertificates = this.database.getAllCertificates();
       const now = Date.now();
@@ -272,18 +272,7 @@ export class CertRequirementManager {
           // Check if certificate has been invalid for 90+ days
           const timeSinceExpiry = now - cert.expiryDate;
           if (timeSinceExpiry >= this.CLEANUP_DELAY_MS) {
-            // Delete certificate files
-            try {
-              await Deno.remove(cert.certPath);
-              await Deno.remove(cert.keyPath);
-              await Deno.remove(cert.fullChainPath);
-            } catch (error) {
-              logger.debug(
-                `Failed to delete certificate files for ${cert.certDomain}: ${getErrorMessage(error)}`
-              );
-            }
-
-            // Delete from database
+            // Delete from database (PEM content is stored in DB, no files to delete)
             this.database.deleteCertificate(cert.id!);
             deletedCount++;
             logger.info(