Fix doctor summary after repairs

cli/src/__tests__/doctor.test.ts

@@ -0,0 +1,99 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { doctor } from "../commands/doctor.js";
+import { writeConfig } from "../config/store.js";
+import type { PaperclipConfig } from "../config/schema.js";
+
+const ORIGINAL_ENV = { ...process.env };
+
+function createTempConfig(): string {
+  const root = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-doctor-"));
+  const configPath = path.join(root, ".paperclip", "config.json");
+  const runtimeRoot = path.join(root, "runtime");
+
+  const config: PaperclipConfig = {
+    $meta: {
+      version: 1,
+      updatedAt: "2026-03-10T00:00:00.000Z",
+      source: "configure",
+    },
+    database: {
+      mode: "embedded-postgres",
+      embeddedPostgresDataDir: path.join(runtimeRoot, "db"),
+      embeddedPostgresPort: 55432,
+      backup: {
+        enabled: true,
+        intervalMinutes: 60,
+        retentionDays: 30,
+        dir: path.join(runtimeRoot, "backups"),
+      },
+    },
+    logging: {
+      mode: "file",
+      logDir: path.join(runtimeRoot, "logs"),
+    },
+    server: {
+      deploymentMode: "local_trusted",
+      exposure: "private",
+      host: "127.0.0.1",
+      port: 3199,
+      allowedHostnames: [],
+      serveUi: true,
+    },
+    auth: {
+      baseUrlMode: "auto",
+      disableSignUp: false,
+    },
+    storage: {
+      provider: "local_disk",
+      localDisk: {
+        baseDir: path.join(runtimeRoot, "storage"),
+      },
+      s3: {
+        bucket: "paperclip",
+        region: "us-east-1",
+        prefix: "",
+        forcePathStyle: false,
+      },
+    },
+    secrets: {
+      provider: "local_encrypted",
+      strictMode: false,
+      localEncrypted: {
+        keyFilePath: path.join(runtimeRoot, "secrets", "master.key"),
+      },
+    },
+  };
+
+  writeConfig(config, configPath);
+  return configPath;
+}
+
+describe("doctor", () => {
+  beforeEach(() => {
+    process.env = { ...ORIGINAL_ENV };
+    delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
+    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
+    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+  });
+
+  afterEach(() => {
+    process.env = { ...ORIGINAL_ENV };
+  });
+
+  it("re-runs repairable checks so repaired failures do not remain blocking", async () => {
+    const configPath = createTempConfig();
+
+    const summary = await doctor({
+      config: configPath,
+      repair: true,
+      yes: true,
+    });
+
+    expect(summary.failed).toBe(0);
+    expect(summary.warned).toBe(0);
+    expect(process.env.PAPERCLIP_AGENT_JWT_SECRET).toBeTruthy();
+  });
+});

cli/src/commands/doctor.ts

@@ -66,28 +66,40 @@ export async function doctor(opts: {
   printResult(deploymentAuthResult);
 
   // 3. Agent JWT check
-  const jwtResult = agentJwtSecretCheck(opts.config);
+  results.push(
-  results.push(jwtResult);
+    await runRepairableCheck({
-  printResult(jwtResult);
+      run: () => agentJwtSecretCheck(opts.config),
-  await maybeRepair(jwtResult, opts);
+      configPath,
+      opts,
+    }),
+  );
 
   // 4. Secrets adapter check
-  const secretsResult = secretsCheck(config, configPath);
+  results.push(
-  results.push(secretsResult);
+    await runRepairableCheck({
-  printResult(secretsResult);
+      run: () => secretsCheck(config, configPath),
-  await maybeRepair(secretsResult, opts);
+      configPath,
+      opts,
+    }),
+  );
 
   // 5. Storage check
-  const storageResult = storageCheck(config, configPath);
+  results.push(
-  results.push(storageResult);
+    await runRepairableCheck({
-  printResult(storageResult);
+      run: () => storageCheck(config, configPath),
-  await maybeRepair(storageResult, opts);
+      configPath,
+      opts,
+    }),
+  );
 
   // 6. Database check
-  const dbResult = await databaseCheck(config, configPath);
+  results.push(
-  results.push(dbResult);
+    await runRepairableCheck({
-  printResult(dbResult);
+      run: () => databaseCheck(config, configPath),
-  await maybeRepair(dbResult, opts);
+      configPath,
+      opts,
+    }),
+  );
 
   // 7. LLM check
   const llmResult = await llmCheck(config);
@@ -95,10 +107,13 @@ export async function doctor(opts: {
   printResult(llmResult);
 
   // 8. Log directory check
-  const logResult = logCheck(config, configPath);
+  results.push(
-  results.push(logResult);
+    await runRepairableCheck({
-  printResult(logResult);
+      run: () => logCheck(config, configPath),
-  await maybeRepair(logResult, opts);
+      configPath,
+      opts,
+    }),
+  );
 
   // 9. Port check
   const portResult = await portCheck(config);
@@ -120,9 +135,9 @@ function printResult(result: CheckResult): void {
 async function maybeRepair(
   result: CheckResult,
   opts: { repair?: boolean; yes?: boolean },
-): Promise<void> {
+): Promise<boolean> {
-  if (result.status === "pass" || !result.canRepair || !result.repair) return;
+  if (result.status === "pass" || !result.canRepair || !result.repair) return false;
-  if (!opts.repair) return;
+  if (!opts.repair) return false;
 
   let shouldRepair = opts.yes;
   if (!shouldRepair) {
@@ -130,7 +145,7 @@ async function maybeRepair(
       message: `Repair "${result.name}"?`,
       initialValue: true,
     });
-    if (p.isCancel(answer)) return;
+    if (p.isCancel(answer)) return false;
     shouldRepair = answer;
   }
 
@@ -138,10 +153,30 @@ async function maybeRepair(
     try {
       await result.repair();
       p.log.success(`Repaired: ${result.name}`);
+      return true;
     } catch (err) {
       p.log.error(`Repair failed: ${err instanceof Error ? err.message : String(err)}`);
     }
   }
+  return false;
+}
+
+async function runRepairableCheck(input: {
+  run: () => CheckResult | Promise<CheckResult>;
+  configPath: string;
+  opts: { repair?: boolean; yes?: boolean };
+}): Promise<CheckResult> {
+  let result = await input.run();
+  printResult(result);
+
+  const repaired = await maybeRepair(result, input.opts);
+  if (!repaired) return result;
+
+  // Repairs may create/update the adjacent .env file or other local resources.
+  loadPaperclipEnvFile(input.configPath);
+  result = await input.run();
+  printResult(result);
+  return result;
 }
 
 function printSummary(results: CheckResult[]): { passed: number; warned: number; failed: number } {