Merge remote-tracking branch 'public-gh/master' into paperclip-routines

* public-gh/master: (46 commits)
  chore(lockfile): refresh pnpm-lock.yaml (#1377)
  fix: manage codex home per company by default
  Ensure agent home directories exist before use
  Handle directory entries in imported zip archives
  Fix portability import and org chart test blockers
  Fix PR verify failures after merge
  fix: address greptile follow-up feedback
  Address remaining Greptile portability feedback
  docs: clarify quickstart npx usage
  Add guarded dev restart handling
  Fix PAP-576 settings toggles and transcript default
  Add username log censor setting
  fix: use standard toggle component for permission controls
  fix: add missing setPrincipalPermission mock in portability tests
  fix: use fixed 1280x640 dimensions for org chart export image
  Adjust default CEO onboarding task copy
  fix: link Agent Company to agentcompanies.io in export README
  fix: strip agents and projects sections from COMPANY.md export body
  fix: default company export page to README.md instead of first file
  Add default agent instructions bundle
  ...

# Conflicts:
#	packages/adapters/pi-local/src/server/execute.ts
#	packages/db/src/migrations/meta/0039_snapshot.json
#	packages/db/src/migrations/meta/_journal.json
#	server/src/__tests__/agent-permissions-routes.test.ts
#	server/src/__tests__/agent-skills-routes.test.ts
#	server/src/services/company-portability.ts
#	skills/paperclip/references/company-skills.md
#	ui/src/api/agents.ts

ui/src/components/AgentConfigForm.tsx

@@ -44,6 +44,7 @@ import { ClaudeLocalAdvancedFields } from "../adapters/claude-local/config-field
 import { MarkdownEditor } from "./MarkdownEditor";
 import { ChoosePathButton } from "./PathInstructionsModal";
 import { OpenCodeLogoIcon } from "./OpenCodeLogoIcon";
+import { shouldShowLegacyWorkingDirectoryField } from "../lib/legacy-agent-config";
 
 /* ---- Create mode values ---- */
 
@@ -297,6 +298,8 @@ export function AgentConfigForm(props: AgentConfigFormProps) {
     adapterType === "opencode_local" ||
     adapterType === "pi_local" ||
     adapterType === "cursor";
+  const showLegacyWorkingDirectoryField =
+    isLocal && shouldShowLegacyWorkingDirectoryField({ isCreate, adapterConfig: config });
   const uiAdapter = useMemo(() => getUIAdapter(adapterType), [adapterType]);
 
   // Fetch adapter models for the effective adapter type
@@ -590,8 +593,8 @@ export function AgentConfigForm(props: AgentConfigFormProps) {
           )}
 
           {/* Working directory */}
-          {isLocal && (
-            <Field label="Working directory" hint={help.cwd}>
+          {showLegacyWorkingDirectoryField && (
+            <Field label="Working directory (deprecated)" hint={help.cwd}>
               <div className="flex items-center gap-2 rounded-md border border-border px-2.5 py-1.5">
                 <FolderOpen className="h-3.5 w-3.5 text-muted-foreground shrink-0" />
                 <DraftInput

ui/src/components/DevRestartBanner.tsx

@@ -0,0 +1,89 @@
+import { AlertTriangle, RotateCcw, TimerReset } from "lucide-react";
+import type { DevServerHealthStatus } from "../api/health";
+
+function formatRelativeTimestamp(value: string | null): string | null {
+  if (!value) return null;
+  const timestamp = new Date(value).getTime();
+  if (Number.isNaN(timestamp)) return null;
+
+  const deltaMs = Date.now() - timestamp;
+  if (deltaMs < 60_000) return "just now";
+  const deltaMinutes = Math.round(deltaMs / 60_000);
+  if (deltaMinutes < 60) return `${deltaMinutes}m ago`;
+  const deltaHours = Math.round(deltaMinutes / 60);
+  if (deltaHours < 24) return `${deltaHours}h ago`;
+  const deltaDays = Math.round(deltaHours / 24);
+  return `${deltaDays}d ago`;
+}
+
+function describeReason(devServer: DevServerHealthStatus): string {
+  if (devServer.reason === "backend_changes_and_pending_migrations") {
+    return "backend files changed and migrations are pending";
+  }
+  if (devServer.reason === "pending_migrations") {
+    return "pending migrations need a fresh boot";
+  }
+  return "backend files changed since this server booted";
+}
+
+export function DevRestartBanner({ devServer }: { devServer?: DevServerHealthStatus }) {
+  if (!devServer?.enabled || !devServer.restartRequired) return null;
+
+  const changedAt = formatRelativeTimestamp(devServer.lastChangedAt);
+  const sample = devServer.changedPathsSample.slice(0, 3);
+
+  return (
+    <div className="border-b border-amber-300/60 bg-amber-50 text-amber-950 dark:border-amber-500/25 dark:bg-amber-500/10 dark:text-amber-100">
+      <div className="flex flex-col gap-3 px-3 py-2.5 md:flex-row md:items-center md:justify-between">
+        <div className="min-w-0">
+          <div className="flex items-center gap-2 text-[12px] font-semibold uppercase tracking-[0.18em]">
+            <AlertTriangle className="h-3.5 w-3.5 shrink-0" />
+            <span>Restart Required</span>
+            {devServer.autoRestartEnabled ? (
+              <span className="rounded-full bg-amber-900/10 px-2 py-0.5 text-[10px] tracking-[0.14em] dark:bg-amber-100/10">
+                Auto-Restart On
+              </span>
+            ) : null}
+          </div>
+          <p className="mt-1 text-sm">
+            {describeReason(devServer)}
+            {changedAt ? ` · updated ${changedAt}` : ""}
+          </p>
+          <div className="mt-2 flex flex-wrap items-center gap-2 text-xs text-amber-900/80 dark:text-amber-100/75">
+            {sample.length > 0 ? (
+              <span>
+                Changed: {sample.join(", ")}
+                {devServer.changedPathCount > sample.length ? ` +${devServer.changedPathCount - sample.length} more` : ""}
+              </span>
+            ) : null}
+            {devServer.pendingMigrations.length > 0 ? (
+              <span>
+                Pending migrations: {devServer.pendingMigrations.slice(0, 2).join(", ")}
+                {devServer.pendingMigrations.length > 2 ? ` +${devServer.pendingMigrations.length - 2} more` : ""}
+              </span>
+            ) : null}
+          </div>
+        </div>
+
+        <div className="flex shrink-0 items-center gap-2 text-xs font-medium">
+          {devServer.waitingForIdle ? (
+            <div className="inline-flex items-center gap-2 rounded-full bg-amber-900/10 px-3 py-1.5 dark:bg-amber-100/10">
+              <TimerReset className="h-3.5 w-3.5" />
+              <span>Waiting for {devServer.activeRunCount} live run{devServer.activeRunCount === 1 ? "" : "s"} to finish</span>
+            </div>
+          ) : devServer.autoRestartEnabled ? (
+            <div className="inline-flex items-center gap-2 rounded-full bg-amber-900/10 px-3 py-1.5 dark:bg-amber-100/10">
+              <RotateCcw className="h-3.5 w-3.5" />
+              <span>Auto-restart will trigger when the instance is idle</span>
+            </div>
+          ) : (
+            <div className="inline-flex items-center gap-2 rounded-full bg-amber-900/10 px-3 py-1.5 dark:bg-amber-100/10">
+              <RotateCcw className="h-3.5 w-3.5" />
+              <span>Restart <code>pnpm dev:once</code> after the active work is safe to interrupt</span>
+            </div>
+          )}
+        </div>
+      </div>
+    </div>
+  );
+}

ui/src/components/InstanceSidebar.tsx

@@ -1,5 +1,5 @@
 import { useQuery } from "@tanstack/react-query";
-import { Clock3, FlaskConical, Puzzle, Settings } from "lucide-react";
+import { Clock3, FlaskConical, Puzzle, Settings, SlidersHorizontal } from "lucide-react";
 import { NavLink } from "@/lib/router";
 import { pluginsApi } from "@/api/plugins";
 import { queryKeys } from "@/lib/queryKeys";
@@ -22,6 +22,7 @@ export function InstanceSidebar() {
 
       <nav className="flex-1 min-h-0 overflow-y-auto scrollbar-auto-hide flex flex-col gap-4 px-3 py-2">
         <div className="flex flex-col gap-0.5">
+          <SidebarNavItem to="/instance/settings/general" label="General" icon={SlidersHorizontal} end />
           <SidebarNavItem to="/instance/settings/heartbeats" label="Heartbeats" icon={Clock3} end />
           <SidebarNavItem to="/instance/settings/experimental" label="Experimental" icon={FlaskConical} />
           <SidebarNavItem to="/instance/settings/plugins" label="Plugins" icon={Puzzle} />

ui/src/components/Layout.tsx

@@ -15,6 +15,7 @@ import { NewAgentDialog } from "./NewAgentDialog";
 import { ToastViewport } from "./ToastViewport";
 import { MobileBottomNav } from "./MobileBottomNav";
 import { WorktreeBanner } from "./WorktreeBanner";
+import { DevRestartBanner } from "./DevRestartBanner";
 import { useDialog } from "../context/DialogContext";
 import { usePanel } from "../context/PanelContext";
 import { useCompany } from "../context/CompanyContext";
@@ -78,6 +79,11 @@ export function Layout() {
     queryKey: queryKeys.health,
     queryFn: () => healthApi.get(),
     retry: false,
+    refetchInterval: (query) => {
+      const data = query.state.data as { devServer?: { enabled?: boolean } } | undefined;
+      return data?.devServer?.enabled ? 2000 : false;
+    },
+    refetchIntervalInBackground: true,
   });
 
   useEffect(() => {
@@ -266,6 +272,7 @@ export function Layout() {
         Skip to Main Content
       </a>
       <WorktreeBanner />
+      <DevRestartBanner devServer={health?.devServer} />
       <div className={cn("min-h-0 flex-1", isMobile ? "w-full" : "flex overflow-hidden")}>
         {isMobile && sidebarOpen && (
           <button

ui/src/components/MarkdownBody.test.tsx

@@ -0,0 +1,31 @@
+// @vitest-environment node
+
+import { describe, expect, it } from "vitest";
+import { renderToStaticMarkup } from "react-dom/server";
+import { ThemeProvider } from "../context/ThemeContext";
+import { MarkdownBody } from "./MarkdownBody";
+
+describe("MarkdownBody", () => {
+  it("renders markdown images without a resolver", () => {
+    const html = renderToStaticMarkup(
+      <ThemeProvider>
+        <MarkdownBody>{"![](/api/attachments/test/content)"}</MarkdownBody>
+      </ThemeProvider>,
+    );
+
+    expect(html).toContain('<img src="/api/attachments/test/content" alt=""/>');
+  });
+
+  it("resolves relative image paths when a resolver is provided", () => {
+    const html = renderToStaticMarkup(
+      <ThemeProvider>
+        <MarkdownBody resolveImageSrc={(src) => `/resolved/${src}`}>
+          {"![Org chart](images/org-chart.png)"}
+        </MarkdownBody>
+      </ThemeProvider>,
+    );
+
+    expect(html).toContain('src="/resolved/images/org-chart.png"');
+    expect(html).toContain('alt="Org chart"');
+  });
+});

ui/src/components/MarkdownBody.tsx

@@ -1,5 +1,5 @@
 import { isValidElement, useEffect, useId, useState, type CSSProperties, type ReactNode } from "react";
-import Markdown from "react-markdown";
+import Markdown, { type Components } from "react-markdown";
 import remarkGfm from "remark-gfm";
 import { parseProjectMentionHref } from "@paperclipai/shared";
 import { cn } from "../lib/utils";
@@ -8,6 +8,8 @@ import { useTheme } from "../context/ThemeContext";
 interface MarkdownBodyProps {
   children: string;
   className?: string;
+  /** Optional resolver for relative image paths (e.g. within export packages) */
+  resolveImageSrc?: (src: string) => string | null;
 }
 
 let mermaidLoaderPromise: Promise<typeof import("mermaid").default> | null = null;
@@ -112,8 +114,44 @@ function MermaidDiagramBlock({ source, darkMode }: { source: string; darkMode: b
   );
 }
 
-export function MarkdownBody({ children, className }: MarkdownBodyProps) {
+export function MarkdownBody({ children, className, resolveImageSrc }: MarkdownBodyProps) {
   const { theme } = useTheme();
+  const components: Components = {
+    pre: ({ node: _node, children: preChildren, ...preProps }) => {
+      const mermaidSource = extractMermaidSource(preChildren);
+      if (mermaidSource) {
+        return <MermaidDiagramBlock source={mermaidSource} darkMode={theme === "dark"} />;
+      }
+      return <pre {...preProps}>{preChildren}</pre>;
+    },
+    a: ({ href, children: linkChildren }) => {
+      const parsed = href ? parseProjectMentionHref(href) : null;
+      if (parsed) {
+        const label = linkChildren;
+        return (
+          <a
+            href={`/projects/${parsed.projectId}`}
+            className="paperclip-project-mention-chip"
+            style={mentionChipStyle(parsed.color)}
+          >
+            {label}
+          </a>
+        );
+      }
+      return (
+        <a href={href} rel="noreferrer">
+          {linkChildren}
+        </a>
+      );
+    },
+  };
+  if (resolveImageSrc) {
+    components.img = ({ node: _node, src, alt, ...imgProps }) => {
+      const resolved = src ? resolveImageSrc(src) : null;
+      return <img {...imgProps} src={resolved ?? src} alt={alt ?? ""} />;
+    };
+  }
+
   return (
     <div
       className={cn(
@@ -122,38 +160,7 @@ export function MarkdownBody({ children, className }: MarkdownBodyProps) {
         className,
       )}
     >
-      <Markdown
-        remarkPlugins={[remarkGfm]}
-        components={{
-          pre: ({ node: _node, children: preChildren, ...preProps }) => {
-            const mermaidSource = extractMermaidSource(preChildren);
-            if (mermaidSource) {
-              return <MermaidDiagramBlock source={mermaidSource} darkMode={theme === "dark"} />;
-            }
-            return <pre {...preProps}>{preChildren}</pre>;
-          },
-          a: ({ href, children: linkChildren }) => {
-            const parsed = href ? parseProjectMentionHref(href) : null;
-            if (parsed) {
-              const label = linkChildren;
-              return (
-                <a
-                  href={`/projects/${parsed.projectId}`}
-                  className="paperclip-project-mention-chip"
-                  style={mentionChipStyle(parsed.color)}
-                >
-                  {label}
-                </a>
-              );
-            }
-            return (
-              <a href={href} rel="noreferrer">
-                {linkChildren}
-              </a>
-            );
-          },
-        }}
-      >
+      <Markdown remarkPlugins={[remarkGfm]} components={components}>
         {children}
       </Markdown>
     </div>

ui/src/components/OnboardingWizard.tsx

@@ -32,8 +32,6 @@ import { DEFAULT_CURSOR_LOCAL_MODEL } from "@paperclipai/adapter-cursor-local";
 import { DEFAULT_GEMINI_LOCAL_MODEL } from "@paperclipai/adapter-gemini-local";
 import { resolveRouteOnboardingOptions } from "../lib/onboarding-route";
 import { AsciiArtAnimation } from "./AsciiArtAnimation";
-import { ChoosePathButton } from "./PathInstructionsModal";
-import { HintIcon } from "./agent-config-primitives";
 import { OpenCodeLogoIcon } from "./OpenCodeLogoIcon";
 import {
   Building2,
@@ -49,7 +47,6 @@ import {
   MousePointer2,
   Check,
   Loader2,
-  FolderOpen,
   ChevronDown,
   X
 } from "lucide-react";
@@ -62,17 +59,14 @@ type AdapterType =
   | "opencode_local"
   | "pi_local"
   | "cursor"
-  | "process"
   | "http"
   | "openclaw_gateway";
 
-const DEFAULT_TASK_DESCRIPTION = `Setup yourself as the CEO. Use the ceo persona found here: 
+const DEFAULT_TASK_DESCRIPTION = `You are the CEO. You set the direction for the company.
 
-https://github.com/paperclipai/companies/blob/main/default/ceo/AGENTS.md
-
-Ensure you have a folder agents/ceo and then download this AGENTS.md, and sibling HEARTBEAT.md, SOUL.md, and TOOLS.md. and set that AGENTS.md as the path to your agents instruction file
-
-After that, hire yourself a Founding Engineer agent and then plan the roadmap and tasks for your new company.`;
+- hire a founding engineer
+- write a hiring plan
+- break the roadmap into concrete tasks and start delegating work`;
 
 export function OnboardingWizard() {
   const { onboardingOpen, onboardingOptions, closeOnboarding } = useDialog();
@@ -113,7 +107,6 @@ export function OnboardingWizard() {
   // Step 2
   const [agentName, setAgentName] = useState("CEO");
   const [adapterType, setAdapterType] = useState<AdapterType>("claude_local");
-  const [cwd, setCwd] = useState("");
   const [model, setModel] = useState("");
   const [command, setCommand] = useState("");
   const [args, setArgs] = useState("");
@@ -128,7 +121,9 @@ export function OnboardingWizard() {
   const [showMoreAdapters, setShowMoreAdapters] = useState(false);
 
   // Step 3
-  const [taskTitle, setTaskTitle] = useState("Create your CEO HEARTBEAT.md");
+  const [taskTitle, setTaskTitle] = useState(
+    "Hire your first engineer and create a hiring plan"
+  );
   const [taskDescription, setTaskDescription] = useState(
     DEFAULT_TASK_DESCRIPTION
   );
@@ -217,7 +212,7 @@ export function OnboardingWizard() {
     if (step !== 2) return;
     setAdapterEnvResult(null);
     setAdapterEnvError(null);
-  }, [step, adapterType, cwd, model, command, args, url]);
+  }, [step, adapterType, model, command, args, url]);
 
   const selectedModel = (adapterModels ?? []).find((m) => m.id === model);
   const hasAnthropicApiKeyOverrideCheck =
@@ -273,7 +268,6 @@ export function OnboardingWizard() {
     setCompanyGoal("");
     setAgentName("CEO");
     setAdapterType("claude_local");
-    setCwd("");
     setModel("");
     setCommand("");
     setArgs("");
@@ -283,7 +277,7 @@ export function OnboardingWizard() {
     setAdapterEnvLoading(false);
     setForceUnsetAnthropicApiKey(false);
     setUnsetAnthropicLoading(false);
-    setTaskTitle("Create your CEO HEARTBEAT.md");
+    setTaskTitle("Hire your first engineer and create a hiring plan");
     setTaskDescription(DEFAULT_TASK_DESCRIPTION);
     setCreatedCompanyId(null);
     setCreatedCompanyPrefix(null);
@@ -301,7 +295,6 @@ export function OnboardingWizard() {
     const config = adapter.buildAdapterConfig({
       ...defaultCreateValues,
       adapterType,
-      cwd,
       model:
         adapterType === "codex_local"
           ? model || DEFAULT_CODEX_LOCAL_MODEL
@@ -787,12 +780,6 @@ export function OnboardingWizard() {
                             icon: Gem,
                             desc: "Local Gemini agent"
                           },
-                          {
-                            value: "process" as const,
-                            label: "Process",
-                            icon: Terminal,
-                            desc: "Run a local command"
-                          },
                           {
                             value: "opencode_local" as const,
                             label: "OpenCode",
@@ -874,24 +861,6 @@ export function OnboardingWizard() {
                     adapterType === "pi_local" ||
                     adapterType === "cursor") && (
                     <div className="space-y-3">
-                      <div>
-                        <div className="flex items-center gap-1.5 mb-1">
-                          <label className="text-xs text-muted-foreground">
-                            Working directory
-                          </label>
-                          <HintIcon text="Paperclip works best if you create a new folder for your agents to keep their memories and stay organized. Create a new folder and put the path here." />
-                        </div>
-                        <div className="flex items-center gap-2 rounded-md border border-border px-2.5 py-1.5">
-                          <FolderOpen className="h-3.5 w-3.5 text-muted-foreground shrink-0" />
-                          <input
-                            className="w-full bg-transparent outline-none text-sm font-mono placeholder:text-muted-foreground/50"
-                            placeholder="/path/to/project"
-                            value={cwd}
-                            onChange={(e) => setCwd(e.target.value)}
-                          />
-                          <ChoosePathButton />
-                        </div>
-                      </div>
                       <div>
                         <label className="text-xs text-muted-foreground mb-1 block">
                           Model
@@ -1110,33 +1079,6 @@ export function OnboardingWizard() {
                     </div>
                   )}
 
-                  {adapterType === "process" && (
-                    <div className="space-y-3">
-                      <div>
-                        <label className="text-xs text-muted-foreground mb-1 block">
-                          Command
-                        </label>
-                        <input
-                          className="w-full rounded-md border border-border bg-transparent px-3 py-2 text-sm font-mono outline-none focus:ring-1 focus:ring-ring placeholder:text-muted-foreground/50"
-                          placeholder="e.g. node, python"
-                          value={command}
-                          onChange={(e) => setCommand(e.target.value)}
-                        />
-                      </div>
-                      <div>
-                        <label className="text-xs text-muted-foreground mb-1 block">
-                          Args (comma-separated)
-                        </label>
-                        <input
-                          className="w-full rounded-md border border-border bg-transparent px-3 py-2 text-sm font-mono outline-none focus:ring-1 focus:ring-ring placeholder:text-muted-foreground/50"
-                          placeholder="e.g. script.js, --flag"
-                          value={args}
-                          onChange={(e) => setArgs(e.target.value)}
-                        />
-                      </div>
-                    </div>
-                  )}
-
                   {(adapterType === "http" ||
                     adapterType === "openclaw_gateway") && (
                     <div>

ui/src/components/agent-config-primitives.tsx

@@ -25,7 +25,7 @@ export const help: Record<string, string> = {
   reportsTo: "The agent this one reports to in the org hierarchy.",
   capabilities: "Describes what this agent can do. Shown in the org chart and used for task routing.",
   adapterType: "How this agent runs: local CLI (Claude/Codex/OpenCode), OpenClaw Gateway, spawned process, or generic HTTP webhook.",
-  cwd: "Default working directory fallback for local adapters. Use an absolute path on the machine running Paperclip.",
+  cwd: "Deprecated legacy working directory fallback for local adapters. Existing agents may still carry this value, but new configurations should use project workspaces instead.",
   promptTemplate: "Sent on every heartbeat. Keep this small and dynamic. Use it for current-task framing, not large static instructions. Supports {{ agent.id }}, {{ agent.name }}, {{ agent.role }} and other template variables.",
   model: "Override the default model used by the adapter.",
   thinkingEffort: "Control model reasoning depth. Supported values vary by adapter/model.",

ui/src/components/transcript/useLiveRunTranscripts.ts

@@ -1,7 +1,10 @@
 import { useEffect, useMemo, useRef, useState } from "react";
+import { useQuery } from "@tanstack/react-query";
 import type { LiveEvent } from "@paperclipai/shared";
+import { instanceSettingsApi } from "../../api/instanceSettings";
 import { heartbeatsApi, type LiveRunForIssue } from "../../api/heartbeats";
 import { buildTranscript, getUIAdapter, type RunLogChunk, type TranscriptEntry } from "../../adapters";
+import { queryKeys } from "../../lib/queryKeys";
 
 const LOG_POLL_INTERVAL_MS = 2000;
 const LOG_READ_LIMIT_BYTES = 256_000;
@@ -65,6 +68,10 @@ export function useLiveRunTranscripts({
   const seenChunkKeysRef = useRef(new Set<string>());
   const pendingLogRowsByRunRef = useRef(new Map<string, string>());
   const logOffsetByRunRef = useRef(new Map<string, number>());
+  const { data: generalSettings } = useQuery({
+    queryKey: queryKeys.instance.generalSettings,
+    queryFn: () => instanceSettingsApi.getGeneral(),
+  });
 
   const runById = useMemo(() => new Map(runs.map((run) => [run.id, run])), [runs]);
   const activeRunIds = useMemo(
@@ -267,12 +274,18 @@ export function useLiveRunTranscripts({
 
   const transcriptByRun = useMemo(() => {
     const next = new Map<string, TranscriptEntry[]>();
+    const censorUsernameInLogs = generalSettings?.censorUsernameInLogs === true;
     for (const run of runs) {
       const adapter = getUIAdapter(run.adapterType);
-      next.set(run.id, buildTranscript(chunksByRun.get(run.id) ?? [], adapter.parseStdoutLine));
+      next.set(
+        run.id,
+        buildTranscript(chunksByRun.get(run.id) ?? [], adapter.parseStdoutLine, {
+          censorUsernameInLogs,
+        }),
+      );
     }
     return next;
-  }, [chunksByRun, runs]);
+  }, [chunksByRun, generalSettings?.censorUsernameInLogs, runs]);
 
   return {
     transcriptByRun,