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/log-check.ts

@@ -8,15 +8,7 @@ export function logCheck(config: PaperclipConfig, configPath?: string): CheckRes
   const reportedDir = logDir;
 
   if (!fs.existsSync(logDir)) {
-    return {
-      name: "Log directory",
-      status: "warn",
-      message: `Log directory does not exist: ${reportedDir}`,
-      canRepair: true,
-      repair: () => {
-        fs.mkdirSync(reportedDir, { recursive: true });
-      },
-    };
+    fs.mkdirSync(reportedDir, { recursive: true });
   }
 
   try {