feat: improve doctor update flow

src/cli/plugins-cli.ts

@@ -454,6 +454,10 @@ export function registerPluginsCli(program: Command) {
       const targets = opts.all ? Object.keys(installs) : id ? [id] : [];
 
       if (targets.length === 0) {
+        if (opts.all) {
+          defaultRuntime.log("No npm-installed plugins to update.");
+          return;
+        }
         defaultRuntime.error("Provide a plugin id or use --all.");
         process.exit(1);
       }

src/cli/update-cli.ts

@@ -623,7 +623,8 @@ export async function updateCommand(opts: UpdateCommandOptions): Promise<void> {
         process.env.CLAWDBOT_UPDATE_IN_PROGRESS = "1";
         try {
           const { doctorCommand } = await import("../commands/doctor.js");
-          await doctorCommand(defaultRuntime, { nonInteractive: true });
+          const interactiveDoctor = Boolean(process.stdin.isTTY) && !opts.json && opts.yes !== true;
+          await doctorCommand(defaultRuntime, { nonInteractive: !interactiveDoctor });
         } catch (err) {
           defaultRuntime.log(theme.warn(`Doctor failed: ${String(err)}`));
         } finally {

src/commands/doctor-config-flow.ts

@@ -121,10 +121,14 @@ export async function loadAndMaybeMigrateDoctorConfig(params: {
   options: DoctorOptions;
   confirm: (p: { message: string; initialValue: boolean }) => Promise<boolean>;
 }) {
-  void params.confirm;
   const shouldRepair = params.options.repair === true || params.options.yes === true;
   const snapshot = await readConfigFileSnapshot();
-  let cfg: ClawdbotConfig = snapshot.config ?? {};
+  const baseCfg = snapshot.config ?? {};
+  let cfg: ClawdbotConfig = baseCfg;
+  let candidate = structuredClone(baseCfg) as ClawdbotConfig;
+  let pendingChanges = false;
+  let shouldWriteConfig = false;
+  const fixHints: string[] = [];
   if (snapshot.exists && !snapshot.valid && snapshot.legacyIssues.length === 0) {
     note("Config invalid; doctor will run with best-effort config.", "Config");
   }
@@ -139,52 +143,76 @@ export async function loadAndMaybeMigrateDoctorConfig(params: {
       snapshot.legacyIssues.map((issue) => `- ${issue.path}: ${issue.message}`).join("\n"),
       "Legacy config keys detected",
     );
+    const { config: migrated, changes } = migrateLegacyConfig(snapshot.parsed);
+    if (changes.length > 0) {
+      note(changes.join("\n"), "Doctor changes");
+    }
+    if (migrated) {
+      candidate = migrated;
+      pendingChanges = pendingChanges || changes.length > 0;
+    }
     if (shouldRepair) {
       // Legacy migration (2026-01-02, commit: 16420e5b) — normalize per-provider allowlists; move WhatsApp gating into channels.whatsapp.allowFrom.
-      const { config: migrated, changes } = migrateLegacyConfig(snapshot.parsed);
-      if (changes.length > 0) note(changes.join("\n"), "Doctor changes");
       if (migrated) cfg = migrated;
     } else {
-      note(
+      fixHints.push(
         `Run "${formatCliCommand("clawdbot doctor --fix")}" to apply legacy migrations.`,
-        "Doctor",
       );
     }
   }
 
-  const normalized = normalizeLegacyConfigValues(cfg);
+  const normalized = normalizeLegacyConfigValues(candidate);
   if (normalized.changes.length > 0) {
     note(normalized.changes.join("\n"), "Doctor changes");
+    candidate = normalized.config;
+    pendingChanges = true;
     if (shouldRepair) {
       cfg = normalized.config;
     } else {
-      note(`Run "${formatCliCommand("clawdbot doctor --fix")}" to apply these changes.`, "Doctor");
+      fixHints.push(`Run "${formatCliCommand("clawdbot doctor --fix")}" to apply these changes.`);
     }
   }
 
-  const autoEnable = applyPluginAutoEnable({ config: cfg, env: process.env });
+  const autoEnable = applyPluginAutoEnable({ config: candidate, env: process.env });
   if (autoEnable.changes.length > 0) {
     note(autoEnable.changes.join("\n"), "Doctor changes");
+    candidate = autoEnable.config;
+    pendingChanges = true;
     if (shouldRepair) {
       cfg = autoEnable.config;
     } else {
-      note(`Run "${formatCliCommand("clawdbot doctor --fix")}" to apply these changes.`, "Doctor");
+      fixHints.push(`Run "${formatCliCommand("clawdbot doctor --fix")}" to apply these changes.`);
     }
   }
 
-  const unknown = stripUnknownConfigKeys(cfg);
+  const unknown = stripUnknownConfigKeys(candidate);
   if (unknown.removed.length > 0) {
     const lines = unknown.removed.map((path) => `- ${path}`).join("\n");
+    candidate = unknown.config;
+    pendingChanges = true;
     if (shouldRepair) {
       cfg = unknown.config;
       note(lines, "Doctor changes");
     } else {
       note(lines, "Unknown config keys");
-      note('Run "clawdbot doctor --fix" to remove these keys.', "Doctor");
+      fixHints.push('Run "clawdbot doctor --fix" to remove these keys.');
+    }
+  }
+
+  if (!shouldRepair && pendingChanges) {
+    const shouldApply = await params.confirm({
+      message: "Apply recommended config repairs now?",
+      initialValue: true,
+    });
+    if (shouldApply) {
+      cfg = candidate;
+      shouldWriteConfig = true;
+    } else if (fixHints.length > 0) {
+      note(fixHints.join("\n"), "Doctor");
     }
   }
 
   noteOpencodeProviderOverrides(cfg);
 
-  return { cfg, path: snapshot.path ?? CONFIG_PATH_CLAWDBOT };
+  return { cfg, path: snapshot.path ?? CONFIG_PATH_CLAWDBOT, shouldWriteConfig };
 }

src/commands/doctor.ts

@@ -250,7 +250,8 @@ export async function doctorCommand(
     healthOk,
   });
 
-  if (prompter.shouldRepair) {
+  const shouldWriteConfig = prompter.shouldRepair || configResult.shouldWriteConfig;
+  if (shouldWriteConfig) {
     cfg = applyWizardMetadata(cfg, { command: "doctor", mode: resolveMode(cfg) });
     await writeConfigFile(cfg);
     runtime.log(`Updated ${CONFIG_PATH_CLAWDBOT}`);