fix: doctor command auto-creates directories and treats LLM as optional

Instead of showing alarming warnings on first run when storage, log,
and database directories don't exist, the doctor checks now silently
create them and report pass. LLM provider is treated as optional
rather than a warning when not configured.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

cli/src/checks/database-check.ts

@@ -39,15 +39,7 @@ export async function databaseCheck(config: PaperclipConfig, configPath?: string
     const dataDir = resolveRuntimeLikePath(config.database.embeddedPostgresDataDir, configPath);
     const reportedPath = dataDir;
     if (!fs.existsSync(dataDir)) {
-      return {
-        name: "Database",
-        status: "warn",
-        message: `Embedded PostgreSQL data directory does not exist: ${reportedPath}`,
-        canRepair: true,
-        repair: () => {
-          fs.mkdirSync(reportedPath, { recursive: true });
-        },
-      };
+      fs.mkdirSync(reportedPath, { recursive: true });
     }
 
     return {