diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d8ba072..ad18bbb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -9,33 +9,20 @@ permissions:
   contents: read
 
 jobs:
-  core:
-    strategy:
-      matrix:
-        os: [ubuntu-latest, windows-latest]
-    runs-on: ${{ matrix.os }}
+  verify:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v7
       - uses: actions/setup-node@v7
         with:
           node-version: 22
           cache: npm
+          cache-dependency-path: |
+            package-lock.json
+            desktop/package-lock.json
       - run: npm ci
       - run: npm run check
-      - run: npm audit --omit=dev
-
-  desktop:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: desktop
-    steps:
-      - uses: actions/checkout@v7
-      - uses: actions/setup-node@v7
-        with:
-          node-version: 22
-          cache: npm
-          cache-dependency-path: desktop/package-lock.json
       - run: npm ci
+        working-directory: desktop
       - run: npm run typecheck
-      - run: npm audit --omit=dev
+        working-directory: desktop
diff --git a/.github/workflows/dependency-audit.yml b/.github/workflows/dependency-audit.yml
new file mode 100644
index 0000000..f149c9b
--- /dev/null
+++ b/.github/workflows/dependency-audit.yml
@@ -0,0 +1,28 @@
+name: Dependency Audit
+
+on:
+  schedule:
+    - cron: "17 9 * * 1"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  audit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-node@v7
+        with:
+          node-version: 22
+          cache: npm
+          cache-dependency-path: |
+            package-lock.json
+            desktop/package-lock.json
+      - run: npm ci
+      - run: npm audit --omit=dev
+      - run: npm ci
+        working-directory: desktop
+      - run: npm audit --omit=dev
+        working-directory: desktop
diff --git a/README.md b/README.md
index 542a00a..13ebaea 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@ Coding agents are effective inside one task and one checkout. The harder problem
 - manager-owned commits retained under `refs/codepilot/runs/...`
 - collision detection, integration branches, repository validation, and deterministic review
 - Git-native task provenance and generated GitHub pull-request descriptions
-- an Electron desktop control plane for projects, task queues, knowledge, and live agent events
+- an Electron desktop control plane with local/remote Git onboarding, project-scoped PM threads, task queues, knowledge, and live agent events
 
 ## Trust boundary
 
@@ -30,6 +30,7 @@ codePilot filters parent conversation identifiers and common unrelated secrets f
 
 - Node.js 22+
 - Git
+- GitHub CLI for repository cloning and pull-request publication
 - Codex CLI and/or Claude Code, already installed and authenticated
 - Windows, macOS, or Linux for the CLI; the packaged desktop flow is currently Windows-first
 
@@ -74,6 +75,10 @@ npm run desktop:dev
 
 Build the Windows package with `npm run desktop:build`; output is written under `desktop/out/`. Automatic task deployment is off by default.
 
+The Projects screen can register an existing local Git checkout or clone an HTTPS/SSH remote into the configured projects directory. Credentials are never accepted in repository URLs; Git's configured credential helper or SSH agent owns authentication. After registration, onboarding asks the operator to review the App Core start command, repository-relative working directory, and local URL before Project Manager begins; this step saves configuration but never launches the app. Each registered repository has its own Project Manager thread, conversation, backlog, knowledge, and run database. Turns are serialized within one project while different projects can think and execute concurrently, even as the desktop switches between them. Removing a project only unregisters it from the workspace; its repository and `.codepilot` data remain on disk so it can be onboarded again later.
+
+Settings includes a GitHub connection panel backed by the official `gh` browser login. GitHub CLI stores the credential in the operating-system credential store; codePilot receives only redacted account/status metadata. GitHub writes require both the global **Allow GitHub write operations** switch and an explicit **Create GitHub pull request** selection for that deployment. Today those writes are limited to pushing the generated integration branch and opening its pull request—codePilot does not merge, delete, change repository settings, or grant access.
+
 The older local Next.js dashboard is deliberately absent from the public tree because it contains a separately licensed UI kit. Electron is the supported public UI.
 
 ## Worker configuration
diff --git a/desktop/src/active-agents.tsx b/desktop/src/active-agents.tsx
index eac6672..2616ade 100644
--- a/desktop/src/active-agents.tsx
+++ b/desktop/src/active-agents.tsx
@@ -3,7 +3,7 @@ import { ChevronDownIcon, FolderOpenIcon, StopCircleIcon } from "@heroicons/reac
 import type { ActiveAgent } from "./types";
 import { collapseLifecycleEvents, EventView } from "./event-view";
 
-export function ActiveAgents() {
+export function ActiveAgents({ projectId }: { projectId: string }) {
   const [agents, setAgents] = useState<ActiveAgent[]>([]),
     [expanded, setExpanded] = useState<Set<string>>(new Set()),
     [messages, setMessages] = useState<Record<string, string>>({}),
@@ -15,7 +15,7 @@ export function ActiveAgents() {
     logs = useRef(new Map<string, HTMLDivElement>());
   async function refresh() {
     try {
-      const next = await window.codepilot.getActiveAgents();
+      const next = await window.codepilot.getActiveAgents(projectId);
       setAgents(next);
       setExpanded((current) => {
         const copy = new Set(current);
@@ -34,7 +34,7 @@ export function ActiveAgents() {
     void refresh();
     const timer = setInterval(() => void refresh(), 1200);
     return () => clearInterval(timer);
-  }, []);
+  }, [projectId]);
   useEffect(() => {
     const frame = requestAnimationFrame(() => {
       for (const [taskId, element] of logs.current)
@@ -55,7 +55,7 @@ export function ActiveAgents() {
     setSending(agent.taskId);
     setError("");
     try {
-      setAgents(await window.codepilot.guideAgent(agent.taskId, message));
+      setAgents(await window.codepilot.guideAgent(projectId, agent.taskId, message));
       setMessages((current) => ({ ...current, [agent.taskId]: "" }));
     } catch (cause) {
       setError(cause instanceof Error ? cause.message : String(cause));
@@ -67,7 +67,7 @@ export function ActiveAgents() {
     setInterrupting(agent.taskId);
     setError("");
     try {
-      const result = await window.codepilot.interruptAgent(agent.taskId);
+      const result = await window.codepilot.interruptAgent(projectId, agent.taskId);
       setFeedback(result.feedback);
       setAgents(result.agents);
     } catch (cause) {
@@ -90,7 +90,7 @@ export function ActiveAgents() {
           </p>
         </div>
         <div className="flex gap-2">
-            <button onClick={() => void window.codepilot.openProjectDirectory()} className="flex items-center gap-2 rounded-lg border border-white/10 px-3 py-2 text-xs text-zinc-300 hover:bg-white/5"><FolderOpenIcon className="size-4" />Open project folder</button>
+            <button onClick={() => void window.codepilot.openProjectDirectory(projectId)} className="flex items-center gap-2 rounded-lg border border-white/10 px-3 py-2 text-xs text-zinc-300 hover:bg-white/5"><FolderOpenIcon className="size-4" />Open project folder</button>
           {agents.length > 1 && <>
             <button
               onClick={() =>
diff --git a/desktop/src/agents.tsx b/desktop/src/agents.tsx
index 769b67e..da5a6b7 100644
--- a/desktop/src/agents.tsx
+++ b/desktop/src/agents.tsx
@@ -1,7 +1,7 @@
 import React, { useEffect, useState } from "react";
 import { PlayIcon } from "@heroicons/react/24/outline";
 import type { AgentRunResult, DesktopState, PMState, PMTask } from "./types";
-export function Agents({ onState }: { onState(state: DesktopState): void }) {
+export function Agents({ projectId, onState }: { projectId: string; onState(state: DesktopState): void }) {
   const [objective, setObjective] = useState(""),
     [codex, setCodex] = useState(true),
     [claude, setClaude] = useState(false),
@@ -13,11 +13,12 @@ export function Agents({ onState }: { onState(state: DesktopState): void }) {
     [error, setError] = useState(""),
     [results, setResults] = useState<AgentRunResult[]>([]);
   const [pmState, setPMState] = useState<PMState>();
+  const [githubReady, setGitHubReady] = useState(false);
   const [showAllTasks, setShowAllTasks] = useState(false);
   const [poofing, setPoofing] = useState<Set<string>>(() => new Set());
-  useEffect(() => { void window.codepilot.getGlobalSettings().then((settings) => { setCodex(settings.defaultProvider === "codex"); setClaude(settings.defaultProvider === "claude"); }); }, []);
-  useEffect(() => { let active = true; const refresh = () => void window.codepilot.getPM().then((next) => active && setPMState(next)); refresh(); const timer = window.setInterval(refresh, 2000); return () => { active = false; window.clearInterval(timer); }; }, []);
-  async function deployTask(task: PMTask) { setError(""); try { setPMState(await window.codepilot.setPMTaskStatus(task.id, "launched")); setPoofing((items) => new Set(items).add(task.id)); await new Promise((resolve) => window.setTimeout(resolve, 900)); const result = await window.codepilot.runAgents({ objective: `${task.title}\n\ncodePilot PM task: ${task.id}\n\n${task.description}\n\nAcceptance criteria:\n${task.acceptanceCriteria.map((item) => `- ${item}`).join("\n")}`, providers: [task.recommendedProvider === "claude" ? "claude" : "codex"], retries: 0, timeoutMinutes: 30, validationCommands: [], integrate, createPullRequest, dryRun }); setResults((current) => [result, ...current].slice(0, 5)); const nextStatus = result.status === "completed" ? "done" : "ready"; const summary = result.review.findings.length ? result.review.findings.join(" ") : `Task did not advance because the agent run returned ${result.status} with review verdict ${result.review.verdict}.`; setPMState(await window.codepilot.setPMTaskStatus(task.id, nextStatus, summary)); } catch (cause) { const reason = cause instanceof Error ? cause.message : String(cause); setError(reason); try { setPMState(await window.codepilot.setPMTaskStatus(task.id, "ready", `Task did not advance because deployment failed: ${reason}`)); } catch {} } finally { setPoofing((items) => { const next = new Set(items); next.delete(task.id); return next; }); } }
+  useEffect(() => { void Promise.all([window.codepilot.getGlobalSettings(), window.codepilot.getGitHubStatus()]).then(([settings, status]) => { setCodex(settings.defaultProvider === "codex"); setClaude(settings.defaultProvider === "claude"); setGitHubReady(status.authenticated && settings.github.allowWrites); }); }, []);
+  useEffect(() => { let active = true; const refresh = () => void window.codepilot.getPM(projectId).then((next) => active && setPMState(next)); refresh(); const timer = window.setInterval(refresh, 2000); return () => { active = false; window.clearInterval(timer); }; }, [projectId]);
+  async function deployTask(task: PMTask) { setError(""); try { setPMState(await window.codepilot.setPMTaskStatus(projectId, task.id, "launched")); setPoofing((items) => new Set(items).add(task.id)); await new Promise((resolve) => window.setTimeout(resolve, 900)); const result = await window.codepilot.runAgents({ projectId, objective: `${task.title}\n\ncodePilot PM task: ${task.id}\n\n${task.description}\n\nAcceptance criteria:\n${task.acceptanceCriteria.map((item) => `- ${item}`).join("\n")}`, providers: [task.recommendedProvider === "claude" ? "claude" : "codex"], retries: 0, timeoutMinutes: 30, validationCommands: [], integrate, createPullRequest, dryRun }); setResults((current) => [result, ...current].slice(0, 5)); const nextStatus = result.status === "completed" ? "done" : "ready"; const summary = result.review.findings.length ? result.review.findings.join(" ") : `Task did not advance because the agent run returned ${result.status} with review verdict ${result.review.verdict}.`; setPMState(await window.codepilot.setPMTaskStatus(projectId, task.id, nextStatus, summary)); } catch (cause) { const reason = cause instanceof Error ? cause.message : String(cause); setError(reason); try { setPMState(await window.codepilot.setPMTaskStatus(projectId, task.id, "ready", `Task did not advance because deployment failed: ${reason}`)); } catch {} } finally { setPoofing((items) => { const next = new Set(items); next.delete(task.id); return next; }); } }
   async function launch() {
     const requestObjective = objective.trim();
     if (!requestObjective) return;
@@ -26,7 +27,7 @@ export function Agents({ onState }: { onState(state: DesktopState): void }) {
     setValidation("");
     try {
       const [title, ...rest] = requestObjective.split(/\r?\n/);
-      const nextPM = await window.codepilot.createPMTask({ title: title.slice(0, 160), description: `${rest.join("\n").trim() || title}${validation.trim() ? `\n\nVerification criteria:\n${validation.trim()}` : ""}`, acceptanceCriteria: validation.split("\n").map((item) => item.trim()).filter(Boolean), recommendedProvider: codex ? "codex" : "claude" });
+      const nextPM = await window.codepilot.createPMTask(projectId, { title: title.slice(0, 160), description: `${rest.join("\n").trim() || title}${validation.trim() ? `\n\nVerification criteria:\n${validation.trim()}` : ""}`, acceptanceCriteria: validation.split("\n").map((item) => item.trim()).filter(Boolean), recommendedProvider: codex ? "codex" : "claude" });
       setPMState(nextPM);
       const created = [...nextPM.tasks].reverse().find((task) => task.title === title.slice(0, 160));
       if (created) void deployTask(created);
@@ -118,8 +119,9 @@ export function Agents({ onState }: { onState(state: DesktopState): void }) {
               set={setIntegrate}
             />
             <Check
-              label="Create GitHub pull request"
+              label={githubReady ? "Create GitHub pull request" : "Connect GitHub in Settings to publish"}
               checked={createPullRequest}
+              disabled={!githubReady}
               set={(value) => { setCreatePullRequest(value); if (value) { setIntegrate(true); setDryRun(false); } }}
             />
             <Check label="Dry run only" checked={dryRun} set={setDryRun} />
@@ -154,16 +156,19 @@ function Check({
   label,
   checked,
   set,
+  disabled = false,
 }: {
   label: string;
   checked: boolean;
   set(value: boolean): void;
+  disabled?: boolean;
 }) {
   return (
-    <label className="mb-3 flex cursor-pointer items-center justify-between text-sm text-zinc-300">
+    <label className={`mb-3 flex items-center justify-between text-sm text-zinc-300 ${disabled ? "cursor-not-allowed opacity-50" : "cursor-pointer"}`}>
       <span>{label}</span>
       <input
         type="checkbox"
+        disabled={disabled}
         checked={checked}
         onChange={(e) => set(e.target.checked)}
         className="size-4 accent-indigo-500"
diff --git a/desktop/src/app-control.tsx b/desktop/src/app-control.tsx
index 3939267..f5f5666 100644
--- a/desktop/src/app-control.tsx
+++ b/desktop/src/app-control.tsx
@@ -1,4 +1,4 @@
-import { ArrowTopRightOnSquareIcon, PlayIcon, StopIcon, XMarkIcon } from "@heroicons/react/24/outline";
+import { ArrowPathIcon, ArrowTopRightOnSquareIcon, PlayIcon, StopIcon, XMarkIcon } from "@heroicons/react/24/outline";
 import { useEffect, useRef, useState } from "react";
 import type { AppConfig, AppStatus } from "./types";
 
@@ -6,6 +6,7 @@ export function AppControl({ projectId, status, onStatus }: { projectId: string;
   const [config, setConfig] = useState<AppConfig>({ command: "", workingDirectory: ".", url: "http://localhost:3000" });
   const [busy, setBusy] = useState("");
   const [message, setMessage] = useState("");
+  const [previewKey, setPreviewKey] = useState(0);
   const loaded = useRef(false);
   useEffect(() => {
     loaded.current = false;
@@ -21,17 +22,24 @@ export function AppControl({ projectId, status, onStatus }: { projectId: string;
     <div className="text-xs font-semibold uppercase tracking-[.2em] text-indigo-400">Project runtime</div>
     <div className="mt-3 flex items-center gap-4"><span className={`runtime-glyph runtime-glyph-large ${status?.running ? "runtime-glyph-on" : ""}`} aria-hidden="true"><span className="runtime-orbit" /><span className="runtime-core" /><span className="runtime-node runtime-node-a" /><span className="runtime-node runtime-node-b" /><span className="runtime-node runtime-node-c" /></span><div><div className="flex items-baseline gap-3"><h1 className="font-mono text-2xl font-semibold tracking-wide">APP CORE</h1><span className={`font-mono text-sm font-semibold tracking-[.22em] ${status?.running ? "text-emerald-300" : "text-zinc-600"}`}>// {status?.running ? "ON" : "OFF"}</span></div><div className={`mt-1 flex items-center gap-1 ${status?.running ? "text-emerald-400/60" : "text-zinc-700"}`} aria-hidden="true"><span className="core-signal h-1" /><span className="core-signal h-2" /><span className="core-signal h-3" /><span className="core-signal h-1.5" /><span className="ml-2 font-mono text-[9px] tracking-widest">{status?.running ? "PROCESS LINK ACTIVE" : "PROCESS LINK DORMANT"}</span></div></div></div>
     <p className="mt-2 text-sm text-zinc-400">Configure how codePilot launches this project. The PM can update these values when you ask it to configure the app.</p>
+    {config.url && <section className="mt-8 overflow-hidden rounded-2xl border border-white/10 bg-white/[.025]">
+      <header className="flex items-center justify-between gap-4 border-b border-white/10 px-5 py-4">
+        <div className="min-w-0"><h2 className="text-sm font-semibold">Live preview</h2><p className="mt-1 truncate font-mono text-[10px] text-zinc-600">{config.url}</p></div>
+        <button onClick={() => setPreviewKey(value => value + 1)} className="flex shrink-0 items-center gap-2 rounded-lg border border-white/10 px-3 py-2 text-xs text-zinc-300 hover:bg-white/5"><ArrowPathIcon className="size-3.5"/>Refresh</button>
+      </header>
+      <iframe key={`${config.url}-${previewKey}`} src={config.url} title="Project application preview" sandbox="allow-scripts allow-same-origin allow-forms allow-popups allow-pointer-lock" referrerPolicy="no-referrer" className="h-[680px] w-full border-0 bg-zinc-950"/>
+    </section>}
     <div className="mt-8 grid grid-cols-[minmax(0,1fr)_minmax(320px,.8fr)] gap-6">
       <section className="rounded-2xl border border-white/10 bg-white/[.025] p-6">
         <div className="flex items-center justify-between"><h2 className="text-sm font-semibold">Launch configuration</h2><span className={`rounded-full px-2.5 py-1 text-[10px] font-semibold uppercase ${status?.running ? "bg-emerald-400/10 text-emerald-300" : "bg-zinc-400/10 text-zinc-500"}`}>{status?.running ? `Running · ${status.pid}` : "Stopped"}</span></div>
         <Label text="Start command"><input value={config.command} onChange={(event) => setConfig({ ...config, command: event.target.value })} placeholder="npm start" className="field" /></Label>
         <Label text="Working directory"><input value={config.workingDirectory} onChange={(event) => setConfig({ ...config, workingDirectory: event.target.value })} placeholder="." className="field" /></Label>
-        <Label text="App URL"><div className="flex gap-2"><input value={config.url} onChange={(event) => setConfig({ ...config, url: event.target.value })} placeholder="http://localhost:3000" className="field min-w-0 flex-1" /><button disabled={Boolean(busy) || !config.url} onClick={() => void act("clear-port", () => (window.codepilot as typeof window.codepilot & { clearProjectPort: () => Promise<AppStatus> }).clearProjectPort())} className="flex shrink-0 items-center gap-1 rounded-lg border border-amber-400/20 px-3 text-xs text-amber-300 hover:bg-amber-400/10 disabled:opacity-40"><XMarkIcon className="size-3.5" />Clear port</button></div></Label>
+        <Label text="App URL"><div className="flex gap-2"><input value={config.url} onChange={(event) => setConfig({ ...config, url: event.target.value })} placeholder="http://localhost:3000" className="field min-w-0 flex-1" /><button disabled={Boolean(busy) || !config.url} onClick={() => void act("clear-port", () => window.codepilot.clearProjectPort(projectId))} className="flex shrink-0 items-center gap-1 rounded-lg border border-amber-400/20 px-3 text-xs text-amber-300 hover:bg-amber-400/10 disabled:opacity-40"><XMarkIcon className="size-3.5" />Clear port</button></div></Label>
         {message && <p className="mt-4 text-xs text-amber-300">{message}</p>}
         <div className="mt-6 flex flex-wrap gap-3">
-          <button disabled={Boolean(busy)} onClick={() => void act("save", () => window.codepilot.saveAppConfig(config))} className="rounded-lg border border-white/10 px-4 py-2.5 text-sm text-zinc-300 hover:bg-white/5 disabled:opacity-50">Save configuration</button>
-          <button disabled={Boolean(busy)} onClick={() => void (status?.running ? act("stop", () => window.codepilot.stopProjectApp()) : act("start", () => window.codepilot.startProjectApp()))} className={`analog-control flex items-center gap-2 rounded-lg border px-5 py-2.5 text-sm font-semibold transition disabled:opacity-40 ${status?.running ? "analog-red" : "analog-green"}`}>{status?.running ? <StopIcon className="size-4" /> : <PlayIcon className="size-4" />}{busy ? "Working…" : status?.running ? "Stop app" : "Start app"}</button>
-          <button disabled={!config.url} onClick={() => void window.codepilot.openProjectApp()} className="flex items-center gap-2 rounded-lg border border-white/10 px-4 py-2.5 text-sm text-zinc-300 disabled:opacity-40"><ArrowTopRightOnSquareIcon className="size-4" />Open app</button>
+          <button disabled={Boolean(busy)} onClick={() => void act("save", () => window.codepilot.saveAppConfig(projectId, config))} className="rounded-lg border border-white/10 px-4 py-2.5 text-sm text-zinc-300 hover:bg-white/5 disabled:opacity-50">Save configuration</button>
+          <button disabled={Boolean(busy)} onClick={() => void (status?.running ? act("stop", () => window.codepilot.stopProjectApp(projectId)) : act("start", () => window.codepilot.startProjectApp(projectId)))} className={`analog-control flex items-center gap-2 rounded-lg border px-5 py-2.5 text-sm font-semibold transition disabled:opacity-40 ${status?.running ? "analog-red" : "analog-green"}`}>{status?.running ? <StopIcon className="size-4" /> : <PlayIcon className="size-4" />}{busy ? "Working…" : status?.running ? "Stop app" : "Start app"}</button>
+          <button disabled={!config.url} onClick={() => void window.codepilot.openProjectApp(projectId)} className="flex items-center gap-2 rounded-lg border border-white/10 px-4 py-2.5 text-sm text-zinc-300 disabled:opacity-40"><ArrowTopRightOnSquareIcon className="size-4" />Open app</button>
         </div>
       </section>
       <section className="flex min-h-96 flex-col overflow-hidden rounded-2xl border border-white/10 bg-white/[.025]"><header className="border-b border-white/10 p-5 text-sm font-semibold">App output</header><pre className="min-h-0 flex-1 overflow-auto whitespace-pre-wrap bg-black/20 p-5 text-[11px] leading-5 text-zinc-500">{status?.logs.length ? status.logs.join("") : "Start the app to see its output here."}</pre></section>
diff --git a/desktop/src/knowledge.tsx b/desktop/src/knowledge.tsx
index 5cb06df..b65bc28 100644
--- a/desktop/src/knowledge.tsx
+++ b/desktop/src/knowledge.tsx
@@ -1,15 +1,15 @@
 import { PaperAirplaneIcon, SparklesIcon } from "@heroicons/react/20/solid";
 import { useEffect, useRef, useState } from "react";
 import type { KnowledgeState } from "./types";
-export function Knowledge() {
+export function Knowledge({ projectId }: { projectId: string }) {
   const [state, setState] = useState<KnowledgeState>(),
     [input, setInput] = useState(""),
     [busy, setBusy] = useState(false),
     [error, setError] = useState("");
   const chat = useRef<HTMLDivElement>(null);
   useEffect(() => {
-    void window.codepilot.getKnowledge().then(setState);
-  }, []);
+    void window.codepilot.getKnowledge(projectId).then(setState);
+  }, [projectId]);
   useEffect(() => {
     const frame = requestAnimationFrame(() => {
       if (chat.current) chat.current.scrollTop = chat.current.scrollHeight;
@@ -23,7 +23,7 @@ export function Knowledge() {
     setError("");
     setInput("");
     try {
-      setState(await window.codepilot.chatKnowledge(message));
+      setState(await window.codepilot.chatKnowledge(projectId, message));
     } catch (cause) {
       setError(cause instanceof Error ? cause.message : String(cause));
     } finally {
diff --git a/desktop/src/main.ts b/desktop/src/main.ts
index 7447aac..29bc081 100644
--- a/desktop/src/main.ts
+++ b/desktop/src/main.ts
@@ -24,6 +24,7 @@ import type {
   NewPMTask,
   TaskBin,
   Project,
+  ProjectOnboardingInput,
 } from "./types";
 import { Manager } from "../../src/manager";
 import type { ProviderName } from "../../src/domain";
@@ -45,15 +46,26 @@ import {
   savePMTasks,
 } from "../../src/pm-store";
 import { CodexAppServer } from "./codex-app-server";
+import { KeyedSerialQueue } from "../../src/keyed-queue";
+import {
+  canonicalGitRepository,
+  cloneGitRepository,
+  repositoryNameFromRemote,
+  suggestedProjectName,
+} from "../../src/project-onboarding";
+import { removeProjectRegistration } from "../../src/project-registry";
+import { assertGitHubPublicationAllowed, parseGitHubAuthStatus, type GitHubStatus } from "../../src/github-auth";
 declare const MAIN_WINDOW_VITE_DEV_SERVER_URL: string | undefined;
 declare const MAIN_WINDOW_VITE_NAME: string;
 if (started) app.quit();
 let window: BrowserWindow | null = null;
 const pmServer = new CodexAppServer();
 const pmThreads = new Map<string, string>();
+const pmTurns = new KeyedSerialQueue();
+const pmActivity = new Map<string, number>();
 const appProcesses = new Map<string, ReturnType<typeof spawn>>();
 const appProcessState = new Map<string, { startedAt?: string; logs: string[] }>();
-const defaultGlobalSettings: GlobalSettings = { defaultProvider: "codex", scaffold: { mode: "guided", autoDeploy: false, onboardingPrompt: "You are onboarding me into a new project. Begin by asking focused questions about the users, problem, core workflow, constraints, technology preferences, and definition of success. Summarize decisions as we go. Create small implementation tasks only after requirements are agreed, then continue helping me shape and build the project incrementally." } };
+const defaultGlobalSettings: GlobalSettings = { defaultProvider: "codex", scaffold: { mode: "guided", autoDeploy: false, onboardingPrompt: "You are onboarding me into a new project. Begin by asking focused questions about the users, problem, core workflow, constraints, technology preferences, and definition of success. Summarize decisions as we go. Create small implementation tasks only after requirements are agreed, then continue helping me shape and build the project incrementally." }, github: { allowWrites: false } };
 const file = () => join(app.getPath("userData"), "state.json");
 function load(): DesktopState {
   try {
@@ -81,7 +93,7 @@ function save(state: DesktopState) {
 }
 function hydrate() {
   const state = load();
-  state.globalSettings = { ...defaultGlobalSettings, ...state.globalSettings, scaffold: { ...defaultGlobalSettings.scaffold, ...state.globalSettings?.scaffold } };
+  state.globalSettings = { ...defaultGlobalSettings, ...state.globalSettings, scaffold: { ...defaultGlobalSettings.scaffold, ...state.globalSettings?.scaffold }, github: { ...defaultGlobalSettings.github, ...state.globalSettings?.github } };
   const
     project =
       state.projects.find((item) => item.id === state.activeProjectId) ??
@@ -107,6 +119,48 @@ function hydrate() {
   }
   return state;
 }
+function githubStatus(): GitHubStatus {
+  try {
+    execFileSync("gh", ["--version"], { encoding: "utf8", windowsHide: true, stdio: ["ignore", "pipe", "pipe"] });
+  } catch {
+    return { installed: false, authenticated: false, host: "github.com", scopes: [], error: "GitHub CLI is not installed or is not available on PATH" };
+  }
+  try {
+    const output = execFileSync("gh", ["auth", "status", "--hostname", "github.com"], { encoding: "utf8", windowsHide: true, stdio: ["ignore", "pipe", "pipe"] });
+    return { installed: true, ...parseGitHubAuthStatus(output) };
+  } catch {
+    return { installed: true, authenticated: false, host: "github.com", scopes: [], error: "Connect a GitHub account to publish branches and pull requests" };
+  }
+}
+async function loginGitHub(): Promise<GitHubStatus> {
+  if (!githubStatus().installed) throw new Error("Install GitHub CLI before connecting a GitHub account");
+  await new Promise<void>((resolveLogin, rejectLogin) => {
+    const child = spawn("gh", ["auth", "login", "--hostname", "github.com", "--git-protocol", "https", "--web", "--clipboard", "--scopes", "workflow"], {
+      windowsHide: true,
+      stdio: ["ignore", "ignore", "ignore"],
+    });
+    const timeout = setTimeout(() => {
+      child.kill();
+      rejectLogin(new Error("GitHub sign-in timed out. Start it again when you are ready to finish in the browser."));
+    }, 10 * 60_000);
+    child.once("error", () => {
+      clearTimeout(timeout);
+      rejectLogin(new Error("GitHub sign-in could not start. Confirm that GitHub CLI is installed."));
+    });
+    child.once("close", (code) => {
+      clearTimeout(timeout);
+      if (code === 0) resolveLogin();
+      else rejectLogin(new Error("GitHub sign-in did not complete. No credentials were stored by CodePilot."));
+    });
+  });
+  execFileSync("gh", ["auth", "setup-git", "--hostname", "github.com"], { windowsHide: true, stdio: "ignore" });
+  const status = githubStatus();
+  if (!status.authenticated) throw new Error("GitHub CLI did not report a connected account after sign-in");
+  return status;
+}
+function assertGitHubWriteAccess() {
+  assertGitHubPublicationAllowed(Boolean(load().globalSettings?.github?.allowWrites), githubStatus());
+}
 function recoverInterruptedRuns() {
   for (const project of load().projects) {
     const db = join(project.repo, ".codepilot", "codepilot.db");
@@ -129,8 +183,8 @@ function recoverInterruptedRuns() {
     }
   }
 }
-function runDetail(id: string) {
-  const db = join(active().repo, ".codepilot", "codepilot.db");
+function runDetail(project: Project, id: string) {
+  const db = join(project.repo, ".codepilot", "codepilot.db");
   if (!existsSync(db)) throw new Error("Run database not found");
   using database = new DatabaseSync(db, { readOnly: true });
   const run = database.prepare("SELECT * FROM runs WHERE id = ?").get(id) as
@@ -171,26 +225,29 @@ function runDetail(id: string) {
 }
 function registerIPC() {
   ipcMain.handle("state:get", () => hydrate());
-  ipcMain.handle("project:brief-get",()=>projectBrief());
-  ipcMain.handle("project:brief-save",(_event,content:string)=>saveProjectBrief(String(content).slice(0,100000)));
+  ipcMain.handle("project:brief-get",(_event,projectId:string)=>projectBrief(projectById(projectId)));
+  ipcMain.handle("project:brief-save",(_event,projectId:string,content:string)=>saveProjectBrief(projectById(projectId),String(content).slice(0,100000)));
   ipcMain.handle("projects:activity",()=>projectActivity());
-  ipcMain.handle("settings:get", () => ({ ...defaultGlobalSettings, ...load().globalSettings, scaffold: { ...defaultGlobalSettings.scaffold, ...load().globalSettings?.scaffold } }));
+  ipcMain.handle("settings:get", () => ({ ...defaultGlobalSettings, ...load().globalSettings, scaffold: { ...defaultGlobalSettings.scaffold, ...load().globalSettings?.scaffold }, github: { ...defaultGlobalSettings.github, ...load().globalSettings?.github } }));
   ipcMain.handle("settings:save", (_event, settings: GlobalSettings) => {
     const state = load();
-    state.globalSettings = { defaultProvider: settings.defaultProvider === "claude" ? "claude" : "codex", scaffold: { mode: settings.scaffold?.mode === "blank" ? "blank" : "guided", autoDeploy: Boolean(settings.scaffold?.autoDeploy), onboardingPrompt: String(settings.scaffold?.onboardingPrompt || defaultGlobalSettings.scaffold.onboardingPrompt).trim().slice(0, 12000) } };
+    state.globalSettings = { defaultProvider: settings.defaultProvider === "claude" ? "claude" : "codex", scaffold: { mode: settings.scaffold?.mode === "blank" ? "blank" : "guided", autoDeploy: Boolean(settings.scaffold?.autoDeploy), onboardingPrompt: String(settings.scaffold?.onboardingPrompt || defaultGlobalSettings.scaffold.onboardingPrompt).trim().slice(0, 12000) }, github: { allowWrites: Boolean(settings.github?.allowWrites) } };
     save(state); return state.globalSettings;
   });
-  ipcMain.handle("run:detail", (_event, id: string) => runDetail(id));
-  ipcMain.handle("app:status", () => projectAppStatus());
-  ipcMain.handle("app:save-config", (_event, config: AppConfig) => {
-    saveAppConfig(config);
-    return projectAppStatus();
+  ipcMain.handle("github:status", () => githubStatus());
+  ipcMain.handle("github:login", () => loginGitHub());
+  ipcMain.handle("run:detail", (_event, projectId: string, id: string) => runDetail(projectById(projectId), id));
+  ipcMain.handle("app:status", (_event, projectId: string) => projectAppStatus(projectById(projectId)));
+  ipcMain.handle("app:save-config", (_event, projectId: string, config: AppConfig) => {
+    const project = projectById(projectId);
+    saveAppConfig(config, project);
+    return projectAppStatus(project);
   });
-  ipcMain.handle("app:start", () => startProjectApp());
-  ipcMain.handle("app:stop", () => stopProjectApp());
-  ipcMain.handle("app:clear-port", () => clearProjectPort());
-  ipcMain.handle("app:open", async () => {
-    const { config } = projectAppStatus();
+  ipcMain.handle("app:start", (_event, projectId: string) => startProjectApp(projectById(projectId)));
+  ipcMain.handle("app:stop", (_event, projectId: string) => stopProjectApp(projectById(projectId)));
+  ipcMain.handle("app:clear-port", (_event, projectId: string) => clearProjectPort(projectById(projectId)));
+  ipcMain.handle("app:open", async (_event, projectId: string) => {
+    const { config } = projectAppStatus(projectById(projectId));
     if (!/^https?:\/\//i.test(config.url)) throw new Error("Configure an http:// or https:// app URL first");
     await shell.openExternal(config.url);
   });
@@ -212,56 +269,67 @@ function registerIPC() {
   });
   ipcMain.handle(
     "project:add",
-    (_event, input: { name: string; repo?: string }) => {
+    (_event, input: { name: string }) => {
       const state = load(),
         name = input.name.trim();
       if (!name) throw new Error("Project name is required");
-      let repo = input.repo
-        ? resolve(input.repo)
-        : resolve(
-            state.projectsDirectory,
-            name.replace(/[^a-zA-Z0-9._-]+/g, "-"),
-          );
-      if (!input.repo) {
-        const rel = relative(resolve(state.projectsDirectory), repo);
-        if (!rel || rel.startsWith(".."))
-          throw new Error("Invalid generated project path");
-        if (existsSync(repo))
-          throw new Error("Project directory already exists");
-        ensureProjectGit(repo, true);
-        execFileSync("git", [
-          "-C",
-          repo,
-          "-c",
-          "user.name=codePilot",
-          "-c",
-          "user.email=codepilot@local",
-          "commit",
-          "--allow-empty",
-          "-m",
-          "Initialize project",
-        ]);
-      } else execFileSync("git", ["-C", repo, "rev-parse", "--show-toplevel"]);
-      if (input.repo) ensureProjectGit(repo);
-      const existing = state.projects.find(
-        (project) => project.repo.toLowerCase() === repo.toLowerCase(),
-      );
-      const project: Project = existing ?? {
+      const repo = resolve(state.projectsDirectory, name.replace(/[^a-zA-Z0-9._-]+/g, "-"));
+      const rel = relative(resolve(state.projectsDirectory), repo);
+      if (!rel || rel.startsWith("..")) throw new Error("Invalid generated project path");
+      if (existsSync(repo)) throw new Error("Project directory already exists");
+      ensureProjectGit(repo, true);
+      execFileSync("git", ["-C", repo, "-c", "user.name=codePilot", "-c", "user.email=codepilot@local", "commit", "--allow-empty", "-m", "Initialize project"]);
+      const project: Project = {
         id: randomUUID(),
         name,
         repo,
         createdAt: new Date().toISOString(),
       };
-      if (!existing) state.projects.push(project);
+      state.projects.push(project);
       state.activeProjectId = project.id;
       save(state);
       return hydrate();
     },
   );
+  ipcMain.handle("project:onboard", async (_event, input: ProjectOnboardingInput) => {
+    const state = load();
+    const repo = input.source === "local"
+      ? canonicalGitRepository(input.repo)
+      : await cloneGitRepository({
+          url: input.url,
+          projectsDirectory: state.projectsDirectory,
+          ...(input.directoryName?.trim() ? { directoryName: input.directoryName } : {}),
+        });
+    ensureProjectGit(repo);
+    const existing = state.projects.find((project) => samePath(project.repo, repo));
+    const fallbackName = input.source === "local" ? suggestedProjectName(repo) : repositoryNameFromRemote(input.url);
+    const name = input.name?.trim() || fallbackName;
+    const project: Project = existing ?? { id: randomUUID(), name, repo, createdAt: new Date().toISOString() };
+    if (!existing) state.projects.push(project);
+    state.activeProjectId = project.id;
+    save(state);
+    return hydrate();
+  });
+  ipcMain.handle("project:remove", (_event, projectId: string) => {
+    const state = load();
+    const project = state.projects.find((candidate) => candidate.id === projectId);
+    if (!project) throw new Error("Project not found. Refresh the workspace and try again.");
+    const activity = projectActivity()[project.id] ?? 0;
+    const appProcess = appProcesses.get(project.id);
+    if (activity > 0 || appProcess?.exitCode === null)
+      throw new Error("Stop this project's PM, agents, and app process before removing it.");
+    const next = removeProjectRegistration(state.projects, state.activeProjectId, project.id);
+    state.projects = next.projects;
+    state.activeProjectId = next.activeProjectId;
+    state.runs = [];
+    pmThreads.delete(project.id);
+    appProcessState.delete(project.id);
+    save(state);
+    return hydrate();
+  });
 }
-function activeAgents() {
-  const project = active(),
-    db = join(project.repo, ".codepilot", "codepilot.db");
+function activeAgents(project: Project) {
+  const db = join(project.repo, ".codepilot", "codepilot.db");
   if (!existsSync(db)) return [];
   using database = new DatabaseSync(db, { readOnly: true });
   const tasks = database
@@ -276,6 +344,7 @@ function activeAgents() {
       )
       .all(String(task.id)) as Array<Record<string, unknown>>;
     return {
+      projectId: project.id,
       taskId: String(task.id),
       runId: String(task.run_id),
       provider: String(task.provider),
@@ -292,27 +361,32 @@ function activeAgents() {
   });
 }
 function registerAgentIPC() {
-  ipcMain.handle("agents:active", () => activeAgents());
-  ipcMain.handle("agents:guide", (_event, taskId: string, message: string) => {
-    if (!activeAgents().some((agent) => agent.taskId === taskId))
+  ipcMain.handle("agents:active", (_event, projectId: string) => activeAgents(projectById(projectId)));
+  ipcMain.handle("agents:guide", (_event, projectId: string, taskId: string, message: string) => {
+    const project = projectById(projectId);
+    if (!activeAgents(project).some((agent) => agent.taskId === taskId))
       throw new Error("That agent is no longer active");
     queueAgentGuidance(taskId, message.slice(0, 4000));
-    return activeAgents();
+    return activeAgents(project);
   });
-  ipcMain.handle("agents:interrupt", (_event, taskId: string) => {
+  ipcMain.handle("agents:interrupt", (_event, projectId: string, taskId: string) => {
+    const project = projectById(projectId);
+    if (!activeAgents(project).some((agent) => agent.taskId === taskId))
+      throw new Error("That agent is no longer active");
     if (!interruptAgent(taskId)) throw new Error("That agent is no longer interruptible");
     return {
       feedback: "Interrupt received. I’m stopping safely now; completed changes and the available handoff evidence will be preserved in session history.",
-      agents: activeAgents(),
+      agents: activeAgents(project),
     };
   });
-  ipcMain.handle("project:open-directory", async () => {
-    const error = await shell.openPath(active().repo);
+  ipcMain.handle("project:open-directory", async (_event, projectId: string) => {
+    const error = await shell.openPath(projectById(projectId).repo);
     if (error) throw new Error(error);
   });
   ipcMain.handle("agents:run", async (_event, input: AgentRunInput) => {
-    const project = active();
-    if (!project || typeof project.repo !== "string" || !project.repo.trim()) throw new Error("The active project has no repository path. Re-select the project or add it again before deploying an agent.");
+    const project = projectById(input.projectId);
+    if (input.createPullRequest) assertGitHubWriteAccess();
+    if (typeof project.repo !== "string" || !project.repo.trim()) throw new Error("The selected project has no repository path. Re-select the project or add it again before deploying an agent.");
     const
       objective = input.objective.trim(),
       providers = input.providers.filter(
@@ -351,8 +425,9 @@ function registerAgentIPC() {
     };
   });
   ipcMain.handle("agents:run-batch", async (_event, input: AgentBatchRunInput) => {
-    const project = active();
-    if (!project?.repo?.trim()) throw new Error("The active project has no repository path.");
+    const project = projectById(input.projectId);
+    if (input.createPullRequest) assertGitHubWriteAccess();
+    if (!project.repo?.trim()) throw new Error("The selected project has no repository path.");
     const items = input.items.slice(0, 20).map((item) => ({
       id: item.id.trim(),
       objective: item.objective.trim(),
@@ -388,19 +463,21 @@ function registerAgentIPC() {
     };
   });
 }
-function active() {
-  const state = load();
-  return (
-    state.projects.find((project) => project.id === state.activeProjectId) ??
-    state.projects[0]!
-  );
+function projectById(projectId: string): Project {
+  const project = load().projects.find((candidate) => candidate.id === projectId);
+  if (!project) throw new Error("Project not found. Refresh the workspace and try again.");
+  return project;
 }
-function projectBrief(project = active()) { const path=join(project.repo,"PROJECT.md"); return {path,content:existsSync(path)?readFileSync(path,"utf8"):"",exists:existsSync(path)}; }
-function saveProjectBrief(content:string){const brief=projectBrief();writeFileSync(brief.path,`${content.trim()}\n`);return projectBrief()}
-function projectActivity(){return Object.fromEntries(load().projects.map(project=>{const path=join(project.repo,".codepilot","codepilot.db");if(!existsSync(path))return[project.id,0];try{using database=new DatabaseSync(path,{readOnly:true});const row=database.prepare("SELECT COUNT(*) AS count FROM tasks WHERE status IN ('leased','running','validating')").get() as Record<string,unknown>;return[project.id,Number(row.count)]}catch{return[project.id,0]}}))}
+function samePath(left: string, right: string): boolean {
+  const normalize = (value: string) => resolve(value).replace(/[\\/]+$/, "").toLowerCase();
+  return normalize(left) === normalize(right);
+}
+function projectBrief(project: Project) { const path=join(project.repo,"PROJECT.md"); return {path,content:existsSync(path)?readFileSync(path,"utf8"):"",exists:existsSync(path)}; }
+function saveProjectBrief(project: Project,content:string){const brief=projectBrief(project);writeFileSync(brief.path,`${content.trim()}\n`);return projectBrief(project)}
+function projectActivity(){return Object.fromEntries(load().projects.map(project=>{const path=join(project.repo,".codepilot","codepilot.db"),pm=pmActivity.get(project.id)??0;if(!existsSync(path))return[project.id,pm];try{using database=new DatabaseSync(path,{readOnly:true});const row=database.prepare("SELECT COUNT(*) AS count FROM tasks WHERE status IN ('leased','running','validating')").get() as Record<string,unknown>;return[project.id,Number(row.count)+pm]}catch{return[project.id,pm]}}))}
 const defaultAppConfig: AppConfig = { command: "", workingDirectory: ".", url: "http://localhost:3000" };
-function appConfigPath(project = active()) { return join(project.repo, ".codepilot", "app-config.json"); }
-function readAppConfig(project = active()): AppConfig {
+function appConfigPath(project: Project) { return join(project.repo, ".codepilot", "app-config.json"); }
+function readAppConfig(project: Project): AppConfig {
   try { return { ...defaultAppConfig, ...(JSON.parse(readFileSync(appConfigPath(project), "utf8")) as Partial<AppConfig>) }; }
   catch {
     try {
@@ -410,7 +487,7 @@ function readAppConfig(project = active()): AppConfig {
     return { ...defaultAppConfig };
   }
 }
-function saveAppConfig(input: AppConfig, project = active()) {
+function saveAppConfig(input: AppConfig, project: Project) {
   const command = String(input.command ?? "").trim().slice(0, 1000);
   const workingDirectory = String(input.workingDirectory ?? ".").trim() || ".";
   const cwd = resolve(project.repo, workingDirectory);
@@ -421,7 +498,7 @@ function saveAppConfig(input: AppConfig, project = active()) {
   mkdirSync(dirname(appConfigPath(project)), { recursive: true });
   writeFileSync(appConfigPath(project), JSON.stringify({ command, workingDirectory, url }, null, 2));
 }
-function projectAppStatus(project = active()) {
+function projectAppStatus(project: Project) {
   const process = appProcesses.get(project.id), state = appProcessState.get(project.id) ?? { logs: [] };
   return { configured: Boolean(readAppConfig(project).command), running: Boolean(process && process.exitCode === null), ...(process?.pid ? { pid: process.pid } : {}), ...(state.startedAt ? { startedAt: state.startedAt } : {}), config: readAppConfig(project), logs: state.logs };
 }
@@ -443,8 +520,8 @@ function projectEnvironment(...directories: string[]): NodeJS.ProcessEnv {
   }
   return values;
 }
-function startProjectApp() {
-  const project = active(), current = appProcesses.get(project.id);
+function startProjectApp(project: Project) {
+  const current = appProcesses.get(project.id);
   if (current?.exitCode === null) return projectAppStatus(project);
   const config = readAppConfig(project);
   if (!config.command) throw new Error("Configure a start command first");
@@ -460,8 +537,8 @@ function startProjectApp() {
   appProcesses.set(project.id, child); appProcessState.set(project.id, state);
   return projectAppStatus(project);
 }
-function stopProjectApp() {
-  const project = active(), child = appProcesses.get(project.id);
+function stopProjectApp(project: Project) {
+  const child = appProcesses.get(project.id);
   if (child?.pid) {
     if (process.platform === "win32") { try { execFileSync("taskkill", ["/pid", String(child.pid), "/T", "/F"], { windowsHide: true }); } catch { child.kill(); } }
     else child.kill("SIGTERM");
@@ -470,9 +547,8 @@ function stopProjectApp() {
   }
   return projectAppStatus(project);
 }
-function clearProjectPort() {
-  const project = active();
-  stopProjectApp();
+function clearProjectPort(project: Project) {
+  stopProjectApp(project);
   const config = readAppConfig(project);
   let parsed: URL;
   try { parsed = new URL(config.url); } catch { throw new Error("Configure a valid http:// or https:// app URL before clearing its port."); }
@@ -494,10 +570,10 @@ function clearProjectPort() {
   }
   return projectAppStatus(project);
 }
-function knowledgeDir() {
-  return join(active().repo, ".codepilot", "knowledge");
+function knowledgeDir(project: Project) {
+  return join(project.repo, ".codepilot", "knowledge");
 }
-function entries(directory = knowledgeDir()): KnowledgeEntry[] {
+function entries(directory: string): KnowledgeEntry[] {
   if (!existsSync(directory)) return [];
   return readdirSync(directory)
     .filter((name) => name.endsWith(".json"))
@@ -514,11 +590,11 @@ function entries(directory = knowledgeDir()): KnowledgeEntry[] {
     })
     .sort((a, b) => b.updatedAt.localeCompare(a.updatedAt));
 }
-function history(): ChatMessage[] {
+function history(project: Project): ChatMessage[] {
   try {
     return JSON.parse(
       readFileSync(
-        join(active().repo, ".codepilot", "knowledge-chat.json"),
+        join(project.repo, ".codepilot", "knowledge-chat.json"),
         "utf8",
       ),
     ) as ChatMessage[];
@@ -526,18 +602,18 @@ function history(): ChatMessage[] {
     return [];
   }
 }
-function knowledgeState(): KnowledgeState {
-  return { entries: entries(), messages: history() };
+function knowledgeState(project: Project): KnowledgeState {
+  return { entries: entries(knowledgeDir(project)), messages: history(project) };
 }
-function saveEntry(entry: KnowledgeEntry) {
-  mkdirSync(knowledgeDir(), { recursive: true });
+function saveEntry(project: Project, entry: KnowledgeEntry) {
+  mkdirSync(knowledgeDir(project), { recursive: true });
   writeFileSync(
-    join(knowledgeDir(), `${entry.id}.json`),
+    join(knowledgeDir(project), `${entry.id}.json`),
     JSON.stringify(entry, null, 2),
   );
 }
-function saveChat(messages: ChatMessage[]) {
-  const path = join(active().repo, ".codepilot", "knowledge-chat.json");
+function saveChat(project: Project, messages: ChatMessage[]) {
+  const path = join(project.repo, ".codepilot", "knowledge-chat.json");
   mkdirSync(dirname(path), { recursive: true });
   writeFileSync(path, JSON.stringify(messages.slice(-100), null, 2));
 }
@@ -564,7 +640,7 @@ function matchesPMTask(objective: string, title: string, taskId?: string): boole
   const overlap = [...taskWords].filter((word) => runWords.has(word)).length;
   return overlap / Math.min(taskWords.size, runWords.size) >= 0.8;
 }
-function pmState(repo = active().repo): PMState {
+function pmState(repo: string): PMState {
   const paths = pmPaths(repo);
   const storedTasks = loadPMTasks(repo) as PMTask[];
   const committedTaskIds = new Set(
@@ -646,8 +722,8 @@ function pmState(repo = active().repo): PMState {
     messages: readJson<ChatMessage[]>(paths.chat, []),
   };
 }
-function pmTaskDetail(id: string) {
-  const project = active(), state = pmState(project.repo), task = state.tasks.find((item) => item.id === id);
+function pmTaskDetail(project: Project, id: string) {
+  const state = pmState(project.repo), task = state.tasks.find((item) => item.id === id);
   if (!task) throw new Error("Task not found");
   const prerequisites = task.dependencies.map((dependency) => {
     const prerequisite = state.tasks.find((item) => item.id === dependency)!;
@@ -678,18 +754,20 @@ function ensureProjectGit(repo: string, initialize = false) {
     mkdirSync(root, { recursive: true });
     execFileSync("git", ["init", root]);
   } else {
-    const gitRoot = resolve(execFileSync("git", ["-C", root, "rev-parse", "--show-toplevel"], { encoding: "utf8" }).trim());
-    if (gitRoot.toLowerCase() !== root.toLowerCase()) throw new Error("Each codePilot project must be its own Git repository, not a subdirectory of another repository.");
+    const gitRoot = canonicalGitRepository(root);
+    if (!samePath(gitRoot, root)) throw new Error("Each codePilot project must be its own Git repository, not a subdirectory of another repository.");
   }
-  const ignorePath = join(root, ".gitignore");
+  const ignorePath = initialize
+    ? join(root, ".gitignore")
+    : resolve(root, execFileSync("git", ["-C", root, "rev-parse", "--git-path", "info/exclude"], { encoding: "utf8", windowsHide: true }).trim());
   const existing = existsSync(ignorePath) ? readFileSync(ignorePath, "utf8") : "";
   if (!/(^|\r?\n)\.codepilot\/?(?:\r?\n|$)/m.test(existing)) {
+    mkdirSync(dirname(ignorePath), { recursive: true });
     writeFileSync(ignorePath, `${existing.trimEnd()}${existing.trim() ? "\n\n" : ""}.codepilot/\n`);
     if (initialize) execFileSync("git", ["-C", root, "add", ".gitignore"]);
   }
 }
-function commitPMTaskBin(taskIds: string[]): TaskBin {
-  const project = active();
+function commitPMTaskBin(project: Project, taskIds: string[]): TaskBin {
   const state = pmState(project.repo);
   const selected = [...new Set(taskIds)].map((id) => state.tasks.find((task) => task.id === id)).filter((task): task is PMTask => Boolean(task));
   if (!selected.length) throw new Error("Select at least one task to create a commit bin.");
@@ -706,18 +784,18 @@ function commitPMTaskBin(taskIds: string[]): TaskBin {
   saveCommittedTaskBin(project.repo, bin, state.tasks);
   return bin;
 }
-function createPMTask(input: NewPMTask): PMState {
+function createPMTask(project: Project, input: NewPMTask): PMState {
   const title = input.title.trim(), description = input.description.trim();
   if (!title || !description) throw new Error("Task title and description are required.");
-  const project = active(), state = pmState(project.repo), now = new Date().toISOString();
+  const state = pmState(project.repo), now = new Date().toISOString();
   const task: PMTask = { id: randomUUID(), title, description, acceptanceCriteria: (input.acceptanceCriteria ?? []).map((item) => item.trim()).filter(Boolean), priority: input.priority === "high" || input.priority === "low" ? input.priority : "medium", status: "ready", queueId: "deploy", queueTitle: "Deploy queue", dependencies: [], recommendedProvider: input.recommendedProvider === "claude" ? "claude" : "codex", createdAt: now, updatedAt: now };
   state.tasks.push(task);
   state.tasks = reconcileTaskStatuses(state.tasks);
   savePM(project.repo, state);
   return pmState(project.repo);
 }
-function deletePMTask(id: string): PMState {
-  const project = active(), state = pmState(project.repo);
+function deletePMTask(project: Project, id: string): PMState {
+  const state = pmState(project.repo);
   if (!state.tasks.some((task) => task.id === id)) throw new Error("Task not found");
   state.tasks = omitTaskDependencies(state.tasks.filter((task) => task.id !== id), new Set([id]));
   state.tasks = reconcileTaskStatuses(state.tasks);
@@ -748,11 +826,10 @@ const schema = {
   required: ["message", "operations"],
   additionalProperties: false,
 };
-async function chat(message: string) {
+async function chat(project: Project, message: string) {
   if (!message.trim()) throw new Error("Message required");
-  const project = active(),
-    before = entries(),
-    messages = history(),
+  const before = entries(knowledgeDir(project)),
+    messages = history(project),
     temp = join(app.getPath("temp"), `codepilot-chat-${randomUUID()}`);
   mkdirSync(temp, { recursive: true });
   const schemaPath = join(temp, "schema.json"),
@@ -791,7 +868,7 @@ async function chat(message: string) {
       operation.content.trim()
     ) {
       const now = new Date().toISOString();
-      saveEntry({
+      saveEntry(project, {
         id: randomUUID(),
         title: operation.title.trim(),
         content: operation.content.trim(),
@@ -804,7 +881,7 @@ async function chat(message: string) {
     } else if (operation.action === "update") {
       const old = before.find((item) => item.id === operation.id);
       if (old && operation.title.trim() && operation.content.trim()) {
-        saveEntry({
+        saveEntry(project, {
           ...old,
           title: operation.title.trim(),
           content: operation.content.trim(),
@@ -818,12 +895,12 @@ async function chat(message: string) {
       operation.action === "delete" &&
       before.some((item) => item.id === operation.id)
     ) {
-      rmSync(join(knowledgeDir(), `${operation.id}.json`), { force: true });
+      rmSync(join(knowledgeDir(project), `${operation.id}.json`), { force: true });
       applied++;
     }
   }
   const now = new Date().toISOString();
-  saveChat([
+  saveChat(project, [
     ...messages,
     { role: "user", content: message, timestamp: now },
     {
@@ -834,7 +911,7 @@ async function chat(message: string) {
     },
   ]);
   rmSync(temp, { recursive: true, force: true });
-  return knowledgeState();
+  return knowledgeState(project);
 }
 function run(command: string, args: string[], input = ""): Promise<void> {
   return new Promise((done, fail) => {
@@ -859,9 +936,9 @@ function run(command: string, args: string[], input = ""): Promise<void> {
   });
 }
 function registerKnowledgeIPC() {
-  ipcMain.handle("knowledge:get", () => knowledgeState());
-  ipcMain.handle("knowledge:chat", (_event, message: string) =>
-    chat(message.slice(0, 8000)),
+  ipcMain.handle("knowledge:get", (_event, projectId: string) => knowledgeState(projectById(projectId)));
+  ipcMain.handle("knowledge:chat", (_event, projectId: string, message: string) =>
+    chat(projectById(projectId), message.slice(0, 8000)),
   );
 }
 const pmSchema = {
@@ -960,7 +1037,7 @@ async function persistentPMReply(project: Project, prompt: string): Promise<stri
   pmThreads.set(project.id, threadId);
   return await pmServer.turn(threadId, project.repo, prompt, pmSchema);
 }
-async function chatPM(message: string, targetProject = active()) {
+async function chatPM(message: string, targetProject: Project) {
   if (!message.trim()) throw new Error("Message required");
   const project = targetProject,
     before = pmState(project.repo),
@@ -1113,17 +1190,25 @@ async function chatPM(message: string, targetProject = active()) {
   }
 }
 function registerPMIPC() {
-  ipcMain.handle("pm:get", () => pmState());
-  ipcMain.handle("pm:task-detail", (_event, id: string) => pmTaskDetail(id));
-  ipcMain.handle("pm:chat", async (_event, message: string) => {
-    const state = await chatPM(message.slice(0, 8000));
-    if (state.requiresUserInput)
-      for (const browserWindow of BrowserWindow.getAllWindows())
-        browserWindow.webContents.send("pm:user-input-required");
-    return state;
+  ipcMain.handle("pm:get", (_event, projectId: string) => pmState(projectById(projectId).repo));
+  ipcMain.handle("pm:task-detail", (_event, projectId: string, id: string) => pmTaskDetail(projectById(projectId), id));
+  ipcMain.handle("pm:chat", async (_event, projectId: string, message: string) => {
+    const project = projectById(projectId);
+    pmActivity.set(project.id, (pmActivity.get(project.id) ?? 0) + 1);
+    try {
+      const state = await pmTurns.run(project.id, () => chatPM(message.slice(0, 8000), project));
+      if (state.requiresUserInput)
+        for (const browserWindow of BrowserWindow.getAllWindows())
+          browserWindow.webContents.send("pm:user-input-required", project.id);
+      return state;
+    } finally {
+      const remaining = (pmActivity.get(project.id) ?? 1) - 1;
+      if (remaining > 0) pmActivity.set(project.id, remaining);
+      else pmActivity.delete(project.id);
+    }
   });
-  ipcMain.handle("pm:clear-chat", () => {
-    const project = active(),
+  ipcMain.handle("pm:clear-chat", (_event, projectId: string) => {
+    const project = projectById(projectId),
       state = pmState(project.repo),
       next = { ...state, messages: [] };
     pmThreads.delete(project.id);
@@ -1133,10 +1218,10 @@ function registerPMIPC() {
   });
   ipcMain.handle(
     "pm:task-status",
-      (_event, id: string, status: PMTask["status"], summary?: string) => {
+      (_event, projectId: string, id: string, status: PMTask["status"], summary?: string) => {
       if (!["backlog", "blocked", "ready", "launched", "done", "committed"].includes(status))
         throw new Error("Invalid task status");
-      const project = active(),
+      const project = projectById(projectId),
         state = pmState(project.repo),
         task = state.tasks.find((item) => item.id === id);
       if (!task) throw new Error("Task not found");
@@ -1151,8 +1236,8 @@ function registerPMIPC() {
       return pmState(project.repo);
     },
   );
-  ipcMain.handle("pm:task-failure", (_event, id: string, summary: string) => {
-    const project = active(),
+  ipcMain.handle("pm:task-failure", (_event, projectId: string, id: string, summary: string) => {
+    const project = projectById(projectId),
       state = pmState(project.repo),
       task = state.tasks.find((item) => item.id === id);
     if (!task) throw new Error("Task not found");
@@ -1169,9 +1254,9 @@ function registerPMIPC() {
     savePM(project.repo, state);
     return pmState(project.repo);
   });
-  ipcMain.handle("pm:commit-bin", (_event, taskIds: string[]) => commitPMTaskBin(taskIds));
-  ipcMain.handle("pm:create-task", (_event, input: NewPMTask) => createPMTask(input));
-  ipcMain.handle("pm:delete-task", (_event, id: string) => deletePMTask(id));
+  ipcMain.handle("pm:commit-bin", (_event, projectId: string, taskIds: string[]) => commitPMTaskBin(projectById(projectId), taskIds));
+  ipcMain.handle("pm:create-task", (_event, projectId: string, input: NewPMTask) => createPMTask(projectById(projectId), input));
+  ipcMain.handle("pm:delete-task", (_event, projectId: string, id: string) => deletePMTask(projectById(projectId), id));
 }
 function createWindow() {
   window = new BrowserWindow({
diff --git a/desktop/src/pm.tsx b/desktop/src/pm.tsx
index 9ed6536..d8494d2 100644
--- a/desktop/src/pm.tsx
+++ b/desktop/src/pm.tsx
@@ -6,7 +6,7 @@ import {
   ArrowsPointingInIcon,
 } from "@heroicons/react/24/outline";
 import type { PMState, PMTask } from "./types";
-export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible, projectName, expanded, onExpand }: { initialMessage?: string; triageMessage?: string; triageTaskIds?: string[]; visible: boolean; projectName: string; expanded?: boolean; onExpand?: () => void }) {
+export function PM({ projectId, initialMessage, triageMessage, triageTaskIds = [], visible, projectName, expanded, onExpand }: { projectId: string; initialMessage?: string; triageMessage?: string; triageTaskIds?: string[]; visible: boolean; projectName: string; expanded?: boolean; onExpand?: () => void }) {
   const [state, setState] = useState<PMState>(),
     [message, setMessage] = useState(""),
     [queue, setQueue] = useState<string[]>([]),
@@ -21,8 +21,8 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
     autonomousReviewQueued = useRef(false),
     chat = useRef<HTMLDivElement>(null);
   useEffect(() => {
-    void window.codepilot.getPM().then(setState);
-  }, []);
+    void window.codepilot.getPM(projectId).then(setState);
+  }, [projectId]);
   useEffect(() => { if (initialMessage && !onboardingStarted.current) { onboardingStarted.current = true; setQueue([initialMessage]); } }, [initialMessage]);
   useEffect(() => {
     if (!triageMessage || triageMessage === lastTriageMessage.current) return;
@@ -38,7 +38,7 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
     processing.current = true;
     setBusy(true);
     void window.codepilot
-      .chatPM(next)
+      .chatPM(projectId, next)
       .then(async (nextState) => {
         setState(nextState);
         const settings = await window.codepilot.getGlobalSettings();
@@ -80,7 +80,7 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
     )
       return;
     setQueue([]);
-    setState(await window.codepilot.clearPMChat());
+    setState(await window.codepilot.clearPMChat(projectId));
   }
   async function launch(task: PMTask, provider: "codex" | "claude") {
     if (dispatchedTaskIdsRef.current.has(task.id)) return;
@@ -94,9 +94,10 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
     setDispatchedTaskIds((items) => new Set(items).add(task.id));
     setError("");
     try {
-      setState(await window.codepilot.setPMTaskStatus(task.id, "launched"));
+      setState(await window.codepilot.setPMTaskStatus(projectId, task.id, "launched"));
       void window.codepilot
         .runAgents({
+          projectId,
           objective: `${task.title}\n\ncodePilot PM task: ${task.id}\nQueue: ${task.queueTitle}\n\n${task.description}\n\nAcceptance criteria:\n${task.acceptanceCriteria.map((item) => `- ${item}`).join("\n")}`,
           providers: [provider],
           retries: 0,
@@ -108,7 +109,7 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
         .then(async (result) => {
           if (result.status === "completed") {
             const summary = result.review.findings.length ? result.review.findings.join(" ") : `Agent run completed with review verdict: ${result.review.verdict}.`;
-            const nextState = await window.codepilot.setPMTaskStatus(task.id, "done", summary);
+            const nextState = await window.codepilot.setPMTaskStatus(projectId, task.id, "done", summary);
             setState(nextState);
             const settings = await window.codepilot.getGlobalSettings();
             const readyTasks = nextState.tasks.filter((item) => item.status === "ready" && !dispatchedTaskIdsRef.current.has(item.id));
@@ -118,7 +119,7 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
             if (!readyTasks.length) queueAutonomousReview(`Completed "${task.title}". ${summary}`);
           } else {
             const reason = result.review.findings.length ? result.review.findings.join(" ") : `The agent run returned ${result.status} with review verdict ${result.review.verdict}.`;
-            setState(await window.codepilot.recordPMTaskFailure(task.id, `Task did not advance because it was not eligible for completion: ${reason}`));
+            setState(await window.codepilot.recordPMTaskFailure(projectId, task.id, `Task did not advance because it was not eligible for completion: ${reason}`));
             restoreForTriage();
             queueAutonomousReview(`"${task.title}" needs re-triage after ${result.status}: ${reason}`);
             setError(
@@ -128,21 +129,21 @@ export function PM({ initialMessage, triageMessage, triageTaskIds = [], visible,
         })
         .catch(async (cause) => {
           setError(cause instanceof Error ? cause.message : String(cause));
-          setState(await window.codepilot.recordPMTaskFailure(task.id, `Task did not advance because the agent run failed: ${cause instanceof Error ? cause.message : String(cause)}`));
+          setState(await window.codepilot.recordPMTaskFailure(projectId, task.id, `Task did not advance because the agent run failed: ${cause instanceof Error ? cause.message : String(cause)}`));
           restoreForTriage();
           queueAutonomousReview(`"${task.title}" failed: ${cause instanceof Error ? cause.message : String(cause)}`);
         })
         .finally(() => setLaunching((items) => { const next = new Set(items); next.delete(task.id); return next; }));
     } catch (cause) {
       setError(cause instanceof Error ? cause.message : String(cause));
-      try { setState(await window.codepilot.recordPMTaskFailure(task.id, `Task did not advance because launch failed: ${cause instanceof Error ? cause.message : String(cause)}`)); } catch {}
+      try { setState(await window.codepilot.recordPMTaskFailure(projectId, task.id, `Task did not advance because launch failed: ${cause instanceof Error ? cause.message : String(cause)}`)); } catch {}
       restoreForTriage();
       queueAutonomousReview(`"${task.title}" could not launch: ${cause instanceof Error ? cause.message : String(cause)}`);
       setLaunching((items) => { const next = new Set(items); next.delete(task.id); return next; });
     }
   }
   async function requeueTask(task: PMTask) {
-    setState(await window.codepilot.setPMTaskStatus(task.id, "ready", "Requeued from the Project Manager recent work list."));
+    setState(await window.codepilot.setPMTaskStatus(projectId, task.id, "ready", "Requeued from the Project Manager recent work list."));
     setTriagedTaskIds((items) => { const next = new Set(items); next.delete(task.id); return next; });
     setDispatchedTaskIds((items) => { const next = new Set(items); next.delete(task.id); return next; });
     dispatchedTaskIdsRef.current.delete(task.id);
diff --git a/desktop/src/preload.ts b/desktop/src/preload.ts
index 03eee6e..ac81b9c 100644
--- a/desktop/src/preload.ts
+++ b/desktop/src/preload.ts
@@ -5,41 +5,45 @@ const api: CodePilotAPI = {
   getState: () => ipcRenderer.invoke("state:get"),
   getGlobalSettings: () => ipcRenderer.invoke("settings:get"),
   saveGlobalSettings: (settings) => ipcRenderer.invoke("settings:save", settings),
-  getProjectBrief: () => ipcRenderer.invoke("project:brief-get"),
-  saveProjectBrief: (content) => ipcRenderer.invoke("project:brief-save", content),
+  getGitHubStatus: () => ipcRenderer.invoke("github:status"),
+  loginGitHub: () => ipcRenderer.invoke("github:login"),
+  getProjectBrief: (projectId) => ipcRenderer.invoke("project:brief-get", projectId),
+  saveProjectBrief: (projectId, content) => ipcRenderer.invoke("project:brief-save", projectId, content),
   getProjectActivity: () => ipcRenderer.invoke("projects:activity"),
   selectDirectory: (defaultPath) => ipcRenderer.invoke("dialog:directory", defaultPath),
   addProject: (input) => ipcRenderer.invoke("project:add", input),
+  onboardProject: (input) => ipcRenderer.invoke("project:onboard", input),
+  removeProject: (projectId) => ipcRenderer.invoke("project:remove", projectId),
   switchProject: (id) => ipcRenderer.invoke("project:switch", id),
-  openProjectDirectory: () => ipcRenderer.invoke("project:open-directory"),
-  getAppStatus: () => ipcRenderer.invoke("app:status"),
-  saveAppConfig: (config) => ipcRenderer.invoke("app:save-config", config),
-  startProjectApp: () => ipcRenderer.invoke("app:start"),
-  stopProjectApp: () => ipcRenderer.invoke("app:stop"),
-  openProjectApp: () => ipcRenderer.invoke("app:open"),
-  getKnowledge: () => ipcRenderer.invoke("knowledge:get"),
-  chatKnowledge: (message) => ipcRenderer.invoke("knowledge:chat", message),
+  openProjectDirectory: (projectId) => ipcRenderer.invoke("project:open-directory", projectId),
+  getAppStatus: (projectId) => ipcRenderer.invoke("app:status", projectId),
+  saveAppConfig: (projectId, config) => ipcRenderer.invoke("app:save-config", projectId, config),
+  startProjectApp: (projectId) => ipcRenderer.invoke("app:start", projectId),
+  stopProjectApp: (projectId) => ipcRenderer.invoke("app:stop", projectId),
+  clearProjectPort: (projectId) => ipcRenderer.invoke("app:clear-port", projectId),
+  openProjectApp: (projectId) => ipcRenderer.invoke("app:open", projectId),
+  getKnowledge: (projectId) => ipcRenderer.invoke("knowledge:get", projectId),
+  chatKnowledge: (projectId, message) => ipcRenderer.invoke("knowledge:chat", projectId, message),
   runAgents: (input) => ipcRenderer.invoke("agents:run", input),
   runAgentBatch: (input) => ipcRenderer.invoke("agents:run-batch", input),
-  getActiveAgents: () => ipcRenderer.invoke("agents:active"),
-  guideAgent: (taskId, message) => ipcRenderer.invoke("agents:guide", taskId, message),
-  interruptAgent: (taskId) => ipcRenderer.invoke("agents:interrupt", taskId),
-  getRunDetail: (id) => ipcRenderer.invoke("run:detail", id),
-  getPM: () => ipcRenderer.invoke("pm:get"),
-  getPMTaskDetail: (id) => ipcRenderer.invoke("pm:task-detail", id),
-  chatPM: (message) => ipcRenderer.invoke("pm:chat", message),
-  clearPMChat: () => ipcRenderer.invoke("pm:clear-chat"),
-  setPMTaskStatus: (id, status, summary) => ipcRenderer.invoke("pm:task-status", id, status, summary),
-  recordPMTaskFailure: (id, summary) => ipcRenderer.invoke("pm:task-failure", id, summary),
+  getActiveAgents: (projectId) => ipcRenderer.invoke("agents:active", projectId),
+  guideAgent: (projectId, taskId, message) => ipcRenderer.invoke("agents:guide", projectId, taskId, message),
+  interruptAgent: (projectId, taskId) => ipcRenderer.invoke("agents:interrupt", projectId, taskId),
+  getRunDetail: (projectId, id) => ipcRenderer.invoke("run:detail", projectId, id),
+  getPM: (projectId) => ipcRenderer.invoke("pm:get", projectId),
+  getPMTaskDetail: (projectId, id) => ipcRenderer.invoke("pm:task-detail", projectId, id),
+  chatPM: (projectId, message) => ipcRenderer.invoke("pm:chat", projectId, message),
+  clearPMChat: (projectId) => ipcRenderer.invoke("pm:clear-chat", projectId),
+  setPMTaskStatus: (projectId, id, status, summary) => ipcRenderer.invoke("pm:task-status", projectId, id, status, summary),
+  recordPMTaskFailure: (projectId, id, summary) => ipcRenderer.invoke("pm:task-failure", projectId, id, summary),
   onPMUserInputRequired: (listener) => {
-    const handler = () => listener();
+    const handler = (_event: Electron.IpcRendererEvent, projectId: string) => listener(projectId);
     ipcRenderer.on("pm:user-input-required", handler);
     return () => ipcRenderer.removeListener("pm:user-input-required", handler);
   },
-  createPMTask: (input) => ipcRenderer.invoke("pm:create-task", input),
-  commitPMTaskBin: (taskIds) => ipcRenderer.invoke("pm:commit-bin", taskIds),
+  createPMTask: (projectId, input) => ipcRenderer.invoke("pm:create-task", projectId, input),
+  commitPMTaskBin: (projectId, taskIds) => ipcRenderer.invoke("pm:commit-bin", projectId, taskIds),
+  deletePMTask: (projectId, id) => ipcRenderer.invoke("pm:delete-task", projectId, id),
 };
-(api as CodePilotAPI & { clearProjectPort: () => Promise<unknown> }).clearProjectPort = () => ipcRenderer.invoke("app:clear-port");
-(api as CodePilotAPI & { deletePMTask: (id: string) => Promise<unknown> }).deletePMTask = (id) => ipcRenderer.invoke("pm:delete-task", id);
 
 contextBridge.exposeInMainWorld("codepilot", api);
diff --git a/desktop/src/project-settings.tsx b/desktop/src/project-settings.tsx
index 24e0c78..f24c778 100644
--- a/desktop/src/project-settings.tsx
+++ b/desktop/src/project-settings.tsx
@@ -9,7 +9,7 @@ export function ProjectSettings({ projectId, projectName }: { projectId: string;
   const [saved, setSaved] = useState(false);
   useEffect(() => {
     let mounted = true;
-    Promise.all([window.codepilot.getProjectBrief(), window.codepilot.getAppStatus()]).then(([nextBrief, runtime]) => {
+    Promise.all([window.codepilot.getProjectBrief(projectId), window.codepilot.getAppStatus(projectId)]).then(([nextBrief, runtime]) => {
       if (!mounted) return;
       setBrief(nextBrief);
       setContent(withRunInstructions(nextBrief.content, runtime.config));
@@ -18,7 +18,7 @@ export function ProjectSettings({ projectId, projectName }: { projectId: string;
   }, [projectId]);
   async function save() {
     setBusy(true);
-    try { const next = await window.codepilot.saveProjectBrief(content); setBrief(next); setContent(next.content); setSaved(true); window.setTimeout(() => setSaved(false), 1800); }
+    try { const next = await window.codepilot.saveProjectBrief(projectId, content); setBrief(next); setContent(next.content); setSaved(true); window.setTimeout(() => setSaved(false), 1800); }
     finally { setBusy(false); }
   }
   return <div className="mx-auto max-w-5xl"><div className="text-xs font-semibold uppercase tracking-[.2em] text-indigo-400">Project README · {projectName}</div><div className="mt-2 flex items-center gap-3"><BookOpenIcon className="size-7 text-indigo-300" /><div><h1 className="text-2xl font-semibold">README</h1><p className="mt-1 text-sm text-zinc-400">User-facing documentation for running and understanding this project.</p></div></div><section className="mt-8 rounded-2xl border border-white/10 bg-white/[.025] p-6"><div className="flex items-start justify-between gap-5"><p className="text-xs text-zinc-600">{brief?.path ?? "Loading README path…"}</p><span className={`rounded-full px-2.5 py-1 text-[10px] font-semibold uppercase ${brief?.exists ? "bg-emerald-400/10 text-emerald-300" : "bg-amber-400/10 text-amber-300"}`}>{brief?.exists ? "Tracked" : "Not created"}</span></div><textarea value={content} onChange={(event) => setContent(event.target.value)} rows={34} className="mt-6 w-full resize-y rounded-xl border border-white/10 bg-black/25 p-5 font-mono text-xs leading-6 text-zinc-300 outline-none focus:border-indigo-400/40" placeholder={'# Project name\n\n## Run locally\n\n## Purpose\n\n## Current architecture\n\n## Active work'} /><div className="mt-5 flex items-center justify-between"><p className="text-xs text-zinc-600">Run instructions are generated at the top; the remaining sections document the app and active project work.</p><div className="flex items-center gap-4">{saved && <span className="text-xs text-emerald-400">README saved.</span>}<button disabled={busy || !content.trim()} onClick={() => void save()} className="rounded-xl bg-indigo-500 px-5 py-2.5 text-sm font-semibold disabled:opacity-40">{busy ? "Saving…" : "Save README"}</button></div></div></section></div>;
diff --git a/desktop/src/renderer.tsx b/desktop/src/renderer.tsx
index c37ff7e..3278eb0 100644
--- a/desktop/src/renderer.tsx
+++ b/desktop/src/renderer.tsx
@@ -1,7 +1,7 @@
 import React, { useEffect, useRef, useState } from "react";
 import { createRoot, type Root } from "react-dom/client";
-import { ArrowsPointingInIcon, ArrowsPointingOutIcon, BoltIcon, ChevronLeftIcon, ChevronRightIcon, CircleStackIcon, ClipboardDocumentListIcon, Cog6ToothIcon, CommandLineIcon, FolderIcon, PlayIcon, QueueListIcon, SignalIcon, Squares2X2Icon, StopIcon, WrenchScrewdriverIcon } from "@heroicons/react/24/outline";
-import type { AppStatus, DesktopState, PMTask } from "./types";
+import { ArrowsPointingInIcon, ArrowsPointingOutIcon, BoltIcon, ChevronLeftIcon, ChevronRightIcon, CircleStackIcon, ClipboardDocumentListIcon, Cog6ToothIcon, CommandLineIcon, FolderIcon, PlayIcon, PlusIcon, QueueListIcon, RocketLaunchIcon, SignalIcon, Squares2X2Icon, StopIcon, TrashIcon, WrenchScrewdriverIcon, XMarkIcon } from "@heroicons/react/24/outline";
+import type { AppConfig, AppStatus, DesktopState, PMTask } from "./types";
 import { Agents } from "./agents";
 import { ActiveAgents } from "./active-agents";
 import { Knowledge } from "./knowledge";
@@ -14,11 +14,20 @@ import { ProjectSettings } from "./project-settings";
 import "./styles.css";
 
 type View = "overview" | "pm" | "tasks" | "agents" | "active-agents" | "runtime" | "projects" | "knowledge" | "settings" | "project-settings" | "global-chat";
+type ProjectDialog = "choose" | "github" | "new";
+type LaunchSetup = { projectId: string; projectName: string; onboardingMessage?: string };
 
 function App() {
   const [state, setState] = useState<DesktopState>();
   const [view, setView] = useState<View>("overview");
   const [name, setName] = useState("");
+  const [remoteUrl, setRemoteUrl] = useState("");
+  const [projectDialog, setProjectDialog] = useState<ProjectDialog>();
+  const [launchSetup, setLaunchSetup] = useState<LaunchSetup>();
+  const [launchConfig, setLaunchConfig] = useState<AppConfig>({ command: "", workingDirectory: ".", url: "http://localhost:3000" });
+  const [launchSetupBusy, setLaunchSetupBusy] = useState(false);
+  const [launchSetupError, setLaunchSetupError] = useState("");
+  const [onboardingBusy, setOnboardingBusy] = useState<"local"|"remote"|"">("");
   const [onboardingMessage, setOnboardingMessage] = useState<string>();
   const [triageMessage, setTriageMessage] = useState<string>();
   const [triageTaskIds, setTriageTaskIds] = useState<string[]>([]);
@@ -37,6 +46,12 @@ function App() {
     window.addEventListener("resize", resize);
     return () => window.removeEventListener("resize", resize);
   }, []);
+  useEffect(() => {
+    if (!projectDialog || onboardingBusy) return;
+    const closeOnEscape = (event: KeyboardEvent) => { if (event.key === "Escape") setProjectDialog(undefined); };
+    window.addEventListener("keydown", closeOnEscape);
+    return () => window.removeEventListener("keydown", closeOnEscape);
+  }, [projectDialog, onboardingBusy]);
   useEffect(() => {
     const audio = new Audio(new URL("./assets/user-input-required.wav", import.meta.url).href);
     audio.preload = "auto";
@@ -48,7 +63,9 @@ function App() {
   useEffect(()=>{if(typeof window.codepilot.getProjectActivity!=="function")return;let mounted=true;const refresh=()=>void window.codepilot.getProjectActivity().then(next=>mounted&&setProjectActivity(next)).catch(()=>{});refresh();const timer=window.setInterval(refresh,2000);return()=>{mounted=false;window.clearInterval(timer)}},[]);
   useEffect(() => {
     let mounted = true;
-    const refresh = () => void window.codepilot.getActiveAgents().then((agents) => mounted && setAgentsActive(agents.length > 0)).catch(() => mounted && setAgentsActive(false));
+    if (!state?.activeProjectId) return;
+    const projectId = state.activeProjectId;
+    const refresh = () => void window.codepilot.getActiveAgents(projectId).then((agents) => mounted && setAgentsActive(agents.length > 0)).catch(() => mounted && setAgentsActive(false));
     refresh(); const timer = window.setInterval(refresh, 2000);
     return () => { mounted = false; window.clearInterval(timer); };
   }, [state?.activeProjectId]);
@@ -57,14 +74,17 @@ function App() {
     if (!state?.activeProjectId) return;
     setAppStatus(undefined);
     let mounted = true;
-    const refresh = () => void window.codepilot.getAppStatus().then((status) => mounted && setAppStatus(status)).catch(() => mounted && setAppStatus(undefined));
+    const projectId = state.activeProjectId;
+    const refresh = () => void window.codepilot.getAppStatus(projectId).then((status) => mounted && setAppStatus(status)).catch(() => mounted && setAppStatus(undefined));
     refresh(); const timer = window.setInterval(refresh, 2000);
     return () => { mounted = false; window.clearInterval(timer); };
   }, [state?.activeProjectId]);
   if (!state) return <div className="grid h-full place-items-center text-zinc-500">Starting codePilot…</div>;
-  state.globalSettings ??= { defaultProvider: "codex", scaffold: { mode: "guided", autoDeploy: true, onboardingPrompt: "" } };
+  state.globalSettings ??= { defaultProvider: "codex", scaffold: { mode: "guided", autoDeploy: true, onboardingPrompt: "" }, github: { allowWrites: false } };
   state.globalSettings.scaffold ??= { mode: "guided", autoDeploy: true, onboardingPrompt: "" };
+  state.globalSettings.github ??= { allowWrites: false };
   const active = state.projects.find((project) => project.id === state.activeProjectId)!;
+  const projectsDirectory = state.projectsDirectory;
   const sidebarCompact = sidebarCollapsed || windowWidth < 1180;
   function triageTasks(tasks: PMTask[]) {
     const single = tasks.length === 1 ? tasks[0] : undefined;
@@ -80,7 +100,58 @@ function App() {
     setView("pm");
   }
   async function switchProject(projectId: string) { const nextProject = state?.projects.find((project) => project.id === projectId); if (!nextProject || nextProject.id === active.id) return; setProjectTransition({ from: active.name, to: nextProject.name }); setOnboardingMessage(undefined); try { setState(await window.codepilot.switchProject(projectId)); } finally { window.setTimeout(() => setProjectTransition(undefined), 650); } }
-  async function add() { try { const settings=await window.codepilot.getGlobalSettings();const scaffold=settings.scaffold??{mode:"guided",autoDeploy:true,onboardingPrompt:"Help me define the requirements for this new project."};const projectName=name.trim();const next=await window.codepilot.addProject({name:projectName});setState(next);setName("");setError("");if(scaffold.mode==="guided"){setOnboardingMessage(`We just created a new project named ${projectName}. ${scaffold.onboardingPrompt}`);setView("pm")}else setOnboardingMessage(undefined); } catch (cause) { setError(cause instanceof Error ? cause.message : String(cause)); } }
+  async function removeProject(projectId: string, projectName: string) {
+    if (!window.confirm(`Remove "${projectName}" from codePilot?\n\nThe repository and its .codepilot data will stay on disk.`)) return;
+    setError("");
+    setOnboardingMessage(undefined);
+    try { setState(await window.codepilot.removeProject(projectId)); }
+    catch (cause) { setError(cause instanceof Error ? cause.message : String(cause)); }
+  }
+  function openProjectDialog() { setName(""); setRemoteUrl(""); setError(""); setProjectDialog("choose"); }
+  async function beginLaunchSetup(next: DesktopState, message?: string) {
+    const project = next.projects.find((candidate) => candidate.id === next.activeProjectId)!;
+    setState(next);
+    setProjectDialog(undefined);
+    setError("");
+    const runtime = await window.codepilot.getAppStatus(project.id);
+    setAppStatus(runtime);
+    setLaunchConfig(runtime.config);
+    setLaunchSetup({ projectId: project.id, projectName: project.name, ...(message ? { onboardingMessage: message } : {}) });
+    setLaunchSetupError("");
+  }
+  function continueAfterLaunchSetup(setup = launchSetup, configured = false) {
+    if (!setup) return;
+    setLaunchSetup(undefined);
+    setLaunchSetupError("");
+    if (setup.onboardingMessage) { setOnboardingMessage(`${setup.onboardingMessage} ${configured ? "The App Core launch configuration was saved during onboarding; keep it accurate as the project evolves." : "App Core launch configuration was skipped for now; configure it once the project has a runnable application."}`); setView("pm"); }
+    else { setOnboardingMessage(undefined); setView("projects"); }
+  }
+  async function saveLaunchSetup() {
+    if (!launchSetup) return;
+    setLaunchSetupBusy(true); setLaunchSetupError("");
+    try { setAppStatus(await window.codepilot.saveAppConfig(launchSetup.projectId, launchConfig)); continueAfterLaunchSetup(launchSetup, true); }
+    catch (cause) { setLaunchSetupError(cause instanceof Error ? cause.message : String(cause)); }
+    finally { setLaunchSetupBusy(false); }
+  }
+  async function add() { try { const settings=await window.codepilot.getGlobalSettings();const scaffold=settings.scaffold??{mode:"guided",autoDeploy:true,onboardingPrompt:"Help me define the requirements for this new project."};const projectName=name.trim();const next=await window.codepilot.addProject({name:projectName});setName("");await beginLaunchSetup(next,scaffold.mode==="guided"?`We just created a new project named ${projectName}. ${scaffold.onboardingPrompt}`:undefined); } catch (cause) { setError(cause instanceof Error ? cause.message : String(cause)); } }
+  async function finishRepositoryOnboarding(next: DesktopState, source: "local"|"remote") {
+    const project = next.projects.find((candidate) => candidate.id === next.activeProjectId)!;
+    const settings = await window.codepilot.getGlobalSettings();
+    await beginLaunchSetup(next, settings.scaffold.mode === "guided" ? `We just onboarded the ${source === "remote" ? "cloned" : "local"} Git repository for ${project.name}. Inspect the repository and existing PROJECT.md read-only, summarize its current architecture and maturity, identify missing context, then help me establish goals and a safe initial backlog. ${settings.scaffold.onboardingPrompt}` : undefined);
+  }
+  async function onboardLocal() {
+    setProjectDialog(undefined); setOnboardingBusy("local"); setError("");
+    try { const repo = await window.codepilot.selectDirectory(projectsDirectory); if (repo) await finishRepositoryOnboarding(await window.codepilot.onboardProject({ source: "local", repo }), "local"); }
+    catch (cause) { setError(cause instanceof Error ? cause.message : String(cause)); }
+    finally { setOnboardingBusy(""); }
+  }
+  async function onboardRemote() {
+    const url = remoteUrl.trim(); if (!url) return;
+    setOnboardingBusy("remote"); setError("");
+    try { const next = await window.codepilot.onboardProject({ source: "remote", url }); setRemoteUrl(""); await finishRepositoryOnboarding(next, "remote"); }
+    catch (cause) { setError(cause instanceof Error ? cause.message : String(cause)); }
+    finally { setOnboardingBusy(""); }
+  }
   return <div className="grid-bg flex h-full overflow-hidden bg-zinc-950 pt-10">
     <div className="drag fixed inset-x-0 top-0 h-10 border-b border-white/5" />
     <aside data-compact={sidebarCompact} className={`${view === "pm" && pmExpanded ? "hidden" : "flex"} ${sidebarCompact ? "w-[76px] p-3" : "w-72 p-5"} shrink-0 flex-col border-r border-white/10 bg-zinc-950/90 transition-[width,padding] duration-200`}>
@@ -98,23 +169,33 @@ function App() {
         <Nav on={() => setView("projects")} active={view === "projects"} icon={<FolderIcon />}>Projects</Nav>
         <Nav on={() => setView("settings")} active={view === "settings"} icon={<Cog6ToothIcon />}>Settings</Nav>
       </nav>
-      <div className={`mt-auto rounded-xl border border-white/10 bg-white/[.03] ${sidebarCompact ? "p-2" : "p-4"}`}>{!sidebarCompact && <><div className="text-[10px] uppercase tracking-widest text-zinc-600">Active project</div><div className="mt-2 truncate text-sm font-medium">{active.name}</div><div className="mt-1 truncate font-mono text-[10px] text-zinc-600">{active.repo}</div></>}<div className={`${sidebarCompact ? "grid-cols-1" : "mt-4 grid-cols-2"} grid gap-2`}><button title="Open project folder" onClick={() => void window.codepilot.openProjectDirectory()} className="flex items-center justify-center gap-2 rounded-lg border border-white/10 bg-white/[.04] px-2 py-2 text-xs text-zinc-300 hover:bg-white/[.08]"><FolderIcon className="size-4" />{!sidebarCompact && "Folder"}</button><button title={appStatus?.running ? "Stop project app" : "Start project app"} onClick={() => void (appStatus?.running ? window.codepilot.stopProjectApp() : window.codepilot.startProjectApp()).then(setAppStatus).catch(() => setView("runtime"))} className={`analog-control flex items-center justify-center gap-2 rounded-lg border px-2 py-2 text-xs ${appStatus?.running ? "analog-red" : "analog-green"}`}>{appStatus?.running ? <StopIcon className="size-4" /> : <PlayIcon className="size-4" />}{!sidebarCompact && (appStatus?.running ? "Stop" : "Start")}</button></div></div>
+      <div className={`mt-auto rounded-xl border border-white/10 bg-white/[.03] ${sidebarCompact ? "p-2" : "p-4"}`}>{!sidebarCompact && <><div className="text-[10px] uppercase tracking-widest text-zinc-600">Active project</div><div className="mt-2 truncate text-sm font-medium">{active.name}</div><div className="mt-1 truncate font-mono text-[10px] text-zinc-600">{active.repo}</div></>}<div className={`${sidebarCompact ? "grid-cols-1" : "mt-4 grid-cols-2"} grid gap-2`}><button title="Open project folder" onClick={() => void window.codepilot.openProjectDirectory(active.id)} className="flex items-center justify-center gap-2 rounded-lg border border-white/10 bg-white/[.04] px-2 py-2 text-xs text-zinc-300 hover:bg-white/[.08]"><FolderIcon className="size-4" />{!sidebarCompact && "Folder"}</button><button title={appStatus?.running ? "Stop project app" : "Start project app"} onClick={() => void (appStatus?.running ? window.codepilot.stopProjectApp(active.id) : window.codepilot.startProjectApp(active.id)).then(setAppStatus).catch(() => setView("runtime"))} className={`analog-control flex items-center justify-center gap-2 rounded-lg border px-2 py-2 text-xs ${appStatus?.running ? "analog-red" : "analog-green"}`}>{appStatus?.running ? <StopIcon className="size-4" /> : <PlayIcon className="size-4" />}{!sidebarCompact && (appStatus?.running ? "Stop" : "Start")}</button></div></div>
     </aside>
     <main className={`min-w-0 flex-1 ${view === "tasks" ? "overflow-hidden" : "overflow-y-auto"} ${view === "pm" && pmExpanded ? "p-4" : "p-10"}`}>
       <div data-pm-expanded={pmExpanded} className={`pm-shell relative ${view === "pm" ? "block" : "hidden"}`}>
-        <PM key={active.id} initialMessage={onboardingMessage} triageMessage={triageMessage} triageTaskIds={triageTaskIds} visible={view === "pm"} projectName={active.name} expanded={pmExpanded} onExpand={() => setPMExpanded(value => !value)} />
+        <PM key={active.id} projectId={active.id} initialMessage={onboardingMessage} triageMessage={triageMessage} triageTaskIds={triageTaskIds} visible={view === "pm"} projectName={active.name} expanded={pmExpanded} onExpand={() => setPMExpanded(value => !value)} />
       </div>
-      {view === "pm" ? null : view === "tasks" ? <TaskBoard key={active.id} projectId={active.id} projectName={active.name} onTriage={triageTasks} onReviewProject={reviewProject} /> : view === "agents" ? <Agents onState={setState} /> : view === "active-agents" ? <ActiveAgents /> : view === "runtime" ? <AppControl key={active.id} projectId={active.id} status={appStatus} onStatus={setAppStatus} /> : view === "knowledge" ? <Knowledge /> : view === "project-settings" ? <ProjectSettings projectId={active.id} projectName={active.name}/> : view === "settings" ? <Settings state={state} onState={setState} /> : view === "projects" ? <>
-        <Title eyebrow="Workspace registry" title="Projects" text={`Create or switch projects under ${state.projectsDirectory}.`} />
-        <div className="mt-8 grid grid-cols-[1fr_380px] gap-6"><div className="space-y-3">{state.projects.map((project) => <button key={project.id} onClick={() => {setOnboardingMessage(undefined);void window.codepilot.switchProject(project.id).then(setState)}} className={`w-full rounded-xl border p-5 text-left ${project.id === active.id ? "border-indigo-400/30 bg-indigo-400/10" : "border-white/10 bg-white/[.025]"}`}><div className="flex items-center justify-between gap-4"><div className="font-medium">{project.name}</div>{Boolean(projectActivity[project.id])&&<span className="flex items-center gap-2 rounded-full bg-emerald-400/10 px-2.5 py-1 text-[10px] font-semibold uppercase text-emerald-300"><span className="size-1.5 animate-pulse rounded-full bg-emerald-400 shadow-[0_0_7px_rgba(52,211,153,.7)]"/>{projectActivity[project.id]} working</span>}</div><div className="mt-2 truncate font-mono text-[10px] text-zinc-600">{project.repo}</div></button>)}</div><div className="h-fit rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6"><div className="text-[10px] font-semibold uppercase tracking-[.2em] text-violet-400">Project genesis</div><h2 className="mt-2 text-lg font-semibold">Create a new project</h2><p className="mt-2 text-xs leading-5 text-zinc-500">{state.globalSettings.scaffold.mode==="guided"?"Create the Git foundation, then enter a guided requirements conversation with Project Manager.":"Create a clean Git repository without starting onboarding."}</p><input value={name} onChange={(event) => setName(event.target.value)} onKeyDown={event=>{if(event.key==="Enter"&&name.trim())void add()}} className="mt-5 w-full rounded-xl border border-white/10 bg-black/25 px-4 py-3 text-sm outline-none focus:border-violet-400/40" placeholder="What should we call it?" />{error && <p className="mt-2 text-xs text-red-400">{error}</p>}<button disabled={!name.trim()} onClick={() => void add()} className="mt-4 w-full rounded-xl bg-violet-500 px-4 py-3 text-sm font-semibold shadow-[0_0_18px_rgba(139,92,246,.18)] hover:bg-violet-400 disabled:opacity-40">{state.globalSettings.scaffold.mode==="guided"?"Create & begin onboarding":"Create blank project"}</button><div className="mt-4 flex items-center justify-between border-t border-white/10 pt-4 text-[10px] text-zinc-600"><span>Model: <span className="capitalize text-zinc-400">{state.globalSettings.defaultProvider}</span></span><span>{state.globalSettings.scaffold.autoDeploy?"Auto-deploy on":"Auto-deploy off"}</span></div></div></div>
-      </> : <RunHistory state={state} />}
+      {view === "pm" ? null : view === "tasks" ? <TaskBoard key={active.id} projectId={active.id} projectName={active.name} onTriage={triageTasks} onReviewProject={reviewProject} /> : view === "agents" ? <Agents key={active.id} projectId={active.id} onState={setState} /> : view === "active-agents" ? <ActiveAgents key={active.id} projectId={active.id} /> : view === "runtime" ? <AppControl key={active.id} projectId={active.id} status={appStatus} onStatus={setAppStatus} /> : view === "knowledge" ? <Knowledge key={active.id} projectId={active.id} /> : view === "project-settings" ? <ProjectSettings projectId={active.id} projectName={active.name}/> : view === "settings" ? <Settings state={state} onState={setState} /> : view === "projects" ? <>
+        <div className="flex items-start justify-between gap-6"><Title eyebrow="Workspace registry" title="Projects" text={`Create, switch, or unregister projects under ${state.projectsDirectory}.`} /><button disabled={Boolean(onboardingBusy)} onClick={openProjectDialog} title="Add project" className="mt-1 flex items-center gap-2 rounded-xl border border-indigo-400/25 bg-indigo-400/10 px-3.5 py-2.5 text-sm font-semibold text-indigo-100 hover:bg-indigo-400/15 disabled:opacity-40"><PlusIcon className="size-5"/><span>Add project</span></button></div>
+        <div className="mt-8 max-w-5xl space-y-3">
+          {state.projects.map((project) => <div key={project.id} className={`flex overflow-hidden rounded-xl border ${project.id === active.id ? "border-indigo-400/30 bg-indigo-400/10" : "border-white/10 bg-white/[.025]"}`}><button onClick={() => {setOnboardingMessage(undefined);void switchProject(project.id)}} className="min-w-0 flex-1 p-5 text-left"><div className="flex items-center justify-between gap-4"><div className="font-medium">{project.name}</div>{Boolean(projectActivity[project.id])&&<span className="flex items-center gap-2 rounded-full bg-emerald-400/10 px-2.5 py-1 text-[10px] font-semibold uppercase text-emerald-300"><span className="size-1.5 animate-pulse rounded-full bg-emerald-400 shadow-[0_0_7px_rgba(52,211,153,.7)]"/>{projectActivity[project.id]} working</span>}</div><div className="mt-2 truncate font-mono text-[10px] text-zinc-600">{project.repo}</div></button><button disabled={state.projects.length === 1} onClick={() => void removeProject(project.id, project.name)} title={state.projects.length === 1 ? "CodePilot needs at least one registered project" : "Remove from codePilot"} className="grid w-14 shrink-0 place-items-center border-l border-white/10 text-zinc-600 hover:bg-red-400/10 hover:text-red-300 disabled:cursor-not-allowed disabled:opacity-25 disabled:hover:bg-transparent disabled:hover:text-zinc-600"><TrashIcon className="size-4"/><span className="sr-only">Remove {project.name} from codePilot</span></button></div>)}
+          {error && !projectDialog && <p className="rounded-xl border border-red-400/20 bg-red-400/10 p-3 text-xs text-red-300">{error}</p>}
+        </div>
+      </> : <RunHistory state={state} projectId={active.id} />}
     </main>
+    {projectDialog && <div role="dialog" aria-modal="true" aria-labelledby="project-dialog-title" onMouseDown={(event) => {if(event.target===event.currentTarget&&!onboardingBusy)setProjectDialog(undefined)}} className="fixed inset-0 z-[90] grid place-items-center bg-zinc-950/75 p-6 backdrop-blur-sm"><section className="w-full max-w-2xl rounded-2xl border border-white/10 bg-zinc-950 p-6 shadow-2xl shadow-black/60"><div className="flex items-start justify-between gap-5"><div>{projectDialog!=="choose"&&<button onClick={()=>{setError("");setProjectDialog("choose")}} className="mb-3 flex items-center gap-1 text-xs text-zinc-500 hover:text-indigo-300"><ChevronLeftIcon className="size-3.5"/>All options</button>}<div className="text-[10px] font-semibold uppercase tracking-[.22em] text-indigo-400">Project registry</div><h2 id="project-dialog-title" className="mt-2 text-xl font-semibold">{projectDialog==="choose"?"Add a project":projectDialog==="github"?"Clone from GitHub":"Create a new project"}</h2><p className="mt-2 text-sm leading-6 text-zinc-500">{projectDialog==="choose"?"Choose how this project should enter your CodePilot workspace.":projectDialog==="github"?"Paste an HTTPS or SSH repository URL. Git's credential helper or SSH agent will handle access.":state.globalSettings.scaffold.mode==="guided"?"Name the project. CodePilot will create its Git repository and begin guided onboarding.":"Name the project. CodePilot will create a clean Git repository."}</p></div><button disabled={Boolean(onboardingBusy)} onClick={()=>setProjectDialog(undefined)} title="Close" className="rounded-lg p-2 text-zinc-600 hover:bg-white/5 hover:text-zinc-200 disabled:opacity-30"><XMarkIcon className="size-5"/></button></div>
+      {projectDialog==="choose"?<div className="mt-7 grid grid-cols-1 gap-3 sm:grid-cols-3"><button onClick={()=>void onboardLocal()} className="group rounded-2xl border border-white/10 bg-white/[.025] p-5 text-left hover:border-indigo-400/30 hover:bg-indigo-400/[.07]"><span className="grid size-11 place-items-center rounded-xl bg-indigo-400/10 text-indigo-300 group-hover:bg-indigo-400/15"><FolderIcon className="size-5"/></span><div className="mt-4 text-sm font-semibold">Local folder</div><p className="mt-1.5 text-xs leading-5 text-zinc-500">Select an existing local Git checkout.</p></button><button onClick={()=>{setError("");setProjectDialog("github")}} className="group rounded-2xl border border-white/10 bg-white/[.025] p-5 text-left hover:border-indigo-400/30 hover:bg-indigo-400/[.07]"><span className="grid size-11 place-items-center rounded-xl bg-indigo-400/10 text-indigo-300 group-hover:bg-indigo-400/15"><GitHubMark className="size-5"/></span><div className="mt-4 text-sm font-semibold">GitHub</div><p className="mt-1.5 text-xs leading-5 text-zinc-500">Clone an HTTPS or SSH Git repository.</p></button><button onClick={()=>{setError("");setProjectDialog("new")}} className="group rounded-2xl border border-white/10 bg-white/[.025] p-5 text-left hover:border-violet-400/30 hover:bg-violet-400/[.07]"><span className="grid size-11 place-items-center rounded-xl bg-violet-400/10 text-violet-300 group-hover:bg-violet-400/15"><PlusIcon className="size-5"/></span><div className="mt-4 text-sm font-semibold">New project</div><p className="mt-1.5 text-xs leading-5 text-zinc-500">Create a new Git project from scratch.</p></button></div>:projectDialog==="github"?<form onSubmit={(event)=>{event.preventDefault();if(remoteUrl.trim())void onboardRemote()}} className="mt-7"><label htmlFor="github-repository-url" className="text-xs font-medium text-zinc-300">Repository URL</label><input id="github-repository-url" autoFocus value={remoteUrl} onChange={(event)=>setRemoteUrl(event.target.value)} className="mt-2 w-full rounded-xl border border-white/10 bg-black/25 px-4 py-3 font-mono text-xs outline-none focus:border-indigo-400/40" placeholder="https://github.com/owner/repository.git"/><p className="mt-2 text-[11px] text-zinc-600">Credentials must not be embedded in the URL.</p><button type="submit" disabled={!remoteUrl.trim()||Boolean(onboardingBusy)} className="mt-5 w-full rounded-xl bg-indigo-500 px-4 py-3 text-sm font-semibold hover:bg-indigo-400 disabled:opacity-40">{onboardingBusy==="remote"?"Cloning repository…":"Clone and onboard"}</button></form>:<form onSubmit={(event)=>{event.preventDefault();if(name.trim())void add()}} className="mt-7"><label htmlFor="new-project-name" className="text-xs font-medium text-zinc-300">Project name</label><input id="new-project-name" autoFocus value={name} onChange={(event)=>setName(event.target.value)} className="mt-2 w-full rounded-xl border border-white/10 bg-black/25 px-4 py-3 text-sm outline-none focus:border-violet-400/40" placeholder="What should we call it?"/><p className="mt-2 truncate text-[11px] text-zinc-600">Created under {projectsDirectory}</p><button type="submit" disabled={!name.trim()||Boolean(onboardingBusy)} className="mt-5 w-full rounded-xl bg-violet-500 px-4 py-3 text-sm font-semibold hover:bg-violet-400 disabled:opacity-40">{state.globalSettings.scaffold.mode==="guided"?"Create and begin onboarding":"Create blank project"}</button></form>}
+      {error&&<p className="mt-4 rounded-xl border border-red-400/20 bg-red-400/10 p-3 text-xs text-red-300">{error}</p>}</section></div>}
+    {launchSetup && <LaunchSetupDialog projectName={launchSetup.projectName} config={launchConfig} busy={launchSetupBusy} error={launchSetupError} onChange={setLaunchConfig} onSave={()=>void saveLaunchSetup()} onSkip={()=>continueAfterLaunchSetup(launchSetup)}/>}
     {projectTransition && <div className="pointer-events-none fixed inset-0 z-[80] grid place-items-center bg-zinc-950/45 backdrop-blur-[2px]"><div className="rounded-2xl border border-indigo-400/25 bg-zinc-950/95 px-8 py-6 text-center shadow-2xl"><div className="text-[10px] font-semibold uppercase tracking-[.24em] text-indigo-400">Switching project</div><div className="mt-3 flex items-center gap-3 text-sm text-zinc-200"><span className="max-w-40 truncate">{projectTransition.from}</span><span className="text-indigo-400">→</span><span className="max-w-40 truncate">{projectTransition.to}</span></div><p className="mt-3 text-[10px] text-zinc-500">Loading the selected project’s files, tasks, and sessions</p></div></div>}
   </div>;
 }
 
 function Nav({ active, on, icon, children }: { active: boolean; on(): void; icon: React.ReactNode; children: React.ReactNode }) { return <button title={typeof children === "string" ? children : "App Core"} onClick={on} className={`sidebar-nav flex w-full items-center gap-3 rounded-lg px-3 py-2.5 text-sm ${active ? "bg-white/10" : "text-zinc-500 hover:bg-white/5"}`}><span className="size-5 shrink-0">{icon}</span><span className="nav-label min-w-0 flex-1 text-left">{children}</span></button>; }
 function RuntimeGlyph({ running }: { running: boolean }) { return <span className={`runtime-glyph ${running ? "runtime-glyph-on" : ""}`} aria-hidden="true"><span className="runtime-orbit" /><span className="runtime-core" /><span className="runtime-node runtime-node-a" /><span className="runtime-node runtime-node-b" /><span className="runtime-node runtime-node-c" /></span>; }
+function LaunchSetupDialog({ projectName, config, busy, error, onChange, onSave, onSkip }: { projectName: string; config: AppConfig; busy: boolean; error: string; onChange(config: AppConfig): void; onSave(): void; onSkip(): void }) { return <div role="dialog" aria-modal="true" aria-labelledby="launch-setup-title" className="fixed inset-0 z-[95] grid place-items-center bg-zinc-950/80 p-6 backdrop-blur-sm"><form onSubmit={(event)=>{event.preventDefault();if(config.command.trim())onSave()}} className="w-full max-w-xl rounded-2xl border border-emerald-400/15 bg-zinc-950 p-6 shadow-2xl shadow-black/60"><div className="flex items-start gap-4"><span className="grid size-11 shrink-0 place-items-center rounded-xl bg-emerald-400/10 text-emerald-300"><RocketLaunchIcon className="size-5"/></span><div><div className="text-[10px] font-semibold uppercase tracking-[.22em] text-emerald-400">Onboarding · launch setup</div><h2 id="launch-setup-title" className="mt-2 text-xl font-semibold">Configure {projectName}</h2><p className="mt-2 text-sm leading-6 text-zinc-500">Review how App Core should launch this project. Saving the configuration will not start the app.</p></div></div><OnboardingField label="Start command" hint="The command CodePilot should run."><input autoFocus value={config.command} onChange={(event)=>onChange({...config,command:event.target.value})} className="field" placeholder="npm run dev"/></OnboardingField><OnboardingField label="Working directory" hint="A path relative to the repository root."><input value={config.workingDirectory} onChange={(event)=>onChange({...config,workingDirectory:event.target.value})} className="field" placeholder="."/></OnboardingField><OnboardingField label="Local app URL" hint="Optional address for Open app and port controls."><input value={config.url} onChange={(event)=>onChange({...config,url:event.target.value})} className="field" placeholder="http://localhost:3000"/></OnboardingField>{error&&<p className="mt-4 rounded-xl border border-red-400/20 bg-red-400/10 p-3 text-xs text-red-300">{error}</p>}<div className="mt-6 flex items-center justify-end gap-3"><button type="button" disabled={busy} onClick={onSkip} className="rounded-xl border border-white/10 px-4 py-2.5 text-sm text-zinc-400 hover:bg-white/5 disabled:opacity-40">Skip for now</button><button type="submit" disabled={busy||!config.command.trim()} className="rounded-xl bg-emerald-500 px-5 py-2.5 text-sm font-semibold text-emerald-950 hover:bg-emerald-400 disabled:opacity-40">{busy?"Saving…":"Save and continue"}</button></div></form></div>; }
+function OnboardingField({ label, hint, children }: { label: string; hint: string; children: React.ReactNode }) { return <label className="mt-5 block"><span className="text-xs font-medium text-zinc-300">{label}</span><span className="ml-2 text-[11px] text-zinc-600">{hint}</span><div className="mt-2">{children}</div></label>; }
+function GitHubMark({ className = "" }: { className?: string }) { return <svg viewBox="0 0 24 24" fill="currentColor" className={className} aria-hidden="true"><path fillRule="evenodd" d="M12 2C6.477 2 2 6.596 2 12.267c0 4.537 2.865 8.385 6.839 9.744.5.094.682-.223.682-.495 0-.245-.009-1.054-.014-1.912-2.782.62-3.369-1.21-3.369-1.21-.455-1.187-1.11-1.502-1.11-1.502-.908-.637.069-.624.069-.624 1.004.073 1.532 1.058 1.532 1.058.892 1.568 2.341 1.115 2.91.853.091-.663.349-1.115.635-1.371-2.221-.26-4.556-1.14-4.556-5.075 0-1.121.39-2.037 1.029-2.756-.103-.259-.446-1.303.098-2.717 0 0 .84-.276 2.75 1.053A9.303 9.303 0 0 1 12 6.967a9.3 9.3 0 0 1 2.504.346c1.909-1.329 2.748-1.053 2.748-1.053.545 1.414.202 2.458.1 2.717.64.719 1.027 1.635 1.027 2.756 0 3.945-2.339 4.812-4.566 5.067.359.318.679.945.679 1.904 0 1.375-.012 2.482-.012 2.82 0 .275.18.594.688.493C19.138 20.385 22 16.537 22 12.267 22 6.596 17.523 2 12 2Z" clipRule="evenodd"/></svg>; }
 function Title({ eyebrow, title, text }: { eyebrow: string; title: string; text: string }) { return <><div className="text-xs font-semibold uppercase tracking-[.2em] text-indigo-400">{eyebrow}</div><h1 className="mt-2 text-2xl font-semibold">{title}</h1><p className="mt-2 text-sm text-zinc-400">{text}</p></>; }
 const rendererWindow = window as Window & { __codepilotRoot?: Root };
 rendererWindow.__codepilotRoot ??= createRoot(document.getElementById("root")!);
diff --git a/desktop/src/run-history.tsx b/desktop/src/run-history.tsx
index b880367..7204018 100644
--- a/desktop/src/run-history.tsx
+++ b/desktop/src/run-history.tsx
@@ -1,12 +1,12 @@
 import React, { useEffect, useState } from "react";
 import type { DesktopState, RunDetail } from "./types";
 
-export function RunHistory({ state }: { state: DesktopState }) {
+export function RunHistory({ state, projectId }: { state: DesktopState; projectId: string }) {
   const [selected, setSelected] = useState<RunDetail>();
   const [summaries, setSummaries] = useState<Record<string, string>>({});
   const [loading, setLoading] = useState("");
-  useEffect(() => { let live = true; void Promise.all(state.runs.map(async (run) => { try { const detail = await window.codepilot.getRunDetail(run.id); return [run.id, detail.workers.find((worker) => worker.report?.summary)?.report?.summary ?? detail.summary?.review?.findings?.[0] ?? `Run ${run.status}.`] as const; } catch { return [run.id, `Run ${run.status}.`] as const; } })).then((items) => { if (live) setSummaries(Object.fromEntries(items)); }); return () => { live = false; }; }, [state.runs]);
-  async function open(id: string) { setLoading(id); try { setSelected(await window.codepilot.getRunDetail(id)); } finally { setLoading(""); } }
+  useEffect(() => { let live = true; void Promise.all(state.runs.map(async (run) => { try { const detail = await window.codepilot.getRunDetail(projectId, run.id); return [run.id, detail.workers.find((worker) => worker.report?.summary)?.report?.summary ?? detail.summary?.review?.findings?.[0] ?? `Run ${run.status}.`] as const; } catch { return [run.id, `Run ${run.status}.`] as const; } })).then((items) => { if (live) setSummaries(Object.fromEntries(items)); }); return () => { live = false; }; }, [projectId, state.runs]);
+  async function open(id: string) { setLoading(id); try { setSelected(await window.codepilot.getRunDetail(projectId, id)); } finally { setLoading(""); } }
   return <><div className="text-xs font-semibold uppercase tracking-[.2em] text-indigo-400">Mission control</div><h1 className="mt-2 text-2xl font-semibold">Agent sessions</h1><p className="mt-2 text-sm text-zinc-400">Open a session to see what was delivered, changed, tested, and flagged.</p><div className="mt-8 grid grid-cols-3 gap-4"><Stat label="Projects" value={state.projects.length} /><Stat label="Sessions" value={state.runs.length} /><Stat label="Needs review" value={state.runs.filter((run) => run.status === "needs_review").length} /></div><div className="mt-8 grid grid-cols-[minmax(320px,0.8fr)_minmax(0,1.2fr)] gap-6"><section className="h-fit overflow-hidden rounded-2xl border border-white/10 bg-white/[.025]">{state.runs.length ? state.runs.map((run) => <button key={run.id} onClick={() => void open(run.id)} className={`w-full border-b border-white/5 p-5 text-left hover:bg-white/5 ${selected?.id === run.id ? "bg-indigo-500/10" : ""}`}><div className="flex items-start justify-between gap-4"><span className="line-clamp-3 text-sm leading-5 text-zinc-200">{summaries[run.id] ?? "Loading result summary…"}</span><Status value={run.status} /></div><div className="mt-2 flex items-center justify-between gap-3"><span className="line-clamp-1 text-[10px] text-zinc-600">Task · {run.objective.split("\n")[0]}</span><span className="shrink-0 text-[10px] text-zinc-600">{new Date(run.createdAt).toLocaleString()}{loading === run.id ? " · loading…" : ""}</span></div></button>) : <div className="py-16 text-center text-sm text-zinc-600">No agent sessions yet.</div>}</section><section className="min-w-0">{selected ? <Detail run={selected} /> : <div className="rounded-2xl border border-dashed border-white/10 py-24 text-center text-sm text-zinc-600">Select a session to inspect its results.</div>}</section></div></>;
 }
 function Detail({ run }: { run: RunDetail }) { return <div className="space-y-4"><div className="rounded-2xl border border-white/10 bg-white/[.025] p-6"><div className="flex items-center justify-between"><Status value={run.status} /><span className="font-mono text-[10px] text-zinc-600">{run.id}</span></div><h2 className="mt-4 text-lg font-semibold">{run.objective}</h2></div>{run.workers.map((worker) => <div key={worker.taskId} className="rounded-2xl border border-white/10 bg-white/[.025] p-6"><div className="flex items-center justify-between"><h3 className="text-sm font-semibold capitalize">{worker.provider} result</h3><Status value={worker.report?.status ?? worker.status} /></div>{worker.report ? <p className="mt-4 text-sm leading-6 text-zinc-300">{worker.report.summary}</p> : <p className="mt-4 text-sm text-zinc-500">No structured worker report was produced.</p>}{worker.verification?.resultCommit && <div className="mt-4 font-mono text-[10px] text-zinc-600">commit {worker.verification.resultCommit}</div>}</div>)}{run.summary?.review && <div className="rounded-2xl border border-white/10 bg-white/[.025] p-6"><h3 className="text-sm font-semibold">Manager review · {run.summary.review.verdict}</h3><List items={run.summary.review.findings} /></div>}</div>; }
diff --git a/desktop/src/settings.tsx b/desktop/src/settings.tsx
index 97c4bb5..bde994a 100644
--- a/desktop/src/settings.tsx
+++ b/desktop/src/settings.tsx
@@ -1,17 +1,93 @@
-import { useState } from "react";
-import { CheckIcon, CpuChipIcon, SparklesIcon } from "@heroicons/react/24/outline";
-import type { DesktopState, GlobalSettings } from "./types";
+import { useEffect, useState } from "react";
+import { CheckIcon, CloudIcon, CpuChipIcon, SparklesIcon } from "@heroicons/react/24/outline";
+import type { DesktopState, GitHubStatus, GlobalSettings } from "./types";
 
 export function Settings({ state, onState }: { state: DesktopState; onState(state: DesktopState): void }) {
-  const [settings,setSettings]=useState<GlobalSettings>(state.globalSettings),[saved,setSaved]=useState(false),[busy,setBusy]=useState(false);
-  async function save(){setBusy(true);try{const next=await window.codepilot.saveGlobalSettings(settings);setSettings(next);onState(await window.codepilot.getState());setSaved(true);window.setTimeout(()=>setSaved(false),1800)}finally{setBusy(false)}}
-  return <div className="mx-auto max-w-4xl"><div className="text-xs font-semibold uppercase tracking-[.2em] text-violet-400">Global configuration</div><h1 className="mt-2 text-2xl font-semibold">Settings</h1><p className="mt-2 text-sm text-zinc-400">Defaults apply across projects and sessions.</p>
-    <section className="mt-8 rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6"><Header icon={<CpuChipIcon className="size-5"/>} title="Default model provider" text="Used by guided scaffolding, automatic tasks, and as the initial choice in Deploy."/><div className="mt-6 grid grid-cols-2 gap-4">{(["codex","claude"] as const).map(provider=><Choice key={provider} active={settings.defaultProvider===provider} on={()=>setSettings({...settings,defaultProvider:provider})} title={provider} text={provider==="codex"?"OpenAI coding agent":"Anthropic Claude Code"}/>)}</div></section>
-    <section className="mt-6 rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6"><Header icon={<SparklesIcon className="size-5"/>} title="Project scaffolding" text="Choose whether new projects open as blank repositories or begin a guided Project Manager onboarding."/><div className="mt-6 grid grid-cols-2 gap-4"><Choice active={settings.scaffold.mode==="guided"} on={()=>setSettings({...settings,scaffold:{...settings.scaffold,mode:"guided"}})} title="Guided onboarding" text="Start a requirements conversation and build through agreed tasks."/><Choice active={settings.scaffold.mode==="blank"} on={()=>setSettings({...settings,scaffold:{...settings.scaffold,mode:"blank"}})} title="Blank repository" text="Create Git foundations without starting a conversation."/></div>
-      <label className="mt-6 block text-sm font-medium text-zinc-300">Onboarding instructions<span className="mt-1 block text-xs font-normal text-zinc-600">Injected as the opening Project Manager message for every guided project.</span><textarea rows={9} value={settings.scaffold.onboardingPrompt} onChange={event=>setSettings({...settings,scaffold:{...settings.scaffold,onboardingPrompt:event.target.value}})} disabled={settings.scaffold.mode==="blank"} className="mt-3 w-full resize-y rounded-xl border border-white/10 bg-black/25 p-4 text-sm leading-6 text-zinc-300 outline-none focus:border-violet-400/40 disabled:opacity-40"/></label>
-      <label className="mt-5 flex cursor-pointer items-center justify-between rounded-xl border border-white/10 bg-black/20 p-4"><div><div className="text-sm font-medium">Auto-deploy agreed tasks</div><div className="mt-1 text-xs text-zinc-600">Use the global model as requirements become implementation-ready.</div></div><input type="checkbox" checked={settings.scaffold.autoDeploy} onChange={event=>setSettings({...settings,scaffold:{...settings.scaffold,autoDeploy:event.target.checked}})} className="size-4 accent-violet-500"/></label>
-    </section><div className="mt-6 flex items-center justify-end gap-4">{saved&&<span className="text-xs text-emerald-400">Global settings saved.</span>}<button disabled={busy||!settings.scaffold.onboardingPrompt.trim()} onClick={()=>void save()} className="rounded-xl bg-violet-500 px-5 py-2.5 text-sm font-semibold hover:bg-violet-400 disabled:opacity-40">{busy?"Saving…":"Save global settings"}</button></div>
+  const [settings, setSettings] = useState<GlobalSettings>(state.globalSettings);
+  const [github, setGitHub] = useState<GitHubStatus>();
+  const [saved, setSaved] = useState(false);
+  const [busy, setBusy] = useState(false);
+  const [githubBusy, setGitHubBusy] = useState(false);
+  const [githubError, setGitHubError] = useState("");
+
+  useEffect(() => {
+    void window.codepilot.getGitHubStatus().then(setGitHub).catch(cause => setGitHubError(cause instanceof Error ? cause.message : String(cause)));
+  }, []);
+
+  async function save() {
+    setBusy(true);
+    try {
+      const next = await window.codepilot.saveGlobalSettings(settings);
+      setSettings(next);
+      onState(await window.codepilot.getState());
+      setSaved(true);
+      window.setTimeout(() => setSaved(false), 1800);
+    } finally {
+      setBusy(false);
+    }
+  }
+
+  async function connectGitHub() {
+    setGitHubBusy(true);
+    setGitHubError("");
+    try {
+      const next = await window.codepilot.loginGitHub();
+      setGitHub(next);
+      setSettings(current => ({ ...current, github: { allowWrites: true } }));
+    } catch (cause) {
+      setGitHubError(cause instanceof Error ? cause.message : String(cause));
+    } finally {
+      setGitHubBusy(false);
+    }
+  }
+
+  return <div className="mx-auto max-w-4xl">
+    <div className="text-xs font-semibold uppercase tracking-[.2em] text-violet-400">Global configuration</div>
+    <h1 className="mt-2 text-2xl font-semibold">Settings</h1>
+    <p className="mt-2 text-sm text-zinc-400">Defaults apply across projects and sessions.</p>
+
+    <section className="mt-8 rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6">
+      <Header icon={<CloudIcon className="size-5"/>} title="GitHub connection" text="Delegate authentication to GitHub CLI and its system credential store. CodePilot never reads or saves your token."/>
+      <div className="mt-6 rounded-xl border border-white/10 bg-black/20 p-4">
+        <div className="flex flex-wrap items-center justify-between gap-4">
+          <div>
+            <div className={`text-sm font-semibold ${github?.authenticated ? "text-emerald-300" : "text-zinc-300"}`}>
+              {github?.authenticated ? `Connected as @${github.account}` : github?.installed === false ? "GitHub CLI not found" : "GitHub is not connected"}
+            </div>
+            <p className="mt-1 text-xs text-zinc-600">
+              {github?.authenticated ? `${github.gitProtocol?.toUpperCase() || "Git"} · ${github.scopes.length ? github.scopes.join(", ") : "permissions managed by GitHub"}` : "Sign-in opens GitHub's browser flow and copies its one-time code to your clipboard."}
+            </p>
+          </div>
+          <button disabled={githubBusy || github?.installed === false} onClick={() => void connectGitHub()} className="rounded-lg border border-violet-400/30 bg-violet-400/10 px-4 py-2 text-xs font-semibold text-violet-200 hover:bg-violet-400/15 disabled:opacity-40">
+            {githubBusy ? "Waiting for GitHub…" : github?.authenticated ? "Reconnect account" : "Connect GitHub"}
+          </button>
+        </div>
+        {githubError && <p className="mt-3 text-xs text-red-300">{githubError}</p>}
+      </div>
+      <label className={`mt-4 flex items-center justify-between rounded-xl border border-white/10 bg-black/20 p-4 ${github?.authenticated ? "cursor-pointer" : "cursor-not-allowed opacity-50"}`}>
+        <div>
+          <div className="text-sm font-medium">Allow GitHub write operations</div>
+          <div className="mt-1 text-xs text-zinc-600">Permits branch pushes and pull-request creation only when a deploy explicitly selects GitHub publishing.</div>
+        </div>
+        <input type="checkbox" disabled={!github?.authenticated} checked={settings.github.allowWrites} onChange={event => setSettings({...settings, github: { allowWrites: event.target.checked }})} className="size-4 accent-violet-500"/>
+      </label>
+    </section>
+
+    <section className="mt-6 rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6">
+      <Header icon={<CpuChipIcon className="size-5"/>} title="Default model provider" text="Used by guided scaffolding, automatic tasks, and as the initial choice in Deploy."/>
+      <div className="mt-6 grid grid-cols-2 gap-4">{(["codex","claude"] as const).map(provider => <Choice key={provider} active={settings.defaultProvider === provider} on={() => setSettings({...settings, defaultProvider: provider})} title={provider} text={provider === "codex" ? "OpenAI coding agent" : "Anthropic Claude Code"}/>)}</div>
+    </section>
+
+    <section className="mt-6 rounded-2xl border border-violet-400/15 bg-violet-400/[.035] p-6">
+      <Header icon={<SparklesIcon className="size-5"/>} title="Project scaffolding" text="Choose whether new projects open as blank repositories or begin a guided Project Manager onboarding."/>
+      <div className="mt-6 grid grid-cols-2 gap-4"><Choice active={settings.scaffold.mode === "guided"} on={() => setSettings({...settings, scaffold: {...settings.scaffold, mode: "guided"}})} title="Guided onboarding" text="Start a requirements conversation and build through agreed tasks."/><Choice active={settings.scaffold.mode === "blank"} on={() => setSettings({...settings, scaffold: {...settings.scaffold, mode: "blank"}})} title="Blank repository" text="Create Git foundations without starting a conversation."/></div>
+      <label className="mt-6 block text-sm font-medium">Onboarding instructions<span className="mt-1 block text-xs font-normal text-zinc-600">Injected as the opening Project Manager message for every guided project.</span><textarea rows={9} value={settings.scaffold.onboardingPrompt} onChange={event => setSettings({...settings, scaffold: {...settings.scaffold, onboardingPrompt: event.target.value}})} disabled={settings.scaffold.mode === "blank"} className="mt-3 w-full resize-y rounded-xl border border-white/10 bg-black/25 p-4 text-sm leading-6 text-zinc-300 outline-none focus:border-violet-400/40 disabled:opacity-40"/></label>
+      <label className="mt-5 flex cursor-pointer items-center justify-between rounded-xl border border-white/10 bg-black/20 p-4"><div><div className="text-sm font-medium">Auto-deploy agreed tasks</div><div className="mt-1 text-xs text-zinc-600">Use the global model as requirements become implementation-ready.</div></div><input type="checkbox" checked={settings.scaffold.autoDeploy} onChange={event => setSettings({...settings, scaffold: {...settings.scaffold, autoDeploy: event.target.checked}})} className="size-4 accent-violet-500"/></label>
+    </section>
+
+    <div className="mt-6 flex items-center justify-end gap-4">{saved && <span className="text-xs text-emerald-400">Global settings saved.</span>}<button disabled={busy || !settings.scaffold.onboardingPrompt.trim()} onClick={() => void save()} className="rounded-xl bg-violet-500 px-5 py-2.5 text-sm font-semibold hover:bg-violet-400 disabled:opacity-40">{busy ? "Saving…" : "Save global settings"}</button></div>
   </div>;
 }
+
 function Header({icon,title,text}:{icon:React.ReactNode;title:string;text:string}){return <div className="flex items-start gap-4"><span className="grid size-10 place-items-center rounded-xl bg-violet-400/10 text-violet-300">{icon}</span><div><h2 className="text-sm font-semibold">{title}</h2><p className="mt-1 text-xs leading-5 text-zinc-500">{text}</p></div></div>}
 function Choice({active,on,title,text}:{active:boolean;on():void;title:string;text:string}){return <button onClick={on} className={`flex items-center justify-between rounded-xl border p-5 text-left transition ${active?"border-violet-400/40 bg-violet-400/10":"border-white/10 bg-black/20 hover:bg-white/5"}`}><div><div className="font-semibold capitalize">{title}</div><div className="mt-1 text-xs text-zinc-500">{text}</div></div>{active&&<CheckIcon className="size-5 text-violet-300"/>}</button>}
diff --git a/desktop/src/task-board.tsx b/desktop/src/task-board.tsx
index 67affe6..4c9b8bb 100644
--- a/desktop/src/task-board.tsx
+++ b/desktop/src/task-board.tsx
@@ -19,7 +19,7 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
   const commitTaskBin = window.codepilot.commitPMTaskBin;
   useEffect(() => {
     let active = true;
-    const refresh = () => void window.codepilot.getPM().then((next) => active && setState(next));
+    const refresh = () => void window.codepilot.getPM(projectId).then((next) => active && setState(next));
     refresh();
     const timer = window.setInterval(refresh, 2000);
     return () => { active = false; window.clearInterval(timer); };
@@ -42,8 +42,8 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
     setRequeueingColumn(column.title);
     try {
       for (const task of column.tasks)
-        await window.codepilot.setPMTaskStatus(task.id, "ready", `Requeued from the ${column.title} task-board column.`);
-      setState(await window.codepilot.getPM());
+        await window.codepilot.setPMTaskStatus(projectId, task.id, "ready", `Requeued from the ${column.title} task-board column.`);
+      setState(await window.codepilot.getPM(projectId));
     } finally {
       setRequeueingColumn("");
     }
@@ -52,7 +52,7 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
     if (requeueingColumn) return;
     setRequeueingColumn("Blocked");
     try {
-      setState(await window.codepilot.getPM());
+      setState(await window.codepilot.getPM(projectId));
     } finally {
       setRequeueingColumn("");
     }
@@ -62,8 +62,9 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
     setRunningReady(true);
     try {
       for (const task of readyTasks)
-        setState(await window.codepilot.setPMTaskStatus(task.id, "launched"));
+        setState(await window.codepilot.setPMTaskStatus(projectId, task.id, "launched"));
       const result = await window.codepilot.runAgentBatch({
+        projectId,
         objective: `Task Board coordinated delivery batch (${readyTasks.length} tasks)`,
         items: readyTasks.map((task) => ({
           id: task.id,
@@ -79,14 +80,14 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
       const summary = result.review.findings.length ? result.review.findings.join(" ") : `Coordinated batch completed with review verdict: ${result.review.verdict}.`;
       for (const task of readyTasks)
         setState(result.status === "completed"
-          ? await window.codepilot.setPMTaskStatus(task.id, "done", summary)
-          : await window.codepilot.recordPMTaskFailure(task.id, summary));
-      setState(await window.codepilot.getPM());
+          ? await window.codepilot.setPMTaskStatus(projectId, task.id, "done", summary)
+          : await window.codepilot.recordPMTaskFailure(projectId, task.id, summary));
+      setState(await window.codepilot.getPM(projectId));
     } catch (cause) {
       const reason = cause instanceof Error ? cause.message : String(cause);
       for (const task of readyTasks)
         try {
-          setState(await window.codepilot.recordPMTaskFailure(task.id, `Coordinated batch failed before delivery: ${reason}`));
+          setState(await window.codepilot.recordPMTaskFailure(projectId, task.id, `Coordinated batch failed before delivery: ${reason}`));
         } catch {}
     } finally {
       setRunningReady(false);
@@ -97,9 +98,9 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
     <div className="text-xs font-semibold uppercase tracking-[.2em] text-indigo-400">Project planning</div>
     <div className="mt-2 flex items-center justify-between gap-4"><div className="flex items-center gap-3"><h1 className="text-2xl font-semibold">Suggested tasks</h1><button onClick={onReviewProject} className="rounded-lg border border-violet-400/30 bg-violet-400/10 px-3 py-2 text-xs font-semibold text-violet-200 hover:bg-violet-400/15">Review</button></div><button disabled={!selectedTaskIds.length || Boolean(commitMessage)} onClick={async () => { setCommitMessage("Committing…"); try {
       if (typeof commitTaskBin !== "function") throw new Error("The desktop bridge is out of date. Restart codePilot, then try the commit again.");
-      const bin = await commitTaskBin(selectedTaskIds);
+      const bin = await commitTaskBin(projectId, selectedTaskIds);
       setCommitMessage(`Bin ${bin.hash} · commit ${bin.commit.slice(0, 8)}`);
-      setState(await window.codepilot.getPM());
+      setState(await window.codepilot.getPM(projectId));
       if (selected && bin.taskIds.includes(selected.task.id)) setSelected(undefined);
       setSelectedTaskIds([]);
     } catch (cause) { setCommitMessage(cause instanceof Error ? cause.message : String(cause)); } finally { window.setTimeout(() => setCommitMessage(""), 5000); } }} className="rounded-lg border border-indigo-400/30 bg-indigo-400/10 px-3 py-2 text-xs font-semibold text-indigo-200 disabled:cursor-not-allowed disabled:opacity-40">Commit selected tasks</button></div>
@@ -111,15 +112,15 @@ export function TaskBoard({ projectId, projectName, onTriage, onReviewProject }:
           <span className="rounded-full bg-white/[.07] px-2.5 py-1 text-xs font-medium text-zinc-300">{column.tasks.length}</span>
         </header>
         <div className="h-[312px] min-h-0 w-full flex-none space-y-2 overflow-y-auto overscroll-contain p-3 [scrollbar-gutter:stable]">
-          {column.tasks.map((task) => <TaskCard key={task.id} task={task} expanded={expandedTaskIds.includes(task.id)} loading={loading === task.id} dependencyTitles={task.dependencies.map((id) => allTasks.find((candidate) => candidate.id === id)?.title ?? id)} onContext={(event) => { event.preventDefault(); event.stopPropagation(); setContext({ task, x: event.clientX, y: event.clientY }); }} onToggle={() => setExpandedTaskIds((ids) => ids.includes(task.id) ? ids.filter((id) => id !== task.id) : [...ids, task.id])} onOpen={async () => { setLoading(task.id); try { setSelected(await window.codepilot.getPMTaskDetail(task.id)); } finally { setLoading(""); } }} />)}
+          {column.tasks.map((task) => <TaskCard key={task.id} task={task} expanded={expandedTaskIds.includes(task.id)} loading={loading === task.id} dependencyTitles={task.dependencies.map((id) => allTasks.find((candidate) => candidate.id === id)?.title ?? id)} onContext={(event) => { event.preventDefault(); event.stopPropagation(); setContext({ task, x: event.clientX, y: event.clientY }); }} onToggle={() => setExpandedTaskIds((ids) => ids.includes(task.id) ? ids.filter((id) => id !== task.id) : [...ids, task.id])} onOpen={async () => { setLoading(task.id); try { setSelected(await window.codepilot.getPMTaskDetail(projectId, task.id)); } finally { setLoading(""); } }} />)}
           {!column.tasks.length && <div className="grid h-32 place-items-center rounded-xl border border-dashed border-white/10 text-xs text-zinc-600">No tasks here</div>}
         </div>
       </section>)}
     </div>
     {commitMessage && <p className="mt-2 text-xs text-zinc-400">{commitMessage}</p>}
-    <AllTasksView tasks={tasks} open={allTasksOpen} setOpen={setAllTasksOpen} selectedTaskIds={selectedTaskIds} setSelectedTaskIds={setSelectedTaskIds} onSelect={async (task) => { setLoading(task.id); try { setSelected(await window.codepilot.getPMTaskDetail(task.id)); } finally { setLoading(""); } }} />
-    {selected && <TaskDrawer detail={selected} close={() => setSelected(undefined)} revise={async () => { setState(await window.codepilot.setPMTaskStatus(selected.task.id, "ready", "Marked for revision after review.")); setSelected(undefined); }} />}
-    {context && <TaskContextMenu task={context.task} x={context.x} y={context.y} close={() => setContext(undefined)} onState={setState} onTriage={(task) => onTriage([task])} />}
+    <AllTasksView tasks={tasks} open={allTasksOpen} setOpen={setAllTasksOpen} selectedTaskIds={selectedTaskIds} setSelectedTaskIds={setSelectedTaskIds} onSelect={async (task) => { setLoading(task.id); try { setSelected(await window.codepilot.getPMTaskDetail(projectId, task.id)); } finally { setLoading(""); } }} />
+    {selected && <TaskDrawer detail={selected} close={() => setSelected(undefined)} revise={async () => { setState(await window.codepilot.setPMTaskStatus(projectId, selected.task.id, "ready", "Marked for revision after review.")); setSelected(undefined); }} />}
+    {context && <TaskContextMenu projectId={projectId} task={context.task} x={context.x} y={context.y} close={() => setContext(undefined)} onState={setState} onTriage={(task) => onTriage([task])} />}
   </div>;
 }
 
@@ -191,13 +192,13 @@ function TaskDrawer({ detail, close, revise }: { detail: PMTaskDetail; close():
 
 function Pill({ value }: { value: string }) { return <span className="rounded-md border border-white/10 bg-white/5 px-2.5 py-1 text-[10px] font-semibold uppercase tracking-wider text-zinc-400">{value.replace("_", " ")}</span>; }
 
-function TaskContextMenu({ task, x, y, close, onState, onTriage }: { task: PMTask; x: number; y: number; close(): void; onState(state: PMState): void; onTriage(task: PMTask): void }) {
-  const api = window.codepilot as typeof window.codepilot & { deletePMTask: (id: string) => Promise<PMState> };
+function TaskContextMenu({ projectId, task, x, y, close, onState, onTriage }: { projectId: string; task: PMTask; x: number; y: number; close(): void; onState(state: PMState): void; onTriage(task: PMTask): void }) {
+  const api = window.codepilot;
   const [busy, setBusy] = useState(false);
   useEffect(() => { if (busy) close(); }, [busy]);
-  async function requeue() { setBusy(true); try { onState(await window.codepilot.setPMTaskStatus(task.id, "ready", "Requeued manually from the task board.")); close(); } finally { setBusy(false); } }
+  async function requeue() { setBusy(true); try { onState(await window.codepilot.setPMTaskStatus(projectId, task.id, "ready", "Requeued manually from the task board.")); close(); } finally { setBusy(false); } }
   function triage() { close(); onTriage(task); }
-  async function remove() { if (!confirm(`Delete task “${task.title}”?`)) return; setBusy(true); try { onState(await api.deletePMTask(task.id)); close(); } finally { setBusy(false); } }
-  async function run() { setBusy(true); try { onState(await window.codepilot.setPMTaskStatus(task.id, "launched")); const result = await window.codepilot.runAgents({ objective: `${task.title}\n\n${task.description}\n\nAcceptance criteria:\n${task.acceptanceCriteria.map((item) => `- ${item}`).join("\n")}`, providers: [task.recommendedProvider === "claude" ? "claude" : "codex"], retries: 0, timeoutMinutes: 30, validationCommands: [], integrate: true, dryRun: false }); const summary = result.review.findings.length ? result.review.findings.join(" ") : `Agent run completed with review verdict: ${result.review.verdict}.`; onState(result.status === "completed" ? await window.codepilot.setPMTaskStatus(task.id, "done", summary) : await window.codepilot.recordPMTaskFailure(task.id, summary)); close(); } catch (cause) { const reason = cause instanceof Error ? cause.message : String(cause); try { onState(await window.codepilot.recordPMTaskFailure(task.id, `Task did not advance because the run failed: ${reason}`)); } catch {} close(); } finally { setBusy(false); } }
+  async function remove() { if (!confirm(`Delete task “${task.title}”?`)) return; setBusy(true); try { onState(await api.deletePMTask(projectId, task.id)); close(); } finally { setBusy(false); } }
+  async function run() { setBusy(true); try { onState(await window.codepilot.setPMTaskStatus(projectId, task.id, "launched")); const result = await window.codepilot.runAgents({ projectId, objective: `${task.title}\n\n${task.description}\n\nAcceptance criteria:\n${task.acceptanceCriteria.map((item) => `- ${item}`).join("\n")}`, providers: [task.recommendedProvider === "claude" ? "claude" : "codex"], retries: 0, timeoutMinutes: 30, validationCommands: [], integrate: true, dryRun: false }); const summary = result.review.findings.length ? result.review.findings.join(" ") : `Agent run completed with review verdict: ${result.review.verdict}.`; onState(result.status === "completed" ? await window.codepilot.setPMTaskStatus(projectId, task.id, "done", summary) : await window.codepilot.recordPMTaskFailure(projectId, task.id, summary)); close(); } catch (cause) { const reason = cause instanceof Error ? cause.message : String(cause); try { onState(await window.codepilot.recordPMTaskFailure(projectId, task.id, `Task did not advance because the run failed: ${reason}`)); } catch {} close(); } finally { setBusy(false); } }
   return <div onClick={(event) => event.stopPropagation()} style={{ left: Math.min(x, window.innerWidth - 190), top: Math.min(y, window.innerHeight - 130) }} className="fixed z-[70] w-44 overflow-hidden rounded-xl border border-white/10 bg-zinc-900 py-1 shadow-2xl ring-1 ring-black/50">{["ready", "backlog"].includes(task.status) && <button disabled={busy} onClick={() => void run()} className="w-full px-3 py-2 text-left text-xs text-indigo-200 hover:bg-indigo-500/15 disabled:opacity-40">Run task</button>}<button disabled={busy} onClick={triage} className="w-full px-3 py-2 text-left text-xs text-violet-200 hover:bg-violet-500/15 disabled:opacity-40">Triage in PM</button><button disabled={busy} onClick={() => void requeue()} className="w-full px-3 py-2 text-left text-xs text-zinc-200 hover:bg-indigo-500/15 disabled:opacity-40">Requeue task</button><button disabled={busy} onClick={() => void remove()} className="w-full px-3 py-2 text-left text-xs text-rose-300 hover:bg-rose-500/15 disabled:opacity-40">Delete task</button></div>;
 }
diff --git a/desktop/src/types.ts b/desktop/src/types.ts
index 72f088a..e00dd49 100644
--- a/desktop/src/types.ts
+++ b/desktop/src/types.ts
@@ -1,14 +1,16 @@
 export type Project={id:string;name:string;repo:string;createdAt:string}
-export type GlobalSettings={defaultProvider:'codex'|'claude';scaffold:{mode:'guided'|'blank';autoDeploy:boolean;onboardingPrompt:string}}
+export type ProjectOnboardingInput={source:'local';repo:string;name?:string}|{source:'remote';url:string;name?:string;directoryName?:string}
+export type GlobalSettings={defaultProvider:'codex'|'claude';scaffold:{mode:'guided'|'blank';autoDeploy:boolean;onboardingPrompt:string};github:{allowWrites:boolean}}
+export type GitHubStatus={installed:boolean;authenticated:boolean;host:'github.com';account?:string;gitProtocol?:'https'|'ssh';scopes:string[];error?:string}
 export type DesktopState={projects:Project[];activeProjectId:string;projectsDirectory:string;globalSettings:GlobalSettings;runs:Array<{id:string;objective:string;status:string;createdAt:string}>}
 export type KnowledgeEntry={id:string;title:string;content:string;tags:string[];published:boolean;createdAt:string;updatedAt:string}
 export type ChatMessage={role:'user'|'assistant';content:string;timestamp:string;operations?:number}
 export type KnowledgeState={entries:KnowledgeEntry[];messages:ChatMessage[]}
 export type ProjectBrief={path:string;content:string;exists:boolean}
-export type AgentRunInput={objective:string;providers:Array<'codex'|'claude'>;retries:number;timeoutMinutes:number;validationCommands:string[];integrate:boolean;createPullRequest?:boolean;dryRun:boolean}
-export type AgentBatchRunInput={objective:string;items:Array<{id:string;objective:string;provider:'codex'|'claude'}>;retries:number;timeoutMinutes:number;validationCommands:string[];integrate:boolean;createPullRequest?:boolean;dryRun:boolean}
+export type AgentRunInput={projectId:string;objective:string;providers:Array<'codex'|'claude'>;retries:number;timeoutMinutes:number;validationCommands:string[];integrate:boolean;createPullRequest?:boolean;dryRun:boolean}
+export type AgentBatchRunInput={projectId:string;objective:string;items:Array<{id:string;objective:string;provider:'codex'|'claude'}>;retries:number;timeoutMinutes:number;validationCommands:string[];integrate:boolean;createPullRequest?:boolean;dryRun:boolean}
 export type AgentRunResult={runId:string;status:string;integrationBranch?:string;pullRequestUrl?:string;review:{verdict:string;findings:string[]}}
-export type ActiveAgent={taskId:string;runId:string;provider:'codex'|'claude';status:string;objective:string;updatedAt:string;pendingGuidance:number;events:Array<{timestamp:string;stream:string;payload:unknown}>}
+export type ActiveAgent={projectId:string;taskId:string;runId:string;provider:'codex'|'claude';status:string;objective:string;updatedAt:string;pendingGuidance:number;events:Array<{timestamp:string;stream:string;payload:unknown}>}
 export type PMTaskStatus='backlog'|'blocked'|'ready'|'launched'|'done'|'committed'
 export type PMTask={id:string;title:string;description:string;acceptanceCriteria:string[];priority:'low'|'medium'|'high';status:PMTaskStatus;queueId:string;queueTitle:string;dependencies:string[];summary?:string;lastRunStatus?:string;failures?:Array<{timestamp:string;summary:string}>;recommendedProvider?:'codex'|'claude'|'either';createdAt:string;updatedAt:string}
 export type PMState={tasks:PMTask[];messages:ChatMessage[];requiresUserInput?:boolean;continueAutonomously?:boolean}
@@ -18,5 +20,5 @@ export type AppConfig={command:string;workingDirectory:string;url:string}
 export type AppStatus={configured:boolean;running:boolean;pid?:number;startedAt?:string;config:AppConfig;logs:string[]}
 export type RunDetail={id:string;objective:string;status:string;createdAt:string;updatedAt:string;summary?:{integrationBranch?:string;pullRequestBody?:string;pullRequestUrl?:string;review?:{verdict:string;findings:string[]};collisions?:Array<{path:string;taskIds:string[]}>;validations?:Array<{command:string;exitCode:number;durationMs:number;stdout:string;stderr:string}>};workers:Array<{taskId:string;provider:string;status:string;report?:{status:string;summary:string;claimedTests:string[];concerns:string[];followUps:string[]};verification?:{changedPaths:string[];dirtyPaths:string[];resultCommit?:string;processExitCode:number};warnings:string[]}>}
 export type NewPMTask={title:string;description:string;acceptanceCriteria?:string[];priority?:PMTask['priority'];recommendedProvider?:PMTask['recommendedProvider']}
-export type CodePilotAPI={getState():Promise<DesktopState>;getGlobalSettings():Promise<GlobalSettings>;saveGlobalSettings(settings:GlobalSettings):Promise<GlobalSettings>;getProjectBrief():Promise<ProjectBrief>;saveProjectBrief(content:string):Promise<ProjectBrief>;getProjectActivity():Promise<Record<string,number>>;selectDirectory(defaultPath?:string):Promise<string|undefined>;addProject(input:{name:string;repo?:string}):Promise<DesktopState>;switchProject(id:string):Promise<DesktopState>;openProjectDirectory():Promise<void>;getAppStatus():Promise<AppStatus>;saveAppConfig(config:AppConfig):Promise<AppStatus>;startProjectApp():Promise<AppStatus>;stopProjectApp():Promise<AppStatus>;openProjectApp():Promise<void>;getKnowledge():Promise<KnowledgeState>;chatKnowledge(message:string):Promise<KnowledgeState>;runAgents(input:AgentRunInput):Promise<AgentRunResult>;runAgentBatch(input:AgentBatchRunInput):Promise<AgentRunResult>;getActiveAgents():Promise<ActiveAgent[]>;guideAgent(taskId:string,message:string):Promise<ActiveAgent[]>;interruptAgent(taskId:string):Promise<{feedback:string;agents:ActiveAgent[]}>;getRunDetail(id:string):Promise<RunDetail>;getPM():Promise<PMState>;getPMTaskDetail(id:string):Promise<PMTaskDetail>;chatPM(message:string):Promise<PMState>;clearPMChat():Promise<PMState>;setPMTaskStatus(id:string,status:PMTask['status'],summary?:string):Promise<PMState>;recordPMTaskFailure(id:string,summary:string):Promise<PMState>;onPMUserInputRequired(listener:()=>void):()=>void;createPMTask(input:NewPMTask):Promise<PMState>;commitPMTaskBin(taskIds:string[]):Promise<TaskBin>}
+export type CodePilotAPI={getState():Promise<DesktopState>;getGlobalSettings():Promise<GlobalSettings>;saveGlobalSettings(settings:GlobalSettings):Promise<GlobalSettings>;getGitHubStatus():Promise<GitHubStatus>;loginGitHub():Promise<GitHubStatus>;getProjectBrief(projectId:string):Promise<ProjectBrief>;saveProjectBrief(projectId:string,content:string):Promise<ProjectBrief>;getProjectActivity():Promise<Record<string,number>>;selectDirectory(defaultPath?:string):Promise<string|undefined>;addProject(input:{name:string}):Promise<DesktopState>;onboardProject(input:ProjectOnboardingInput):Promise<DesktopState>;removeProject(projectId:string):Promise<DesktopState>;switchProject(id:string):Promise<DesktopState>;openProjectDirectory(projectId:string):Promise<void>;getAppStatus(projectId:string):Promise<AppStatus>;saveAppConfig(projectId:string,config:AppConfig):Promise<AppStatus>;startProjectApp(projectId:string):Promise<AppStatus>;stopProjectApp(projectId:string):Promise<AppStatus>;clearProjectPort(projectId:string):Promise<AppStatus>;openProjectApp(projectId:string):Promise<void>;getKnowledge(projectId:string):Promise<KnowledgeState>;chatKnowledge(projectId:string,message:string):Promise<KnowledgeState>;runAgents(input:AgentRunInput):Promise<AgentRunResult>;runAgentBatch(input:AgentBatchRunInput):Promise<AgentRunResult>;getActiveAgents(projectId:string):Promise<ActiveAgent[]>;guideAgent(projectId:string,taskId:string,message:string):Promise<ActiveAgent[]>;interruptAgent(projectId:string,taskId:string):Promise<{feedback:string;agents:ActiveAgent[]}>;getRunDetail(projectId:string,id:string):Promise<RunDetail>;getPM(projectId:string):Promise<PMState>;getPMTaskDetail(projectId:string,id:string):Promise<PMTaskDetail>;chatPM(projectId:string,message:string):Promise<PMState>;clearPMChat(projectId:string):Promise<PMState>;setPMTaskStatus(projectId:string,id:string,status:PMTask['status'],summary?:string):Promise<PMState>;recordPMTaskFailure(projectId:string,id:string,summary:string):Promise<PMState>;onPMUserInputRequired(listener:(projectId:string)=>void):()=>void;createPMTask(projectId:string,input:NewPMTask):Promise<PMState>;commitPMTaskBin(projectId:string,taskIds:string[]):Promise<TaskBin>;deletePMTask(projectId:string,id:string):Promise<PMState>}
 declare global{interface Window{codepilot:CodePilotAPI}}
diff --git a/docs/architecture.md b/docs/architecture.md
index 00de033..b449e8e 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -19,6 +19,14 @@ The manager owns authoritative orchestration state: scheduling, attempts, timeou
 
 Runs targeting the same repository are serialized in one manager process. Tasks within a run may execute concurrently when their dependency graph permits it.
 
+### Desktop project controllers
+
+Every project-scoped desktop request carries an explicit project ID across the typed preload bridge. The main process resolves that ID before reading PM state, changing tasks, launching agents, inspecting runs, curating knowledge, or controlling the project runtime. Switching the visible project therefore cannot retarget an in-flight operation.
+
+Project Manager threads are keyed by project ID and persisted inside their repository. A keyed queue serializes turns for one PM so multiple windows or queued messages cannot race its conversation state; different project keys may run concurrently through the shared Codex app-server. The Projects screen reports PM and worker activity across the registry.
+
+Repository onboarding either canonicalizes an existing local Git root or clones an explicit HTTPS/SSH remote into the configured projects directory. Existing repositories receive `.codepilot/` in their local Git exclude file, avoiding an onboarding-only source change. Git authentication remains delegated to the operator's credential helper or SSH agent. A post-registration launch step reads any existing or inferred App Core configuration and asks the operator to review the start command, repository-relative working directory, and local URL. Saving this step persists `.codepilot/app-config.json` but deliberately does not start a process; guided Project Manager onboarding begins only after the operator saves or skips it. Removing a project only unregisters it from the desktop workspace; the repository and `.codepilot` state are preserved, and removal is blocked while that project's PM, agents, or app process is active.
+
 ### Provider adapters
 
 Adapters translate the stable `AgentTask` contract into official CLI arguments. Authentication remains owned by each provider CLI. Parent conversation identifiers and common unrelated credential variables are removed from child environments; the selected provider's authentication variable may be forwarded.
@@ -39,7 +47,9 @@ Leases are cooperative rather than operating-system locks. Independent filesyste
 
 ### Integration and delivery
 
-Task commits are retained under durable Git refs. The manager normalizes each worker workspace into one provenance-rich commit, assembles eligible commits on a dedicated integration branch, runs validation, and builds the PR description directly from that evidence. It does not stash, reset, fast-forward, or merge the user's primary branch. Push and GitHub PR creation occur only when explicitly requested.
+Task commits are retained under durable Git refs. The manager normalizes each worker workspace into one provenance-rich commit, assembles eligible commits on a dedicated integration branch, runs validation, and builds the PR description directly from that evidence. It does not stash, reset, fast-forward, or merge the user's primary branch. Push and GitHub PR creation occur only when explicitly requested and the operator has enabled GitHub writes in Settings.
+
+GitHub authentication is owned by the official `gh` CLI. The desktop launches its browser/device flow and reads only redacted `gh auth status` output; it never receives a token. The main process checks both authenticated status and the global write policy immediately before any requested publication.
 
 ### Persistence
 
@@ -54,3 +64,4 @@ One SQLite database owns runs, tasks, attempts, bounded events, worker results,
 - Review is deterministic policy, not an independent semantic reviewer.
 - The Docker worker protocol is not yet controlled by the manager.
 - GitHub delivery currently depends directly on the authenticated `gh` CLI; hosting adapters, idempotent retries, and crash-safe resume are not yet implemented.
+- Multiple repositories can operate independently, but one coordinated initiative spanning their task graphs and delivery policies is not yet implemented.
diff --git a/docs/roadmap.md b/docs/roadmap.md
index 6039de5..9e57e4d 100644
--- a/docs/roadmap.md
+++ b/docs/roadmap.md
@@ -7,7 +7,7 @@
 - durable SQLite run evidence and bounded logs
 - cooperative file leases
 - integration branches, validation, review verdicts, Git-native handoffs, and opt-in GitHub pull requests
-- Electron project and task control plane
+- Electron project and task control plane with Git repository onboarding and concurrent project-scoped PMs
 - CI, security policy, and public documentation
 
 ## v0.2 — reviewable planning
diff --git a/docs/threat-model.md b/docs/threat-model.md
index 4b1a223..5a08d66 100644
--- a/docs/threat-model.md
+++ b/docs/threat-model.md
@@ -16,7 +16,7 @@ codePilot v0.1 is local developer tooling for repositories, objectives, provider
 - The manager is trusted and owns commits, integration, persistence, and policy.
 - Provider processes are semi-trusted: they may edit and execute inside a temporary checkout, but their reports are advisory.
 - Repository code and configured validation commands are trusted by the operator.
-- Remote Git hosting is contacted only when the operator explicitly requests pull-request creation for a run.
+- Remote Git hosting is contacted only when the operator explicitly clones a repository or requests pull-request creation for a run.
 
 ## Existing mitigations
 
@@ -30,6 +30,10 @@ codePilot v0.1 is local developer tooling for repositories, objectives, provider
 - bounded process lines, event counts, database event history, validation output, artifact count, and artifact size
 - timeouts on providers and validation commands
 - Electron context isolation and a typed preload bridge
+- explicit project IDs on desktop PM, task, agent, knowledge, run, and runtime operations
+- HTTPS/SSH-only remote onboarding without embedded URL credentials; authentication stays with Git's credential helper or SSH agent
+- GitHub browser authentication is delegated to the official `gh` CLI; tokens never cross the Electron preload bridge or enter codePilot state
+- remote writes require a persisted global opt-in plus an explicit per-run pull-request request
 
 ## Known risks
 
@@ -39,7 +43,8 @@ codePilot v0.1 is local developer tooling for repositories, objectives, provider
 - Cooperative file leases do not prevent a provider from ignoring the protocol.
 - SQLite state is local and is not tamper-evident.
 - The experimental Docker files do not yet represent an enforced manager-owned sandbox.
-- Explicit GitHub publication uses the current user's authenticated `gh` and Git credentials to push the generated branch and open a pull request.
+- Explicit GitHub publication uses the current user's authenticated `gh` and Git credentials to push the generated branch and open a pull request. Repository permissions are enforced by GitHub, not codePilot.
+- Explicit repository cloning runs Git with the current user's network access and credentials; the cloned repository remains untrusted until the operator reviews it.
 
 ## Operator guidance
 
diff --git a/src/github-auth.ts b/src/github-auth.ts
new file mode 100644
index 0000000..5dfd841
--- /dev/null
+++ b/src/github-auth.ts
@@ -0,0 +1,35 @@
+export type GitHubStatus = {
+  installed: boolean;
+  authenticated: boolean;
+  host: "github.com";
+  account?: string;
+  gitProtocol?: "https" | "ssh";
+  scopes: string[];
+  error?: string;
+};
+
+export function parseGitHubAuthStatus(output: string): Omit<GitHubStatus, "installed"> {
+  const account = output.match(/Logged in to github\.com account\s+([^\s(]+)/i)?.[1];
+  const protocol = output.match(/Git operations protocol:\s*(https|ssh)/i)?.[1]?.toLowerCase() as "https" | "ssh" | undefined;
+  const scopeLine = output.match(/Token scopes:\s*(.+)$/im)?.[1] ?? "";
+  const quotedScopes = [...scopeLine.matchAll(/['"]([^'"]+)['"]/g)].map(match => match[1]!);
+  const scopes = (quotedScopes.length ? quotedScopes : scopeLine.split(","))
+    .map(scope => scope.trim().replace(/^['"]|['"]$/g, ""))
+    .filter(Boolean)
+    .sort();
+  return {
+    authenticated: Boolean(account),
+    host: "github.com",
+    ...(account ? { account } : {}),
+    ...(protocol ? { gitProtocol: protocol } : {}),
+    scopes,
+    ...(!account ? { error: "GitHub CLI is not authenticated" } : {}),
+  };
+}
+
+export function assertGitHubPublicationAllowed(allowWrites: boolean, status: GitHubStatus): void {
+  if (!allowWrites)
+    throw new Error("GitHub publishing is disabled. Enable write operations in Settings before creating a pull request.");
+  if (!status.authenticated)
+    throw new Error("Connect GitHub in Settings before creating a pull request.");
+}
diff --git a/src/keyed-queue.ts b/src/keyed-queue.ts
new file mode 100644
index 0000000..cd792da
--- /dev/null
+++ b/src/keyed-queue.ts
@@ -0,0 +1,12 @@
+export class KeyedSerialQueue {
+  readonly #tails = new Map<string, Promise<unknown>>();
+
+  run<T>(key: string, operation: () => Promise<T>): Promise<T> {
+    const previous = this.#tails.get(key) ?? Promise.resolve();
+    const current = previous.catch(() => undefined).then(operation);
+    this.#tails.set(key, current);
+    return current.finally(() => {
+      if (this.#tails.get(key) === current) this.#tails.delete(key);
+    });
+  }
+}
diff --git a/src/project-onboarding.ts b/src/project-onboarding.ts
new file mode 100644
index 0000000..93a24c7
--- /dev/null
+++ b/src/project-onboarding.ts
@@ -0,0 +1,80 @@
+import { execFile, execFileSync } from "node:child_process";
+import { existsSync, mkdirSync, realpathSync, rmSync } from "node:fs";
+import { basename, relative, resolve } from "node:path";
+
+const remoteUrl = /^(?:https:\/\/[^\s]+|ssh:\/\/[^\s]+|git@[\w.-]+:[^\s]+)$/i;
+
+export function canonicalGitRepository(path: string): string {
+  const requested = resolve(path);
+  const root = execFileSync(
+    "git",
+    ["-C", requested, "rev-parse", "--show-toplevel"],
+    { encoding: "utf8", windowsHide: true },
+  ).trim();
+  return realpathSync(root);
+}
+
+export function repositoryNameFromRemote(url: string): string {
+  assertRemoteGitUrl(url);
+  const clean = url.trim().replace(/[?#].*$/, "").replace(/[\\/]+$/, "");
+  const candidate = clean.split(/[\\/:]/).pop()?.replace(/\.git$/i, "") ?? "";
+  const name = candidate.replace(/[^a-zA-Z0-9._-]+/g, "-").replace(/^-+|-+$/g, "");
+  if (!name) throw new Error("Could not derive a project name from the Git URL");
+  return name;
+}
+
+export async function cloneGitRepository(input: {
+  url: string;
+  projectsDirectory: string;
+  directoryName?: string;
+}): Promise<string> {
+  const url = input.url.trim();
+  assertRemoteGitUrl(url);
+  const root = resolve(input.projectsDirectory);
+  mkdirSync(root, { recursive: true });
+  const requestedName = input.directoryName?.trim() || repositoryNameFromRemote(url);
+  const safeName = requestedName
+    .replace(/[^a-zA-Z0-9._-]+/g, "-")
+    .replace(/^-+|-+$/g, "");
+  if (!safeName || safeName === "." || safeName === "..")
+    throw new Error("A valid destination directory name is required");
+  const destination = resolve(root, safeName);
+  const rel = relative(root, destination);
+  if (!rel || rel.startsWith("..") || resolve(root, rel) !== destination)
+    throw new Error("The clone destination must be inside the projects directory");
+  if (existsSync(destination))
+    throw new Error(`The clone destination already exists: ${destination}`);
+
+  try {
+    await new Promise<void>((done, fail) => {
+      execFile("git", ["clone", "--", url, destination], {
+        encoding: "utf8",
+        windowsHide: true,
+        timeout: 10 * 60_000,
+        maxBuffer: 4 * 1024 * 1024,
+      }, (error, _stdout, stderr) => error
+        ? fail(new Error(stderr.trim() || error.message, { cause: error }))
+        : done());
+    });
+    return canonicalGitRepository(destination);
+  } catch (cause) {
+    if (existsSync(destination)) rmSync(destination, { recursive: true, force: true });
+    const detail = cause instanceof Error ? cause.message : String(cause);
+    throw new Error(`Could not clone the Git repository: ${detail}`, { cause });
+  }
+}
+
+export function suggestedProjectName(path: string): string {
+  return basename(resolve(path));
+}
+
+function assertRemoteGitUrl(url: string): void {
+  const value = url.trim();
+  if (!remoteUrl.test(value) || value.includes("\0"))
+    throw new Error("Use an HTTPS or SSH Git repository URL");
+  if (value.startsWith("https://") || value.startsWith("ssh://")) {
+    const parsed = new URL(value);
+    if (parsed.password || (parsed.protocol === "https:" && parsed.username))
+      throw new Error("Do not embed credentials in the Git URL; use your configured Git credential helper");
+  }
+}
diff --git a/src/project-registry.ts b/src/project-registry.ts
new file mode 100644
index 0000000..06a1988
--- /dev/null
+++ b/src/project-registry.ts
@@ -0,0 +1,16 @@
+export function removeProjectRegistration<T extends { id: string }>(
+  projects: T[],
+  activeProjectId: string,
+  projectId: string,
+): { projects: T[]; activeProjectId: string } {
+  if (!projects.some((project) => project.id === projectId))
+    throw new Error("Project not found. Refresh the workspace and try again.");
+  if (projects.length === 1)
+    throw new Error("CodePilot needs at least one registered project.");
+  const remaining = projects.filter((project) => project.id !== projectId);
+  return {
+    projects: remaining,
+    activeProjectId:
+      activeProjectId === projectId ? remaining[0]!.id : activeProjectId,
+  };
+}
diff --git a/test/github-auth.test.ts b/test/github-auth.test.ts
new file mode 100644
index 0000000..53620c2
--- /dev/null
+++ b/test/github-auth.test.ts
@@ -0,0 +1,36 @@
+import assert from "node:assert/strict";
+import test from "node:test";
+import { assertGitHubPublicationAllowed, parseGitHubAuthStatus } from "../src/github-auth.js";
+
+test("parses a connected GitHub CLI account without retaining the token", () => {
+  const result = parseGitHubAuthStatus(`github.com
+  ✓ Logged in to github.com account hhuumm (keyring)
+  - Active account: true
+  - Git operations protocol: https
+  - Token: gho_secret
+  - Token scopes: 'repo', 'read:org', 'workflow'`);
+  assert.deepEqual(result, {
+    authenticated: true,
+    host: "github.com",
+    account: "hhuumm",
+    gitProtocol: "https",
+    scopes: ["read:org", "repo", "workflow"],
+  });
+  assert.equal(JSON.stringify(result).includes("gho_secret"), false);
+});
+
+test("reports a disconnected GitHub CLI", () => {
+  assert.deepEqual(parseGitHubAuthStatus("You are not logged into any GitHub hosts."), {
+    authenticated: false,
+    host: "github.com",
+    scopes: [],
+    error: "GitHub CLI is not authenticated",
+  });
+});
+
+test("requires both authentication and an explicit write opt-in", () => {
+  const connected = { installed: true, authenticated: true, host: "github.com" as const, account: "hhuumm", scopes: ["repo"] };
+  assert.doesNotThrow(() => assertGitHubPublicationAllowed(true, connected));
+  assert.throws(() => assertGitHubPublicationAllowed(false, connected), /disabled/i);
+  assert.throws(() => assertGitHubPublicationAllowed(true, { ...connected, authenticated: false }), /Connect GitHub/i);
+});
diff --git a/test/keyed-queue.test.ts b/test/keyed-queue.test.ts
new file mode 100644
index 0000000..9f7dc19
--- /dev/null
+++ b/test/keyed-queue.test.ts
@@ -0,0 +1,34 @@
+import assert from "node:assert/strict";
+import test from "node:test";
+import { KeyedSerialQueue } from "../src/keyed-queue.js";
+
+test("serializes work for one project while allowing different projects to overlap", async () => {
+  const queue = new KeyedSerialQueue();
+  const events: string[] = [];
+  let releaseFirst!: () => void;
+  const firstGate = new Promise<void>((resolve) => (releaseFirst = resolve));
+
+  const first = queue.run("project-a", async () => {
+    events.push("a1:start");
+    await firstGate;
+    events.push("a1:end");
+  });
+  const second = queue.run("project-a", async () => {
+    events.push("a2:start");
+  });
+  const other = queue.run("project-b", async () => {
+    events.push("b:start");
+  });
+
+  await other;
+  assert.deepEqual(events, ["a1:start", "b:start"]);
+  releaseFirst();
+  await Promise.all([first, second]);
+  assert.deepEqual(events, ["a1:start", "b:start", "a1:end", "a2:start"]);
+});
+
+test("continues a project queue after a failed operation", async () => {
+  const queue = new KeyedSerialQueue();
+  await assert.rejects(queue.run("project", async () => { throw new Error("failed"); }));
+  assert.equal(await queue.run("project", async () => "recovered"), "recovered");
+});
diff --git a/test/project-onboarding.test.ts b/test/project-onboarding.test.ts
new file mode 100644
index 0000000..f859a8a
--- /dev/null
+++ b/test/project-onboarding.test.ts
@@ -0,0 +1,32 @@
+import assert from "node:assert/strict";
+import { execFileSync } from "node:child_process";
+import { mkdtempSync, mkdirSync, rmSync, statSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import test from "node:test";
+import {
+  canonicalGitRepository,
+  repositoryNameFromRemote,
+} from "../src/project-onboarding.js";
+
+test("canonicalizes an existing Git checkout from a nested directory", () => {
+  const root = mkdtempSync(join(tmpdir(), "codepilot-onboard-"));
+  try {
+    execFileSync("git", ["init", root]);
+    mkdirSync(join(root, "nested"));
+    const expected = statSync(root);
+    const actual = statSync(canonicalGitRepository(join(root, "nested")));
+    assert.equal(actual.dev, expected.dev);
+    assert.equal(actual.ino, expected.ino);
+  } finally {
+    rmSync(root, { recursive: true, force: true });
+  }
+});
+
+test("derives safe project names from HTTPS and SSH remotes", () => {
+  assert.equal(repositoryNameFromRemote("https://github.com/hhuumm/codePilot.git"), "codePilot");
+  assert.equal(repositoryNameFromRemote("git@github.com:hhuumm/codePilot.git"), "codePilot");
+  assert.throws(() => repositoryNameFromRemote("file:///private/repo"), /HTTPS or SSH/);
+  assert.throws(() => repositoryNameFromRemote("https://token@github.com/hhuumm/codePilot.git"), /credential helper/);
+  assert.throws(() => repositoryNameFromRemote("ssh://git:secret@github.com/hhuumm/codePilot.git"), /credential helper/);
+});
diff --git a/test/project-registry.test.ts b/test/project-registry.test.ts
new file mode 100644
index 0000000..deae1a1
--- /dev/null
+++ b/test/project-registry.test.ts
@@ -0,0 +1,26 @@
+import assert from "node:assert/strict";
+import test from "node:test";
+import { removeProjectRegistration } from "../src/project-registry.js";
+
+test("removes a project registration and selects a replacement when needed", () => {
+  const projects = [{ id: "a" }, { id: "b" }, { id: "c" }];
+  assert.deepEqual(removeProjectRegistration(projects, "b", "b"), {
+    projects: [{ id: "a" }, { id: "c" }],
+    activeProjectId: "a",
+  });
+  assert.deepEqual(removeProjectRegistration(projects, "a", "c"), {
+    projects: [{ id: "a" }, { id: "b" }],
+    activeProjectId: "a",
+  });
+});
+
+test("refuses to remove an unknown or final project", () => {
+  assert.throws(
+    () => removeProjectRegistration([{ id: "a" }], "a", "missing"),
+    /Project not found/,
+  );
+  assert.throws(
+    () => removeProjectRegistration([{ id: "a" }], "a", "a"),
+    /at least one/,
+  );
+});