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 {

cli/src/checks/llm-check.ts

@@ -5,20 +5,16 @@ export async function llmCheck(config: PaperclipConfig): Promise<CheckResult> {
   if (!config.llm) {
     return {
       name: "LLM provider",
-      status: "warn",
-      message: "No LLM provider configured",
-      canRepair: false,
-      repairHint: "Run `paperclipai configure --section llm` to set one up",
+      status: "pass",
+      message: "No LLM provider configured (optional)",
     };
   }
 
   if (!config.llm.apiKey) {
     return {
       name: "LLM provider",
-      status: "warn",
-      message: `${config.llm.provider} configured but no API key set`,
-      canRepair: false,
-      repairHint: "Run `paperclipai configure --section llm`",
+      status: "pass",
+      message: `${config.llm.provider} configured but no API key set (optional)`,
     };
   }
 

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 {

cli/src/checks/storage-check.ts

@@ -7,16 +7,7 @@ export function storageCheck(config: PaperclipConfig, configPath?: string): Chec
   if (config.storage.provider === "local_disk") {
     const baseDir = resolveRuntimeLikePath(config.storage.localDisk.baseDir, configPath);
     if (!fs.existsSync(baseDir)) {
-      return {
-        name: "Storage",
-        status: "warn",
-        message: `Local storage directory does not exist: ${baseDir}`,
-        canRepair: true,
-        repair: () => {
-          fs.mkdirSync(baseDir, { recursive: true });
-        },
-        repairHint: "Run with --repair to create local storage directory",
-      };
+      fs.mkdirSync(baseDir, { recursive: true });
     }
 
     try {