Merge public-gh/master into review/pr-162

2026-03-16 08:47:05 -05:00
parent fb684f25e9 7034ea5b01
commit 1a5eaba622
536 changed files with 103660 additions and 9971 deletions
--- a/cli/CHANGELOG.md
+++ b/cli/CHANGELOG.md
@@ -1,5 +1,44 @@
 # paperclipai

+## 0.3.1
+
+### Patch Changes
+
+- Stable release preparation for 0.3.1
+- Updated dependencies
+  - @paperclipai/adapter-utils@0.3.1
+  - @paperclipai/adapter-claude-local@0.3.1
+  - @paperclipai/adapter-codex-local@0.3.1
+  - @paperclipai/adapter-cursor-local@0.3.1
+  - @paperclipai/adapter-gemini-local@0.3.1
+  - @paperclipai/adapter-openclaw-gateway@0.3.1
+  - @paperclipai/adapter-opencode-local@0.3.1
+  - @paperclipai/adapter-pi-local@0.3.1
+  - @paperclipai/db@0.3.1
+  - @paperclipai/shared@0.3.1
+  - @paperclipai/server@0.3.1
+
+## 0.3.0
+
+### Minor Changes
+
+- Stable release preparation for 0.3.0
+
+### Patch Changes
+
+- Updated dependencies [6077ae6]
+- Updated dependencies
+  - @paperclipai/shared@0.3.0
+  - @paperclipai/adapter-utils@0.3.0
+  - @paperclipai/adapter-claude-local@0.3.0
+  - @paperclipai/adapter-codex-local@0.3.0
+  - @paperclipai/adapter-cursor-local@0.3.0
+  - @paperclipai/adapter-openclaw-gateway@0.3.0
+  - @paperclipai/adapter-opencode-local@0.3.0
+  - @paperclipai/adapter-pi-local@0.3.0
+  - @paperclipai/db@0.3.0
+  - @paperclipai/server@0.3.0
+
 ## 0.2.7

 ### Patch Changes
--- a/cli/esbuild.config.mjs
+++ b/cli/esbuild.config.mjs
@@ -21,7 +21,7 @@ const workspacePaths = [
  "packages/adapter-utils",
  "packages/adapters/claude-local",
  "packages/adapters/codex-local",
-  "packages/adapters/openclaw",
+  "packages/adapters/openclaw-gateway",
 ];

 // Workspace packages that should NOT be bundled — they'll be published
--- a/cli/package.json
+++ b/cli/package.json
@@ -1,6 +1,6 @@
 {
  "name": "paperclipai",
-  "version": "0.2.7",
+  "version": "0.3.1",
  "description": "Paperclip CLI — orchestrate AI agent teams to run a business",
  "type": "module",
  "bin": {
@@ -37,9 +37,10 @@
    "@paperclipai/adapter-claude-local": "workspace:*",
    "@paperclipai/adapter-codex-local": "workspace:*",
    "@paperclipai/adapter-cursor-local": "workspace:*",
+    "@paperclipai/adapter-gemini-local": "workspace:*",
    "@paperclipai/adapter-opencode-local": "workspace:*",
    "@paperclipai/adapter-pi-local": "workspace:*",
-    "@paperclipai/adapter-openclaw": "workspace:*",
+    "@paperclipai/adapter-openclaw-gateway": "workspace:*",
    "@paperclipai/adapter-utils": "workspace:*",
    "@paperclipai/db": "workspace:*",
    "@paperclipai/server": "workspace:*",
@@ -47,6 +48,7 @@
    "drizzle-orm": "0.38.4",
    "dotenv": "^17.0.1",
    "commander": "^13.1.0",
+    "embedded-postgres": "^18.1.0-beta.16",
    "picocolors": "^1.1.1"
  },
  "devDependencies": {
--- a/cli/src/tests/agent-jwt-env.test.ts
+++ b/cli/src/tests/agent-jwt-env.test.ts
@@ -4,7 +4,9 @@ import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import {
  ensureAgentJwtSecret,
+  mergePaperclipEnvEntries,
  readAgentJwtSecretFromEnv,
+  readPaperclipEnvEntries,
  resolveAgentJwtEnvFile,
 } from "../config/env.js";
 import { agentJwtSecretCheck } from "../checks/agent-jwt-secret-check.js";
@@ -58,4 +60,20 @@ describe("agent jwt env helpers", () => {
    const result = agentJwtSecretCheck(configPath);
    expect(result.status).toBe("pass");
  });
+
+  it("quotes hash-prefixed env values so dotenv round-trips them", () => {
+    const configPath = tempConfigPath();
+    const envPath = resolveAgentJwtEnvFile(configPath);
+
+    mergePaperclipEnvEntries(
+      {
+        PAPERCLIP_WORKTREE_COLOR: "#439edb",
+      },
+      envPath,
+    );
+
+    const contents = fs.readFileSync(envPath, "utf-8");
+    expect(contents).toContain('PAPERCLIP_WORKTREE_COLOR="#439edb"');
+    expect(readPaperclipEnvEntries(envPath).PAPERCLIP_WORKTREE_COLOR).toBe("#439edb");
+  });
 });
--- a/cli/src/tests/allowed-hostname.test.ts
+++ b/cli/src/tests/allowed-hostname.test.ts
@@ -42,6 +42,7 @@ function writeBaseConfig(configPath: string) {
    },
    auth: {
      baseUrlMode: "auto",
+      disableSignUp: false,
    },
    storage: {
      provider: "local_disk",
--- a/cli/src/tests/doctor.test.ts
+++ b/cli/src/tests/doctor.test.ts
@@ -0,0 +1,99 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { doctor } from "../commands/doctor.js";
+import { writeConfig } from "../config/store.js";
+import type { PaperclipConfig } from "../config/schema.js";
+
+const ORIGINAL_ENV = { ...process.env };
+
+function createTempConfig(): string {
+  const root = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-doctor-"));
+  const configPath = path.join(root, ".paperclip", "config.json");
+  const runtimeRoot = path.join(root, "runtime");
+
+  const config: PaperclipConfig = {
+    $meta: {
+      version: 1,
+      updatedAt: "2026-03-10T00:00:00.000Z",
+      source: "configure",
+    },
+    database: {
+      mode: "embedded-postgres",
+      embeddedPostgresDataDir: path.join(runtimeRoot, "db"),
+      embeddedPostgresPort: 55432,
+      backup: {
+        enabled: true,
+        intervalMinutes: 60,
+        retentionDays: 30,
+        dir: path.join(runtimeRoot, "backups"),
+      },
+    },
+    logging: {
+      mode: "file",
+      logDir: path.join(runtimeRoot, "logs"),
+    },
+    server: {
+      deploymentMode: "local_trusted",
+      exposure: "private",
+      host: "127.0.0.1",
+      port: 3199,
+      allowedHostnames: [],
+      serveUi: true,
+    },
+    auth: {
+      baseUrlMode: "auto",
+      disableSignUp: false,
+    },
+    storage: {
+      provider: "local_disk",
+      localDisk: {
+        baseDir: path.join(runtimeRoot, "storage"),
+      },
+      s3: {
+        bucket: "paperclip",
+        region: "us-east-1",
+        prefix: "",
+        forcePathStyle: false,
+      },
+    },
+    secrets: {
+      provider: "local_encrypted",
+      strictMode: false,
+      localEncrypted: {
+        keyFilePath: path.join(runtimeRoot, "secrets", "master.key"),
+      },
+    },
+  };
+
+  writeConfig(config, configPath);
+  return configPath;
+}
+
+describe("doctor", () => {
+  beforeEach(() => {
+    process.env = { ...ORIGINAL_ENV };
+    delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
+    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
+    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+  });
+
+  afterEach(() => {
+    process.env = { ...ORIGINAL_ENV };
+  });
+
+  it("re-runs repairable checks so repaired failures do not remain blocking", async () => {
+    const configPath = createTempConfig();
+
+    const summary = await doctor({
+      config: configPath,
+      repair: true,
+      yes: true,
+    });
+
+    expect(summary.failed).toBe(0);
+    expect(summary.warned).toBe(0);
+    expect(process.env.PAPERCLIP_AGENT_JWT_SECRET).toBeTruthy();
+  });
+});
--- a/cli/src/tests/worktree.test.ts
+++ b/cli/src/tests/worktree.test.ts
@@ -0,0 +1,472 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { execFileSync } from "node:child_process";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import {
+  copyGitHooksToWorktreeGitDir,
+  copySeededSecretsKey,
+  rebindWorkspaceCwd,
+  resolveSourceConfigPath,
+  resolveGitWorktreeAddArgs,
+  resolveWorktreeMakeTargetPath,
+  worktreeInitCommand,
+  worktreeMakeCommand,
+} from "../commands/worktree.js";
+import {
+  buildWorktreeConfig,
+  buildWorktreeEnvEntries,
+  formatShellExports,
+  generateWorktreeColor,
+  resolveWorktreeSeedPlan,
+  resolveWorktreeLocalPaths,
+  rewriteLocalUrlPort,
+  sanitizeWorktreeInstanceId,
+} from "../commands/worktree-lib.js";
+import type { PaperclipConfig } from "../config/schema.js";
+
+const ORIGINAL_CWD = process.cwd();
+const ORIGINAL_ENV = { ...process.env };
+
+afterEach(() => {
+  process.chdir(ORIGINAL_CWD);
+  for (const key of Object.keys(process.env)) {
+    if (!(key in ORIGINAL_ENV)) delete process.env[key];
+  }
+  for (const [key, value] of Object.entries(ORIGINAL_ENV)) {
+    if (value === undefined) delete process.env[key];
+    else process.env[key] = value;
+  }
+});
+
+function buildSourceConfig(): PaperclipConfig {
+  return {
+    $meta: {
+      version: 1,
+      updatedAt: "2026-03-09T00:00:00.000Z",
+      source: "configure",
+    },
+    database: {
+      mode: "embedded-postgres",
+      embeddedPostgresDataDir: "/tmp/main/db",
+      embeddedPostgresPort: 54329,
+      backup: {
+        enabled: true,
+        intervalMinutes: 60,
+        retentionDays: 30,
+        dir: "/tmp/main/backups",
+      },
+    },
+    logging: {
+      mode: "file",
+      logDir: "/tmp/main/logs",
+    },
+    server: {
+      deploymentMode: "authenticated",
+      exposure: "private",
+      host: "127.0.0.1",
+      port: 3100,
+      allowedHostnames: ["localhost"],
+      serveUi: true,
+    },
+    auth: {
+      baseUrlMode: "explicit",
+      publicBaseUrl: "http://127.0.0.1:3100",
+      disableSignUp: false,
+    },
+    storage: {
+      provider: "local_disk",
+      localDisk: {
+        baseDir: "/tmp/main/storage",
+      },
+      s3: {
+        bucket: "paperclip",
+        region: "us-east-1",
+        prefix: "",
+        forcePathStyle: false,
+      },
+    },
+    secrets: {
+      provider: "local_encrypted",
+      strictMode: false,
+      localEncrypted: {
+        keyFilePath: "/tmp/main/secrets/master.key",
+      },
+    },
+  };
+}
+
+describe("worktree helpers", () => {
+  it("sanitizes instance ids", () => {
+    expect(sanitizeWorktreeInstanceId("feature/worktree-support")).toBe("feature-worktree-support");
+    expect(sanitizeWorktreeInstanceId("  ")).toBe("worktree");
+  });
+
+  it("resolves worktree:make target paths under the user home directory", () => {
+    expect(resolveWorktreeMakeTargetPath("paperclip-pr-432")).toBe(
+      path.resolve(os.homedir(), "paperclip-pr-432"),
+    );
+  });
+
+  it("rejects worktree:make names that are not safe directory/branch names", () => {
+    expect(() => resolveWorktreeMakeTargetPath("paperclip/pr-432")).toThrow(
+      "Worktree name must contain only letters, numbers, dots, underscores, or dashes.",
+    );
+  });
+
+  it("builds git worktree add args for new and existing branches", () => {
+    expect(
+      resolveGitWorktreeAddArgs({
+        branchName: "feature-branch",
+        targetPath: "/tmp/feature-branch",
+        branchExists: false,
+      }),
+    ).toEqual(["worktree", "add", "-b", "feature-branch", "/tmp/feature-branch", "HEAD"]);
+
+    expect(
+      resolveGitWorktreeAddArgs({
+        branchName: "feature-branch",
+        targetPath: "/tmp/feature-branch",
+        branchExists: true,
+      }),
+    ).toEqual(["worktree", "add", "/tmp/feature-branch", "feature-branch"]);
+  });
+
+  it("builds git worktree add args with a start point", () => {
+    expect(
+      resolveGitWorktreeAddArgs({
+        branchName: "my-worktree",
+        targetPath: "/tmp/my-worktree",
+        branchExists: false,
+        startPoint: "public-gh/master",
+      }),
+    ).toEqual(["worktree", "add", "-b", "my-worktree", "/tmp/my-worktree", "public-gh/master"]);
+  });
+
+  it("uses start point even when a local branch with the same name exists", () => {
+    expect(
+      resolveGitWorktreeAddArgs({
+        branchName: "my-worktree",
+        targetPath: "/tmp/my-worktree",
+        branchExists: true,
+        startPoint: "origin/main",
+      }),
+    ).toEqual(["worktree", "add", "-b", "my-worktree", "/tmp/my-worktree", "origin/main"]);
+  });
+
+  it("rewrites loopback auth URLs to the new port only", () => {
+    expect(rewriteLocalUrlPort("http://127.0.0.1:3100", 3110)).toBe("http://127.0.0.1:3110/");
+    expect(rewriteLocalUrlPort("https://paperclip.example", 3110)).toBe("https://paperclip.example");
+  });
+
+  it("builds isolated config and env paths for a worktree", () => {
+    const paths = resolveWorktreeLocalPaths({
+      cwd: "/tmp/paperclip-feature",
+      homeDir: "/tmp/paperclip-worktrees",
+      instanceId: "feature-worktree-support",
+    });
+    const config = buildWorktreeConfig({
+      sourceConfig: buildSourceConfig(),
+      paths,
+      serverPort: 3110,
+      databasePort: 54339,
+      now: new Date("2026-03-09T12:00:00.000Z"),
+    });
+
+    expect(config.database.embeddedPostgresDataDir).toBe(
+      path.resolve("/tmp/paperclip-worktrees", "instances", "feature-worktree-support", "db"),
+    );
+    expect(config.database.embeddedPostgresPort).toBe(54339);
+    expect(config.server.port).toBe(3110);
+    expect(config.auth.publicBaseUrl).toBe("http://127.0.0.1:3110/");
+    expect(config.storage.localDisk.baseDir).toBe(
+      path.resolve("/tmp/paperclip-worktrees", "instances", "feature-worktree-support", "data", "storage"),
+    );
+
+    const env = buildWorktreeEnvEntries(paths, {
+      name: "feature-worktree-support",
+      color: "#3abf7a",
+    });
+    expect(env.PAPERCLIP_HOME).toBe(path.resolve("/tmp/paperclip-worktrees"));
+    expect(env.PAPERCLIP_INSTANCE_ID).toBe("feature-worktree-support");
+    expect(env.PAPERCLIP_IN_WORKTREE).toBe("true");
+    expect(env.PAPERCLIP_WORKTREE_NAME).toBe("feature-worktree-support");
+    expect(env.PAPERCLIP_WORKTREE_COLOR).toBe("#3abf7a");
+    expect(formatShellExports(env)).toContain("export PAPERCLIP_INSTANCE_ID='feature-worktree-support'");
+  });
+
+  it("generates vivid worktree colors as hex", () => {
+    expect(generateWorktreeColor()).toMatch(/^#[0-9a-f]{6}$/);
+  });
+
+  it("uses minimal seed mode to keep app state but drop heavy runtime history", () => {
+    const minimal = resolveWorktreeSeedPlan("minimal");
+    const full = resolveWorktreeSeedPlan("full");
+
+    expect(minimal.excludedTables).toContain("heartbeat_runs");
+    expect(minimal.excludedTables).toContain("heartbeat_run_events");
+    expect(minimal.excludedTables).toContain("workspace_runtime_services");
+    expect(minimal.excludedTables).toContain("agent_task_sessions");
+    expect(minimal.nullifyColumns.issues).toEqual(["checkout_run_id", "execution_run_id"]);
+
+    expect(full.excludedTables).toEqual([]);
+    expect(full.nullifyColumns).toEqual({});
+  });
+
+  it("copies the source local_encrypted secrets key into the seeded worktree instance", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-secrets-"));
+    const originalInlineMasterKey = process.env.PAPERCLIP_SECRETS_MASTER_KEY;
+    const originalKeyFile = process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+    try {
+      delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
+      delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+      const sourceConfigPath = path.join(tempRoot, "source", "config.json");
+      const sourceKeyPath = path.join(tempRoot, "source", "secrets", "master.key");
+      const targetKeyPath = path.join(tempRoot, "target", "secrets", "master.key");
+      fs.mkdirSync(path.dirname(sourceKeyPath), { recursive: true });
+      fs.writeFileSync(sourceKeyPath, "source-master-key", "utf8");
+
+      const sourceConfig = buildSourceConfig();
+      sourceConfig.secrets.localEncrypted.keyFilePath = sourceKeyPath;
+
+      copySeededSecretsKey({
+        sourceConfigPath,
+        sourceConfig,
+        sourceEnvEntries: {},
+        targetKeyFilePath: targetKeyPath,
+      });
+
+      expect(fs.readFileSync(targetKeyPath, "utf8")).toBe("source-master-key");
+    } finally {
+      if (originalInlineMasterKey === undefined) {
+        delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
+      } else {
+        process.env.PAPERCLIP_SECRETS_MASTER_KEY = originalInlineMasterKey;
+      }
+      if (originalKeyFile === undefined) {
+        delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+      } else {
+        process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE = originalKeyFile;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("writes the source inline secrets master key into the seeded worktree instance", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-secrets-"));
+    try {
+      const sourceConfigPath = path.join(tempRoot, "source", "config.json");
+      const targetKeyPath = path.join(tempRoot, "target", "secrets", "master.key");
+
+      copySeededSecretsKey({
+        sourceConfigPath,
+        sourceConfig: buildSourceConfig(),
+        sourceEnvEntries: {
+          PAPERCLIP_SECRETS_MASTER_KEY: "inline-source-master-key",
+        },
+        targetKeyFilePath: targetKeyPath,
+      });
+
+      expect(fs.readFileSync(targetKeyPath, "utf8")).toBe("inline-source-master-key");
+    } finally {
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("persists the current agent jwt secret into the worktree env file", async () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-jwt-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const originalCwd = process.cwd();
+    const originalJwtSecret = process.env.PAPERCLIP_AGENT_JWT_SECRET;
+
+    try {
+      fs.mkdirSync(repoRoot, { recursive: true });
+      process.env.PAPERCLIP_AGENT_JWT_SECRET = "worktree-shared-secret";
+      process.chdir(repoRoot);
+
+      await worktreeInitCommand({
+        seed: false,
+        fromConfig: path.join(tempRoot, "missing", "config.json"),
+        home: path.join(tempRoot, ".paperclip-worktrees"),
+      });
+
+      const envPath = path.join(repoRoot, ".paperclip", ".env");
+      const envContents = fs.readFileSync(envPath, "utf8");
+      expect(envContents).toContain("PAPERCLIP_AGENT_JWT_SECRET=worktree-shared-secret");
+      expect(envContents).toContain("PAPERCLIP_WORKTREE_NAME=repo");
+      expect(envContents).toMatch(/PAPERCLIP_WORKTREE_COLOR=\"#[0-9a-f]{6}\"/);
+    } finally {
+      process.chdir(originalCwd);
+      if (originalJwtSecret === undefined) {
+        delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
+      } else {
+        process.env.PAPERCLIP_AGENT_JWT_SECRET = originalJwtSecret;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("defaults the seed source config to the current repo-local Paperclip config", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-source-config-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const localConfigPath = path.join(repoRoot, ".paperclip", "config.json");
+    const originalCwd = process.cwd();
+    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;
+
+    try {
+      fs.mkdirSync(path.dirname(localConfigPath), { recursive: true });
+      fs.writeFileSync(localConfigPath, JSON.stringify(buildSourceConfig()), "utf8");
+      delete process.env.PAPERCLIP_CONFIG;
+      process.chdir(repoRoot);
+
+      expect(fs.realpathSync(resolveSourceConfigPath({}))).toBe(fs.realpathSync(localConfigPath));
+    } finally {
+      process.chdir(originalCwd);
+      if (originalPaperclipConfig === undefined) {
+        delete process.env.PAPERCLIP_CONFIG;
+      } else {
+        process.env.PAPERCLIP_CONFIG = originalPaperclipConfig;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("preserves the source config path across worktree:make cwd changes", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-source-override-"));
+    const sourceConfigPath = path.join(tempRoot, "source", "config.json");
+    const targetRoot = path.join(tempRoot, "target");
+    const originalCwd = process.cwd();
+    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;
+
+    try {
+      fs.mkdirSync(path.dirname(sourceConfigPath), { recursive: true });
+      fs.mkdirSync(targetRoot, { recursive: true });
+      fs.writeFileSync(sourceConfigPath, JSON.stringify(buildSourceConfig()), "utf8");
+      delete process.env.PAPERCLIP_CONFIG;
+      process.chdir(targetRoot);
+
+      expect(resolveSourceConfigPath({ sourceConfigPathOverride: sourceConfigPath })).toBe(
+        path.resolve(sourceConfigPath),
+      );
+    } finally {
+      process.chdir(originalCwd);
+      if (originalPaperclipConfig === undefined) {
+        delete process.env.PAPERCLIP_CONFIG;
+      } else {
+        process.env.PAPERCLIP_CONFIG = originalPaperclipConfig;
+      }
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("rebinds same-repo workspace paths onto the current worktree root", () => {
+    expect(
+      rebindWorkspaceCwd({
+        sourceRepoRoot: "/Users/example/paperclip",
+        targetRepoRoot: "/Users/example/paperclip-pr-432",
+        workspaceCwd: "/Users/example/paperclip",
+      }),
+    ).toBe("/Users/example/paperclip-pr-432");
+
+    expect(
+      rebindWorkspaceCwd({
+        sourceRepoRoot: "/Users/example/paperclip",
+        targetRepoRoot: "/Users/example/paperclip-pr-432",
+        workspaceCwd: "/Users/example/paperclip/packages/db",
+      }),
+    ).toBe("/Users/example/paperclip-pr-432/packages/db");
+  });
+
+  it("does not rebind paths outside the source repo root", () => {
+    expect(
+      rebindWorkspaceCwd({
+        sourceRepoRoot: "/Users/example/paperclip",
+        targetRepoRoot: "/Users/example/paperclip-pr-432",
+        workspaceCwd: "/Users/example/other-project",
+      }),
+    ).toBeNull();
+  });
+
+  it("copies shared git hooks into a linked worktree git dir", () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-hooks-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const worktreePath = path.join(tempRoot, "repo-feature");
+
+    try {
+      fs.mkdirSync(repoRoot, { recursive: true });
+      execFileSync("git", ["init"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["config", "user.email", "test@example.com"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["config", "user.name", "Test User"], { cwd: repoRoot, stdio: "ignore" });
+      fs.writeFileSync(path.join(repoRoot, "README.md"), "# temp\n", "utf8");
+      execFileSync("git", ["add", "README.md"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["commit", "-m", "Initial commit"], { cwd: repoRoot, stdio: "ignore" });
+
+      const sourceHooksDir = path.join(repoRoot, ".git", "hooks");
+      const sourceHookPath = path.join(sourceHooksDir, "pre-commit");
+      const sourceTokensPath = path.join(sourceHooksDir, "forbidden-tokens.txt");
+      fs.writeFileSync(sourceHookPath, "#!/usr/bin/env bash\nexit 0\n", { encoding: "utf8", mode: 0o755 });
+      fs.chmodSync(sourceHookPath, 0o755);
+      fs.writeFileSync(sourceTokensPath, "secret-token\n", "utf8");
+
+      execFileSync("git", ["worktree", "add", "--detach", worktreePath], { cwd: repoRoot, stdio: "ignore" });
+
+      const copied = copyGitHooksToWorktreeGitDir(worktreePath);
+      const worktreeGitDir = execFileSync("git", ["rev-parse", "--git-dir"], {
+        cwd: worktreePath,
+        encoding: "utf8",
+        stdio: ["ignore", "pipe", "ignore"],
+      }).trim();
+      const resolvedSourceHooksDir = fs.realpathSync(sourceHooksDir);
+      const resolvedTargetHooksDir = fs.realpathSync(path.resolve(worktreePath, worktreeGitDir, "hooks"));
+      const targetHookPath = path.join(resolvedTargetHooksDir, "pre-commit");
+      const targetTokensPath = path.join(resolvedTargetHooksDir, "forbidden-tokens.txt");
+
+      expect(copied).toMatchObject({
+        sourceHooksPath: resolvedSourceHooksDir,
+        targetHooksPath: resolvedTargetHooksDir,
+        copied: true,
+      });
+      expect(fs.readFileSync(targetHookPath, "utf8")).toBe("#!/usr/bin/env bash\nexit 0\n");
+      expect(fs.statSync(targetHookPath).mode & 0o111).not.toBe(0);
+      expect(fs.readFileSync(targetTokensPath, "utf8")).toBe("secret-token\n");
+    } finally {
+      execFileSync("git", ["worktree", "remove", "--force", worktreePath], { cwd: repoRoot, stdio: "ignore" });
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it("creates and initializes a worktree from the top-level worktree:make command", async () => {
+    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-make-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const fakeHome = path.join(tempRoot, "home");
+    const worktreePath = path.join(fakeHome, "paperclip-make-test");
+    const originalCwd = process.cwd();
+    const homedirSpy = vi.spyOn(os, "homedir").mockReturnValue(fakeHome);
+
+    try {
+      fs.mkdirSync(repoRoot, { recursive: true });
+      fs.mkdirSync(fakeHome, { recursive: true });
+      execFileSync("git", ["init"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["config", "user.email", "test@example.com"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["config", "user.name", "Test User"], { cwd: repoRoot, stdio: "ignore" });
+      fs.writeFileSync(path.join(repoRoot, "README.md"), "# temp\n", "utf8");
+      execFileSync("git", ["add", "README.md"], { cwd: repoRoot, stdio: "ignore" });
+      execFileSync("git", ["commit", "-m", "Initial commit"], { cwd: repoRoot, stdio: "ignore" });
+
+      process.chdir(repoRoot);
+
+      await worktreeMakeCommand("paperclip-make-test", {
+        seed: false,
+        home: path.join(tempRoot, ".paperclip-worktrees"),
+      });
+
+      expect(fs.existsSync(path.join(worktreePath, ".git"))).toBe(true);
+      expect(fs.existsSync(path.join(worktreePath, ".paperclip", "config.json"))).toBe(true);
+      expect(fs.existsSync(path.join(worktreePath, ".paperclip", ".env"))).toBe(true);
+    } finally {
+      process.chdir(originalCwd);
+      homedirSpy.mockRestore();
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  }, 20_000);
+});
--- a/cli/src/adapters/registry.ts
+++ b/cli/src/adapters/registry.ts
@@ -2,9 +2,10 @@ import type { CLIAdapterModule } from "@paperclipai/adapter-utils";
 import { printClaudeStreamEvent } from "@paperclipai/adapter-claude-local/cli";
 import { printCodexStreamEvent } from "@paperclipai/adapter-codex-local/cli";
 import { printCursorStreamEvent } from "@paperclipai/adapter-cursor-local/cli";
+import { printGeminiStreamEvent } from "@paperclipai/adapter-gemini-local/cli";
 import { printOpenCodeStreamEvent } from "@paperclipai/adapter-opencode-local/cli";
 import { printPiStreamEvent } from "@paperclipai/adapter-pi-local/cli";
-import { printOpenClawStreamEvent } from "@paperclipai/adapter-openclaw/cli";
+import { printOpenClawGatewayStreamEvent } from "@paperclipai/adapter-openclaw-gateway/cli";
 import { processCLIAdapter } from "./process/index.js";
 import { httpCLIAdapter } from "./http/index.js";

@@ -33,13 +34,28 @@ const cursorLocalCLIAdapter: CLIAdapterModule = {
  formatStdoutEvent: printCursorStreamEvent,
 };

-const openclawCLIAdapter: CLIAdapterModule = {
-  type: "openclaw",
-  formatStdoutEvent: printOpenClawStreamEvent,
+const geminiLocalCLIAdapter: CLIAdapterModule = {
+  type: "gemini_local",
+  formatStdoutEvent: printGeminiStreamEvent,
+};
+
+const openclawGatewayCLIAdapter: CLIAdapterModule = {
+  type: "openclaw_gateway",
+  formatStdoutEvent: printOpenClawGatewayStreamEvent,
 };

 const adaptersByType = new Map<string, CLIAdapterModule>(
-  [claudeLocalCLIAdapter, codexLocalCLIAdapter, openCodeLocalCLIAdapter, piLocalCLIAdapter, cursorLocalCLIAdapter, openclawCLIAdapter, processCLIAdapter, httpCLIAdapter].map((a) => [a.type, a]),
+  [
+    claudeLocalCLIAdapter,
+    codexLocalCLIAdapter,
+    openCodeLocalCLIAdapter,
+    piLocalCLIAdapter,
+    cursorLocalCLIAdapter,
+    geminiLocalCLIAdapter,
+    openclawGatewayCLIAdapter,
+    processCLIAdapter,
+    httpCLIAdapter,
+  ].map((a) => [a.type, a]),
 );

 export function getCLIAdapter(type: string): CLIAdapterModule {
--- a/cli/src/client/http.ts
+++ b/cli/src/client/http.ts
@@ -104,8 +104,10 @@ export class PaperclipApiClient {

 function buildUrl(apiBase: string, path: string): string {
  const normalizedPath = path.startsWith("/") ? path : `/${path}`;
+  const [pathname, query] = normalizedPath.split("?");
  const url = new URL(apiBase);
-  url.pathname = `${url.pathname.replace(/\/+$/, "")}${normalizedPath}`;
+  url.pathname = `${url.pathname.replace(/\/+$/, "")}${pathname}`;
+  if (query) url.search = query;
  return url.toString();
 }

--- a/cli/src/commands/allowed-hostname.ts
+++ b/cli/src/commands/allowed-hostname.ts
@@ -26,6 +26,9 @@ export async function addAllowedHostname(host: string, opts: { config?: string }
    p.log.info(`Hostname ${pc.cyan(normalized)} is already allowed.`);
  } else {
    p.log.success(`Added allowed hostname: ${pc.cyan(normalized)}`);
+    p.log.message(
+      pc.dim("Restart the Paperclip server for this change to take effect."),
+    );
  }

  if (!(config.server.deploymentMode === "authenticated" && config.server.exposure === "private")) {
--- a/cli/src/commands/auth-bootstrap-ceo.ts
+++ b/cli/src/commands/auth-bootstrap-ceo.ts
@@ -3,6 +3,7 @@ import * as p from "@clack/prompts";
 import pc from "picocolors";
 import { and, eq, gt, isNull } from "drizzle-orm";
 import { createDb, instanceUserRoles, invites } from "@paperclipai/db";
+import { loadPaperclipEnvFile } from "../config/env.js";
 import { readConfig, resolveConfigPath } from "../config/store.js";

 function hashToken(token: string) {
@@ -13,7 +14,8 @@ function createInviteToken() {
  return `pcp_bootstrap_${randomBytes(24).toString("hex")}`;
 }

-function resolveDbUrl(configPath?: string) {
+function resolveDbUrl(configPath?: string, explicitDbUrl?: string) {
+  if (explicitDbUrl) return explicitDbUrl;
  const config = readConfig(configPath);
  if (process.env.DATABASE_URL) return process.env.DATABASE_URL;
  if (config?.database.mode === "postgres" && config.database.connectionString) {
@@ -49,8 +51,10 @@ export async function bootstrapCeoInvite(opts: {
  force?: boolean;
  expiresHours?: number;
  baseUrl?: string;
+  dbUrl?: string;
 }) {
  const configPath = resolveConfigPath(opts.config);
+  loadPaperclipEnvFile(configPath);
  const config = readConfig(configPath);
  if (!config) {
    p.log.error(`No config found at ${configPath}. Run ${pc.cyan("paperclip onboard")} first.`);
@@ -62,7 +66,7 @@ export async function bootstrapCeoInvite(opts: {
    return;
  }

-  const dbUrl = resolveDbUrl(configPath);
+  const dbUrl = resolveDbUrl(configPath, opts.dbUrl);
  if (!dbUrl) {
    p.log.error(
      "Could not resolve database connection for bootstrap.",
@@ -71,6 +75,11 @@ export async function bootstrapCeoInvite(opts: {
  }

  const db = createDb(dbUrl);
+  const closableDb = db as typeof db & {
+    $client?: {
+      end?: (options?: { timeout?: number }) => Promise<void>;
+    };
+  };
  try {
    const existingAdminCount = await db
      .select()
@@ -118,5 +127,7 @@ export async function bootstrapCeoInvite(opts: {
  } catch (err) {
    p.log.error(`Could not create bootstrap invite: ${err instanceof Error ? err.message : String(err)}`);
    p.log.info("If using embedded-postgres, start the Paperclip server and run this command again.");
+  } finally {
+    await closableDb.$client?.end?.({ timeout: 5 }).catch(() => undefined);
  }
 }
--- a/cli/src/commands/client/agent.ts
+++ b/cli/src/commands/client/agent.ts
@@ -1,5 +1,13 @@
 import { Command } from "commander";
 import type { Agent } from "@paperclipai/shared";
+import {
+  removeMaintainerOnlySkillSymlinks,
+  resolvePaperclipSkillsDir,
+} from "@paperclipai/adapter-utils/server-utils";
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
 import {
  addCommonClientOptions,
  formatInlineRecord,
@@ -13,6 +21,141 @@ interface AgentListOptions extends BaseClientOptions {
  companyId?: string;
 }

+interface AgentLocalCliOptions extends BaseClientOptions {
+  companyId?: string;
+  keyName?: string;
+  installSkills?: boolean;
+}
+
+interface CreatedAgentKey {
+  id: string;
+  name: string;
+  token: string;
+  createdAt: string;
+}
+
+interface SkillsInstallSummary {
+  tool: "codex" | "claude";
+  target: string;
+  linked: string[];
+  removed: string[];
+  skipped: string[];
+  failed: Array<{ name: string; error: string }>;
+}
+
+const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
+
+function codexSkillsHome(): string {
+  const fromEnv = process.env.CODEX_HOME?.trim();
+  const base = fromEnv && fromEnv.length > 0 ? fromEnv : path.join(os.homedir(), ".codex");
+  return path.join(base, "skills");
+}
+
+function claudeSkillsHome(): string {
+  const fromEnv = process.env.CLAUDE_HOME?.trim();
+  const base = fromEnv && fromEnv.length > 0 ? fromEnv : path.join(os.homedir(), ".claude");
+  return path.join(base, "skills");
+}
+
+async function installSkillsForTarget(
+  sourceSkillsDir: string,
+  targetSkillsDir: string,
+  tool: "codex" | "claude",
+): Promise<SkillsInstallSummary> {
+  const summary: SkillsInstallSummary = {
+    tool,
+    target: targetSkillsDir,
+    linked: [],
+    removed: [],
+    skipped: [],
+    failed: [],
+  };
+
+  await fs.mkdir(targetSkillsDir, { recursive: true });
+  const entries = await fs.readdir(sourceSkillsDir, { withFileTypes: true });
+  summary.removed = await removeMaintainerOnlySkillSymlinks(
+    targetSkillsDir,
+    entries.filter((entry) => entry.isDirectory()).map((entry) => entry.name),
+  );
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    const source = path.join(sourceSkillsDir, entry.name);
+    const target = path.join(targetSkillsDir, entry.name);
+    const existing = await fs.lstat(target).catch(() => null);
+    if (existing) {
+      if (existing.isSymbolicLink()) {
+        let linkedPath: string | null = null;
+        try {
+          linkedPath = await fs.readlink(target);
+        } catch (err) {
+          await fs.unlink(target);
+          try {
+            await fs.symlink(source, target);
+            summary.linked.push(entry.name);
+            continue;
+          } catch (linkErr) {
+            summary.failed.push({
+              name: entry.name,
+              error:
+                err instanceof Error && linkErr instanceof Error
+                  ? `${err.message}; then ${linkErr.message}`
+                  : err instanceof Error
+                    ? err.message
+                    : `Failed to recover broken symlink: ${String(err)}`,
+            });
+            continue;
+          }
+        }
+
+        const resolvedLinkedPath = path.isAbsolute(linkedPath)
+          ? linkedPath
+          : path.resolve(path.dirname(target), linkedPath);
+        const linkedTargetExists = await fs
+          .stat(resolvedLinkedPath)
+          .then(() => true)
+          .catch(() => false);
+
+        if (!linkedTargetExists) {
+          await fs.unlink(target);
+        } else {
+          summary.skipped.push(entry.name);
+          continue;
+        }
+      } else {
+        summary.skipped.push(entry.name);
+        continue;
+      }
+    }
+
+    try {
+      await fs.symlink(source, target);
+      summary.linked.push(entry.name);
+    } catch (err) {
+      summary.failed.push({
+        name: entry.name,
+        error: err instanceof Error ? err.message : String(err),
+      });
+    }
+  }
+
+  return summary;
+}
+
+function buildAgentEnvExports(input: {
+  apiBase: string;
+  companyId: string;
+  agentId: string;
+  apiKey: string;
+}): string {
+  const escaped = (value: string) => value.replace(/'/g, "'\"'\"'");
+  return [
+    `export PAPERCLIP_API_URL='${escaped(input.apiBase)}'`,
+    `export PAPERCLIP_COMPANY_ID='${escaped(input.companyId)}'`,
+    `export PAPERCLIP_AGENT_ID='${escaped(input.agentId)}'`,
+    `export PAPERCLIP_API_KEY='${escaped(input.apiKey)}'`,
+  ].join("\n");
+}
+
 export function registerAgentCommands(program: Command): void {
  const agent = program.command("agent").description("Agent operations");

@@ -71,4 +214,102 @@ export function registerAgentCommands(program: Command): void {
        }
      }),
  );
+
+  addCommonClientOptions(
+    agent
+      .command("local-cli")
+      .description(
+        "Create an agent API key, install local Paperclip skills for Codex/Claude, and print shell exports",
+      )
+      .argument("<agentRef>", "Agent ID or shortname/url-key")
+      .requiredOption("-C, --company-id <id>", "Company ID")
+      .option("--key-name <name>", "API key label", "local-cli")
+      .option(
+        "--no-install-skills",
+        "Skip installing Paperclip skills into ~/.codex/skills and ~/.claude/skills",
+      )
+      .action(async (agentRef: string, opts: AgentLocalCliOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts, { requireCompany: true });
+          const query = new URLSearchParams({ companyId: ctx.companyId ?? "" });
+          const agentRow = await ctx.api.get<Agent>(
+            `/api/agents/${encodeURIComponent(agentRef)}?${query.toString()}`,
+          );
+          if (!agentRow) {
+            throw new Error(`Agent not found: ${agentRef}`);
+          }
+
+          const now = new Date().toISOString().replaceAll(":", "-");
+          const keyName = opts.keyName?.trim() ? opts.keyName.trim() : `local-cli-${now}`;
+          const key = await ctx.api.post<CreatedAgentKey>(`/api/agents/${agentRow.id}/keys`, { name: keyName });
+          if (!key) {
+            throw new Error("Failed to create API key");
+          }
+
+          const installSummaries: SkillsInstallSummary[] = [];
+          if (opts.installSkills !== false) {
+            const skillsDir = await resolvePaperclipSkillsDir(__moduleDir, [path.resolve(process.cwd(), "skills")]);
+            if (!skillsDir) {
+              throw new Error(
+                "Could not locate local Paperclip skills directory. Expected ./skills in the repo checkout.",
+              );
+            }
+
+            installSummaries.push(
+              await installSkillsForTarget(skillsDir, codexSkillsHome(), "codex"),
+              await installSkillsForTarget(skillsDir, claudeSkillsHome(), "claude"),
+            );
+          }
+
+          const exportsText = buildAgentEnvExports({
+            apiBase: ctx.api.apiBase,
+            companyId: agentRow.companyId,
+            agentId: agentRow.id,
+            apiKey: key.token,
+          });
+
+          if (ctx.json) {
+            printOutput(
+              {
+                agent: {
+                  id: agentRow.id,
+                  name: agentRow.name,
+                  urlKey: agentRow.urlKey,
+                  companyId: agentRow.companyId,
+                },
+                key: {
+                  id: key.id,
+                  name: key.name,
+                  createdAt: key.createdAt,
+                  token: key.token,
+                },
+                skills: installSummaries,
+                exports: exportsText,
+              },
+              { json: true },
+            );
+            return;
+          }
+
+          console.log(`Agent: ${agentRow.name} (${agentRow.id})`);
+          console.log(`API key created: ${key.name} (${key.id})`);
+          if (installSummaries.length > 0) {
+            for (const summary of installSummaries) {
+              console.log(
+                `${summary.tool}: linked=${summary.linked.length} removed=${summary.removed.length} skipped=${summary.skipped.length} failed=${summary.failed.length} target=${summary.target}`,
+              );
+              for (const failed of summary.failed) {
+                console.log(`  failed ${failed.name}: ${failed.error}`);
+              }
+            }
+          }
+          console.log("");
+          console.log("# Run this in your shell before launching codex/claude:");
+          console.log(exportsText);
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+    { includeCompany: false },
+  );
 }
--- a/cli/src/commands/client/plugin.ts
+++ b/cli/src/commands/client/plugin.ts
@@ -0,0 +1,374 @@
+import path from "node:path";
+import { Command } from "commander";
+import pc from "picocolors";
+import {
+  addCommonClientOptions,
+  handleCommandError,
+  printOutput,
+  resolveCommandContext,
+  type BaseClientOptions,
+} from "./common.js";
+
+// ---------------------------------------------------------------------------
+// Types mirroring server-side shapes
+// ---------------------------------------------------------------------------
+
+interface PluginRecord {
+  id: string;
+  pluginKey: string;
+  packageName: string;
+  version: string;
+  status: string;
+  displayName?: string;
+  lastError?: string | null;
+  installedAt: string;
+  updatedAt: string;
+}
+
+
+// ---------------------------------------------------------------------------
+// Option types
+// ---------------------------------------------------------------------------
+
+interface PluginListOptions extends BaseClientOptions {
+  status?: string;
+}
+
+interface PluginInstallOptions extends BaseClientOptions {
+  local?: boolean;
+  version?: string;
+}
+
+interface PluginUninstallOptions extends BaseClientOptions {
+  force?: boolean;
+}
+
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+
+/**
+ * Resolve a local path argument to an absolute path so the server can find the
+ * plugin on disk regardless of where the user ran the CLI.
+ */
+function resolvePackageArg(packageArg: string, isLocal: boolean): string {
+  if (!isLocal) return packageArg;
+  // Already absolute
+  if (path.isAbsolute(packageArg)) return packageArg;
+  // Expand leading ~ to home directory
+  if (packageArg.startsWith("~")) {
+    const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
+    return path.resolve(home, packageArg.slice(1).replace(/^[\\/]/, ""));
+  }
+  return path.resolve(process.cwd(), packageArg);
+}
+
+function formatPlugin(p: PluginRecord): string {
+  const statusColor =
+    p.status === "ready"
+      ? pc.green(p.status)
+      : p.status === "error"
+        ? pc.red(p.status)
+        : p.status === "disabled"
+          ? pc.dim(p.status)
+          : pc.yellow(p.status);
+
+  const parts = [
+    `key=${pc.bold(p.pluginKey)}`,
+    `status=${statusColor}`,
+    `version=${p.version}`,
+    `id=${pc.dim(p.id)}`,
+  ];
+
+  if (p.lastError) {
+    parts.push(`error=${pc.red(p.lastError.slice(0, 80))}`);
+  }
+
+  return parts.join("  ");
+}
+
+// ---------------------------------------------------------------------------
+// Command registration
+// ---------------------------------------------------------------------------
+
+export function registerPluginCommands(program: Command): void {
+  const plugin = program.command("plugin").description("Plugin lifecycle management");
+
+  // -------------------------------------------------------------------------
+  // plugin list
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("list")
+      .description("List installed plugins")
+      .option("--status <status>", "Filter by status (ready, error, disabled, installed, upgrade_pending)")
+      .action(async (opts: PluginListOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const qs = opts.status ? `?status=${encodeURIComponent(opts.status)}` : "";
+          const plugins = await ctx.api.get<PluginRecord[]>(`/api/plugins${qs}`);
+
+          if (ctx.json) {
+            printOutput(plugins, { json: true });
+            return;
+          }
+
+          const rows = plugins ?? [];
+          if (rows.length === 0) {
+            console.log(pc.dim("No plugins installed."));
+            return;
+          }
+
+          for (const p of rows) {
+            console.log(formatPlugin(p));
+          }
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin install <package-or-path>
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("install <package>")
+      .description(
+        "Install a plugin from a local path or npm package.\n" +
+          "  Examples:\n" +
+          "    paperclipai plugin install ./my-plugin              # local path\n" +
+          "    paperclipai plugin install @acme/plugin-linear      # npm package\n" +
+          "    paperclipai plugin install @acme/plugin-linear@1.2  # pinned version",
+      )
+      .option("-l, --local", "Treat <package> as a local filesystem path", false)
+      .option("--version <version>", "Specific npm version to install (npm packages only)")
+      .action(async (packageArg: string, opts: PluginInstallOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+
+          // Auto-detect local paths: starts with . or / or ~ or is an absolute path
+          const isLocal =
+            opts.local ||
+            packageArg.startsWith("./") ||
+            packageArg.startsWith("../") ||
+            packageArg.startsWith("/") ||
+            packageArg.startsWith("~");
+
+          const resolvedPackage = resolvePackageArg(packageArg, isLocal);
+
+          if (!ctx.json) {
+            console.log(
+              pc.dim(
+                isLocal
+                  ? `Installing plugin from local path: ${resolvedPackage}`
+                  : `Installing plugin: ${resolvedPackage}${opts.version ? `@${opts.version}` : ""}`,
+              ),
+            );
+          }
+
+          const installedPlugin = await ctx.api.post<PluginRecord>("/api/plugins/install", {
+            packageName: resolvedPackage,
+            version: opts.version,
+            isLocalPath: isLocal,
+          });
+
+          if (ctx.json) {
+            printOutput(installedPlugin, { json: true });
+            return;
+          }
+
+          if (!installedPlugin) {
+            console.log(pc.dim("Install returned no plugin record."));
+            return;
+          }
+
+          console.log(
+            pc.green(
+              `✓ Installed ${pc.bold(installedPlugin.pluginKey)} v${installedPlugin.version} (${installedPlugin.status})`,
+            ),
+          );
+
+          if (installedPlugin.lastError) {
+            console.log(pc.red(`  Warning: ${installedPlugin.lastError}`));
+          }
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin uninstall <plugin-key-or-id>
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("uninstall <pluginKey>")
+      .description(
+        "Uninstall a plugin by its plugin key or database ID.\n" +
+          "  Use --force to hard-purge all state and config.",
+      )
+      .option("--force", "Purge all plugin state and config (hard delete)", false)
+      .action(async (pluginKey: string, opts: PluginUninstallOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const purge = opts.force === true;
+          const qs = purge ? "?purge=true" : "";
+
+          if (!ctx.json) {
+            console.log(
+              pc.dim(
+                purge
+                  ? `Uninstalling and purging plugin: ${pluginKey}`
+                  : `Uninstalling plugin: ${pluginKey}`,
+              ),
+            );
+          }
+
+          const result = await ctx.api.delete<PluginRecord | null>(
+            `/api/plugins/${encodeURIComponent(pluginKey)}${qs}`,
+          );
+
+          if (ctx.json) {
+            printOutput(result, { json: true });
+            return;
+          }
+
+          console.log(pc.green(`✓ Uninstalled ${pc.bold(pluginKey)}${purge ? " (purged)" : ""}`));
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin enable <plugin-key-or-id>
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("enable <pluginKey>")
+      .description("Enable a disabled or errored plugin")
+      .action(async (pluginKey: string, opts: BaseClientOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const result = await ctx.api.post<PluginRecord>(
+            `/api/plugins/${encodeURIComponent(pluginKey)}/enable`,
+          );
+
+          if (ctx.json) {
+            printOutput(result, { json: true });
+            return;
+          }
+
+          console.log(pc.green(`✓ Enabled ${pc.bold(pluginKey)} — status: ${result?.status ?? "unknown"}`));
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin disable <plugin-key-or-id>
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("disable <pluginKey>")
+      .description("Disable a running plugin without uninstalling it")
+      .action(async (pluginKey: string, opts: BaseClientOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const result = await ctx.api.post<PluginRecord>(
+            `/api/plugins/${encodeURIComponent(pluginKey)}/disable`,
+          );
+
+          if (ctx.json) {
+            printOutput(result, { json: true });
+            return;
+          }
+
+          console.log(pc.dim(`Disabled ${pc.bold(pluginKey)} — status: ${result?.status ?? "unknown"}`));
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin inspect <plugin-key-or-id>
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("inspect <pluginKey>")
+      .description("Show full details for an installed plugin")
+      .action(async (pluginKey: string, opts: BaseClientOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const result = await ctx.api.get<PluginRecord>(
+            `/api/plugins/${encodeURIComponent(pluginKey)}`,
+          );
+
+          if (ctx.json) {
+            printOutput(result, { json: true });
+            return;
+          }
+
+          if (!result) {
+            console.log(pc.red(`Plugin not found: ${pluginKey}`));
+            process.exit(1);
+          }
+
+          console.log(formatPlugin(result));
+          if (result.lastError) {
+            console.log(`\n${pc.red("Last error:")}\n${result.lastError}`);
+          }
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+
+  // -------------------------------------------------------------------------
+  // plugin examples
+  // -------------------------------------------------------------------------
+  addCommonClientOptions(
+    plugin
+      .command("examples")
+      .description("List bundled example plugins available for local install")
+      .action(async (opts: BaseClientOptions) => {
+        try {
+          const ctx = resolveCommandContext(opts);
+          const examples = await ctx.api.get<
+            Array<{
+              packageName: string;
+              pluginKey: string;
+              displayName: string;
+              description: string;
+              localPath: string;
+              tag: string;
+            }>
+          >("/api/plugins/examples");
+
+          if (ctx.json) {
+            printOutput(examples, { json: true });
+            return;
+          }
+
+          const rows = examples ?? [];
+          if (rows.length === 0) {
+            console.log(pc.dim("No bundled examples available."));
+            return;
+          }
+
+          for (const ex of rows) {
+            console.log(
+              `${pc.bold(ex.displayName)}  ${pc.dim(ex.pluginKey)}\n` +
+                `  ${ex.description}\n` +
+                `  ${pc.cyan(`paperclipai plugin install ${ex.localPath}`)}`,
+            );
+          }
+        } catch (err) {
+          handleCommandError(err);
+        }
+      }),
+  );
+}
--- a/cli/src/commands/configure.ts
+++ b/cli/src/commands/configure.ts
@@ -61,6 +61,7 @@ function defaultConfig(): PaperclipConfig {
    },
    auth: {
      baseUrlMode: "auto",
+      disableSignUp: false,
    },
    storage: defaultStorageConfig(),
    secrets: defaultSecretsConfig(),
--- a/cli/src/commands/doctor.ts
+++ b/cli/src/commands/doctor.ts
@@ -14,6 +14,7 @@ import {
  storageCheck,
  type CheckResult,
 } from "../checks/index.js";
+import { loadPaperclipEnvFile } from "../config/env.js";
 import { printPaperclipCliBanner } from "../utils/banner.js";

 const STATUS_ICON = {
@@ -31,6 +32,7 @@ export async function doctor(opts: {
  p.intro(pc.bgCyan(pc.black(" paperclip doctor ")));

  const configPath = resolveConfigPath(opts.config);
+  loadPaperclipEnvFile(configPath);
  const results: CheckResult[] = [];

  // 1. Config check (must pass before others)
@@ -64,28 +66,40 @@ export async function doctor(opts: {
  printResult(deploymentAuthResult);

  // 3. Agent JWT check
-  const jwtResult = agentJwtSecretCheck(opts.config);
-  results.push(jwtResult);
-  printResult(jwtResult);
-  await maybeRepair(jwtResult, opts);
+  results.push(
+    await runRepairableCheck({
+      run: () => agentJwtSecretCheck(opts.config),
+      configPath,
+      opts,
+    }),
+  );

  // 4. Secrets adapter check
-  const secretsResult = secretsCheck(config, configPath);
-  results.push(secretsResult);
-  printResult(secretsResult);
-  await maybeRepair(secretsResult, opts);
+  results.push(
+    await runRepairableCheck({
+      run: () => secretsCheck(config, configPath),
+      configPath,
+      opts,
+    }),
+  );

  // 5. Storage check
-  const storageResult = storageCheck(config, configPath);
-  results.push(storageResult);
-  printResult(storageResult);
-  await maybeRepair(storageResult, opts);
+  results.push(
+    await runRepairableCheck({
+      run: () => storageCheck(config, configPath),
+      configPath,
+      opts,
+    }),
+  );

  // 6. Database check
-  const dbResult = await databaseCheck(config, configPath);
-  results.push(dbResult);
-  printResult(dbResult);
-  await maybeRepair(dbResult, opts);
+  results.push(
+    await runRepairableCheck({
+      run: () => databaseCheck(config, configPath),
+      configPath,
+      opts,
+    }),
+  );

  // 7. LLM check
  const llmResult = await llmCheck(config);
@@ -93,10 +107,13 @@ export async function doctor(opts: {
  printResult(llmResult);

  // 8. Log directory check
-  const logResult = logCheck(config, configPath);
-  results.push(logResult);
-  printResult(logResult);
-  await maybeRepair(logResult, opts);
+  results.push(
+    await runRepairableCheck({
+      run: () => logCheck(config, configPath),
+      configPath,
+      opts,
+    }),
+  );

  // 9. Port check
  const portResult = await portCheck(config);
@@ -118,9 +135,9 @@ function printResult(result: CheckResult): void {
 async function maybeRepair(
  result: CheckResult,
  opts: { repair?: boolean; yes?: boolean },
-): Promise<void> {
-  if (result.status === "pass" || !result.canRepair || !result.repair) return;
-  if (!opts.repair) return;
+): Promise<boolean> {
+  if (result.status === "pass" || !result.canRepair || !result.repair) return false;
+  if (!opts.repair) return false;

  let shouldRepair = opts.yes;
  if (!shouldRepair) {
@@ -128,7 +145,7 @@ async function maybeRepair(
      message: `Repair "${result.name}"?`,
      initialValue: true,
    });
-    if (p.isCancel(answer)) return;
+    if (p.isCancel(answer)) return false;
    shouldRepair = answer;
  }

@@ -136,10 +153,30 @@ async function maybeRepair(
    try {
      await result.repair();
      p.log.success(`Repaired: ${result.name}`);
+      return true;
    } catch (err) {
      p.log.error(`Repair failed: ${err instanceof Error ? err.message : String(err)}`);
    }
  }
+  return false;
+}
+
+async function runRepairableCheck(input: {
+  run: () => CheckResult | Promise<CheckResult>;
+  configPath: string;
+  opts: { repair?: boolean; yes?: boolean };
+}): Promise<CheckResult> {
+  let result = await input.run();
+  printResult(result);
+
+  const repaired = await maybeRepair(result, input.opts);
+  if (!repaired) return result;
+
+  // Repairs may create/update the adjacent .env file or other local resources.
+  loadPaperclipEnvFile(input.configPath);
+  result = await input.run();
+  printResult(result);
+  return result;
 }

 function printSummary(results: CheckResult[]): { passed: number; warned: number; failed: number } {
--- a/cli/src/commands/onboard.ts
+++ b/cli/src/commands/onboard.ts
@@ -185,6 +185,7 @@ function quickstartDefaultsFromEnv(): {
    },
    auth: {
      baseUrlMode: authBaseUrlMode,
+      disableSignUp: false,
      ...(authPublicBaseUrl ? { publicBaseUrl: authPublicBaseUrl } : {}),
    },
    storage: {
@@ -228,6 +229,10 @@ function quickstartDefaultsFromEnv(): {
  return { defaults, usedEnvKeys, ignoredEnvKeys };
 }

+function canCreateBootstrapInviteImmediately(config: Pick<PaperclipConfig, "database" | "server">): boolean {
+  return config.server.deploymentMode === "authenticated" && config.database.mode !== "embedded-postgres";
+}
+
 export async function onboard(opts: OnboardOptions): Promise<void> {
  printPaperclipCliBanner();
  p.intro(pc.bgCyan(pc.black(" paperclipai onboard ")));
@@ -449,7 +454,7 @@ export async function onboard(opts: OnboardOptions): Promise<void> {
    "Next commands",
  );

-  if (server.deploymentMode === "authenticated") {
+  if (canCreateBootstrapInviteImmediately({ database, server })) {
    p.log.step("Generating bootstrap CEO invite");
    await bootstrapCeoInvite({ config: configPath });
  }
@@ -472,5 +477,15 @@ export async function onboard(opts: OnboardOptions): Promise<void> {
    return;
  }

+  if (server.deploymentMode === "authenticated" && database.mode === "embedded-postgres") {
+    p.log.info(
+      [
+        "Bootstrap CEO invite will be created after the server starts.",
+        `Next: ${pc.cyan("paperclipai run")}`,
+        `Then: ${pc.cyan("paperclipai auth bootstrap-ceo")}`,
+      ].join("\n"),
+    );
+  }
+
  p.outro("You're all set!");
 }
--- a/cli/src/commands/run.ts
+++ b/cli/src/commands/run.ts
@@ -3,9 +3,13 @@ import path from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";
 import * as p from "@clack/prompts";
 import pc from "picocolors";
+import { bootstrapCeoInvite } from "./auth-bootstrap-ceo.js";
 import { onboard } from "./onboard.js";
 import { doctor } from "./doctor.js";
+import { loadPaperclipEnvFile } from "../config/env.js";
 import { configExists, resolveConfigPath } from "../config/store.js";
+import type { PaperclipConfig } from "../config/schema.js";
+import { readConfig } from "../config/store.js";
 import {
  describeLocalInstancePaths,
  resolvePaperclipHomeDir,
@@ -19,6 +23,13 @@ interface RunOptions {
  yes?: boolean;
 }

+interface StartedServer {
+  apiUrl: string;
+  databaseUrl: string;
+  host: string;
+  listenPort: number;
+}
+
 export async function runCommand(opts: RunOptions): Promise<void> {
  const instanceId = resolvePaperclipInstanceId(opts.instance);
  process.env.PAPERCLIP_INSTANCE_ID = instanceId;
@@ -31,6 +42,7 @@ export async function runCommand(opts: RunOptions): Promise<void> {

  const configPath = resolveConfigPath(opts.config);
  process.env.PAPERCLIP_CONFIG = configPath;
+  loadPaperclipEnvFile(configPath);

  p.intro(pc.bgCyan(pc.black(" paperclipai run ")));
  p.log.message(pc.dim(`Home: ${paths.homeDir}`));
@@ -60,8 +72,41 @@ export async function runCommand(opts: RunOptions): Promise<void> {
    process.exit(1);
  }

+  const config = readConfig(configPath);
+  if (!config) {
+    p.log.error(`No config found at ${configPath}.`);
+    process.exit(1);
+  }
+
  p.log.step("Starting Paperclip server...");
-  await importServerEntry();
+  const startedServer = await importServerEntry();
+
+  if (shouldGenerateBootstrapInviteAfterStart(config)) {
+    p.log.step("Generating bootstrap CEO invite");
+    await bootstrapCeoInvite({
+      config: configPath,
+      dbUrl: startedServer.databaseUrl,
+      baseUrl: resolveBootstrapInviteBaseUrl(config, startedServer),
+    });
+  }
+}
+
+function resolveBootstrapInviteBaseUrl(
+  config: PaperclipConfig,
+  startedServer: StartedServer,
+): string {
+  const explicitBaseUrl =
+    process.env.PAPERCLIP_PUBLIC_URL ??
+    process.env.PAPERCLIP_AUTH_PUBLIC_BASE_URL ??
+    process.env.BETTER_AUTH_URL ??
+    process.env.BETTER_AUTH_BASE_URL ??
+    (config.auth.baseUrlMode === "explicit" ? config.auth.publicBaseUrl : undefined);
+
+  if (typeof explicitBaseUrl === "string" && explicitBaseUrl.trim().length > 0) {
+    return explicitBaseUrl.trim().replace(/\/+$/, "");
+  }
+
+  return startedServer.apiUrl.replace(/\/api$/, "");
 }

 function formatError(err: unknown): string {
@@ -101,19 +146,20 @@ function maybeEnableUiDevMiddleware(entrypoint: string): void {
  }
 }

-async function importServerEntry(): Promise<void> {
+async function importServerEntry(): Promise<StartedServer> {
  // Dev mode: try local workspace path (monorepo with tsx)
  const projectRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "../../..");
  const devEntry = path.resolve(projectRoot, "server/src/index.ts");
  if (fs.existsSync(devEntry)) {
    maybeEnableUiDevMiddleware(devEntry);
-    await import(pathToFileURL(devEntry).href);
-    return;
+    const mod = await import(pathToFileURL(devEntry).href);
+    return await startServerFromModule(mod, devEntry);
  }

  // Production mode: import the published @paperclipai/server package
  try {
-    await import("@paperclipai/server");
+    const mod = await import("@paperclipai/server");
+    return await startServerFromModule(mod, "@paperclipai/server");
  } catch (err) {
    const missingSpecifier = getMissingModuleSpecifier(err);
    const missingServerEntrypoint = !missingSpecifier || missingSpecifier === "@paperclipai/server";
@@ -130,3 +176,15 @@ async function importServerEntry(): Promise<void> {
    );
  }
 }
+
+function shouldGenerateBootstrapInviteAfterStart(config: PaperclipConfig): boolean {
+  return config.server.deploymentMode === "authenticated" && config.database.mode === "embedded-postgres";
+}
+
+async function startServerFromModule(mod: unknown, label: string): Promise<StartedServer> {
+  const startServer = (mod as { startServer?: () => Promise<StartedServer> }).startServer;
+  if (typeof startServer !== "function") {
+    throw new Error(`Paperclip server entrypoint did not export startServer(): ${label}`);
+  }
+  return await startServer();
+}
--- a/cli/src/commands/worktree-lib.ts
+++ b/cli/src/commands/worktree-lib.ts
@@ -0,0 +1,274 @@
+import { randomInt } from "node:crypto";
+import path from "node:path";
+import type { PaperclipConfig } from "../config/schema.js";
+import { expandHomePrefix } from "../config/home.js";
+
+export const DEFAULT_WORKTREE_HOME = "~/.paperclip-worktrees";
+export const WORKTREE_SEED_MODES = ["minimal", "full"] as const;
+
+export type WorktreeSeedMode = (typeof WORKTREE_SEED_MODES)[number];
+
+export type WorktreeSeedPlan = {
+  mode: WorktreeSeedMode;
+  excludedTables: string[];
+  nullifyColumns: Record<string, string[]>;
+};
+
+const MINIMAL_WORKTREE_EXCLUDED_TABLES = [
+  "activity_log",
+  "agent_runtime_state",
+  "agent_task_sessions",
+  "agent_wakeup_requests",
+  "cost_events",
+  "heartbeat_run_events",
+  "heartbeat_runs",
+  "workspace_runtime_services",
+];
+
+const MINIMAL_WORKTREE_NULLIFIED_COLUMNS: Record<string, string[]> = {
+  issues: ["checkout_run_id", "execution_run_id"],
+};
+
+export type WorktreeLocalPaths = {
+  cwd: string;
+  repoConfigDir: string;
+  configPath: string;
+  envPath: string;
+  homeDir: string;
+  instanceId: string;
+  instanceRoot: string;
+  contextPath: string;
+  embeddedPostgresDataDir: string;
+  backupDir: string;
+  logDir: string;
+  secretsKeyFilePath: string;
+  storageDir: string;
+};
+
+export type WorktreeUiBranding = {
+  name: string;
+  color: string;
+};
+
+export function isWorktreeSeedMode(value: string): value is WorktreeSeedMode {
+  return (WORKTREE_SEED_MODES as readonly string[]).includes(value);
+}
+
+export function resolveWorktreeSeedPlan(mode: WorktreeSeedMode): WorktreeSeedPlan {
+  if (mode === "full") {
+    return {
+      mode,
+      excludedTables: [],
+      nullifyColumns: {},
+    };
+  }
+  return {
+    mode,
+    excludedTables: [...MINIMAL_WORKTREE_EXCLUDED_TABLES],
+    nullifyColumns: {
+      ...MINIMAL_WORKTREE_NULLIFIED_COLUMNS,
+    },
+  };
+}
+
+function nonEmpty(value: string | null | undefined): string | null {
+  return typeof value === "string" && value.trim().length > 0 ? value.trim() : null;
+}
+
+function isLoopbackHost(hostname: string): boolean {
+  const value = hostname.trim().toLowerCase();
+  return value === "127.0.0.1" || value === "localhost" || value === "::1";
+}
+
+export function sanitizeWorktreeInstanceId(rawValue: string): string {
+  const trimmed = rawValue.trim().toLowerCase();
+  const normalized = trimmed
+    .replace(/[^a-z0-9_-]+/g, "-")
+    .replace(/-+/g, "-")
+    .replace(/^[-_]+|[-_]+$/g, "");
+  return normalized || "worktree";
+}
+
+export function resolveSuggestedWorktreeName(cwd: string, explicitName?: string): string {
+  return nonEmpty(explicitName) ?? path.basename(path.resolve(cwd));
+}
+
+function hslComponentToHex(n: number): string {
+  return Math.round(Math.max(0, Math.min(255, n)))
+    .toString(16)
+    .padStart(2, "0");
+}
+
+function hslToHex(hue: number, saturation: number, lightness: number): string {
+  const s = Math.max(0, Math.min(100, saturation)) / 100;
+  const l = Math.max(0, Math.min(100, lightness)) / 100;
+  const c = (1 - Math.abs((2 * l) - 1)) * s;
+  const h = ((hue % 360) + 360) % 360;
+  const x = c * (1 - Math.abs(((h / 60) % 2) - 1));
+  const m = l - (c / 2);
+
+  let r = 0;
+  let g = 0;
+  let b = 0;
+
+  if (h < 60) {
+    r = c;
+    g = x;
+  } else if (h < 120) {
+    r = x;
+    g = c;
+  } else if (h < 180) {
+    g = c;
+    b = x;
+  } else if (h < 240) {
+    g = x;
+    b = c;
+  } else if (h < 300) {
+    r = x;
+    b = c;
+  } else {
+    r = c;
+    b = x;
+  }
+
+  return `#${hslComponentToHex((r + m) * 255)}${hslComponentToHex((g + m) * 255)}${hslComponentToHex((b + m) * 255)}`;
+}
+
+export function generateWorktreeColor(): string {
+  return hslToHex(randomInt(0, 360), 68, 56);
+}
+
+export function resolveWorktreeLocalPaths(opts: {
+  cwd: string;
+  homeDir?: string;
+  instanceId: string;
+}): WorktreeLocalPaths {
+  const cwd = path.resolve(opts.cwd);
+  const homeDir = path.resolve(expandHomePrefix(opts.homeDir ?? DEFAULT_WORKTREE_HOME));
+  const instanceRoot = path.resolve(homeDir, "instances", opts.instanceId);
+  const repoConfigDir = path.resolve(cwd, ".paperclip");
+  return {
+    cwd,
+    repoConfigDir,
+    configPath: path.resolve(repoConfigDir, "config.json"),
+    envPath: path.resolve(repoConfigDir, ".env"),
+    homeDir,
+    instanceId: opts.instanceId,
+    instanceRoot,
+    contextPath: path.resolve(homeDir, "context.json"),
+    embeddedPostgresDataDir: path.resolve(instanceRoot, "db"),
+    backupDir: path.resolve(instanceRoot, "data", "backups"),
+    logDir: path.resolve(instanceRoot, "logs"),
+    secretsKeyFilePath: path.resolve(instanceRoot, "secrets", "master.key"),
+    storageDir: path.resolve(instanceRoot, "data", "storage"),
+  };
+}
+
+export function rewriteLocalUrlPort(rawUrl: string | undefined, port: number): string | undefined {
+  if (!rawUrl) return undefined;
+  try {
+    const parsed = new URL(rawUrl);
+    if (!isLoopbackHost(parsed.hostname)) return rawUrl;
+    parsed.port = String(port);
+    return parsed.toString();
+  } catch {
+    return rawUrl;
+  }
+}
+
+export function buildWorktreeConfig(input: {
+  sourceConfig: PaperclipConfig | null;
+  paths: WorktreeLocalPaths;
+  serverPort: number;
+  databasePort: number;
+  now?: Date;
+}): PaperclipConfig {
+  const { sourceConfig, paths, serverPort, databasePort } = input;
+  const nowIso = (input.now ?? new Date()).toISOString();
+
+  const source = sourceConfig;
+  const authPublicBaseUrl = rewriteLocalUrlPort(source?.auth.publicBaseUrl, serverPort);
+
+  return {
+    $meta: {
+      version: 1,
+      updatedAt: nowIso,
+      source: "configure",
+    },
+    ...(source?.llm ? { llm: source.llm } : {}),
+    database: {
+      mode: "embedded-postgres",
+      embeddedPostgresDataDir: paths.embeddedPostgresDataDir,
+      embeddedPostgresPort: databasePort,
+      backup: {
+        enabled: source?.database.backup.enabled ?? true,
+        intervalMinutes: source?.database.backup.intervalMinutes ?? 60,
+        retentionDays: source?.database.backup.retentionDays ?? 30,
+        dir: paths.backupDir,
+      },
+    },
+    logging: {
+      mode: source?.logging.mode ?? "file",
+      logDir: paths.logDir,
+    },
+    server: {
+      deploymentMode: source?.server.deploymentMode ?? "local_trusted",
+      exposure: source?.server.exposure ?? "private",
+      host: source?.server.host ?? "127.0.0.1",
+      port: serverPort,
+      allowedHostnames: source?.server.allowedHostnames ?? [],
+      serveUi: source?.server.serveUi ?? true,
+    },
+    auth: {
+      baseUrlMode: source?.auth.baseUrlMode ?? "auto",
+      ...(authPublicBaseUrl ? { publicBaseUrl: authPublicBaseUrl } : {}),
+      disableSignUp: source?.auth.disableSignUp ?? false,
+    },
+    storage: {
+      provider: source?.storage.provider ?? "local_disk",
+      localDisk: {
+        baseDir: paths.storageDir,
+      },
+      s3: {
+        bucket: source?.storage.s3.bucket ?? "paperclip",
+        region: source?.storage.s3.region ?? "us-east-1",
+        endpoint: source?.storage.s3.endpoint,
+        prefix: source?.storage.s3.prefix ?? "",
+        forcePathStyle: source?.storage.s3.forcePathStyle ?? false,
+      },
+    },
+    secrets: {
+      provider: source?.secrets.provider ?? "local_encrypted",
+      strictMode: source?.secrets.strictMode ?? false,
+      localEncrypted: {
+        keyFilePath: paths.secretsKeyFilePath,
+      },
+    },
+  };
+}
+
+export function buildWorktreeEnvEntries(
+  paths: WorktreeLocalPaths,
+  branding?: WorktreeUiBranding,
+): Record<string, string> {
+  return {
+    PAPERCLIP_HOME: paths.homeDir,
+    PAPERCLIP_INSTANCE_ID: paths.instanceId,
+    PAPERCLIP_CONFIG: paths.configPath,
+    PAPERCLIP_CONTEXT: paths.contextPath,
+    PAPERCLIP_IN_WORKTREE: "true",
+    ...(branding?.name ? { PAPERCLIP_WORKTREE_NAME: branding.name } : {}),
+    ...(branding?.color ? { PAPERCLIP_WORKTREE_COLOR: branding.color } : {}),
+  };
+}
+
+function shellEscape(value: string): string {
+  return `'${value.replaceAll("'", `'\"'\"'`)}'`;
+}
+
+export function formatShellExports(entries: Record<string, string>): string {
+  return Object.entries(entries)
+    .filter(([, value]) => typeof value === "string" && value.trim().length > 0)
+    .map(([key, value]) => `export ${key}=${shellEscape(value)}`)
+    .join("\n");
+}
--- a/cli/src/commands/worktree.ts
+++ b/cli/src/commands/worktree.ts
--- a/cli/src/config/env.ts
+++ b/cli/src/config/env.ts
@@ -22,20 +22,35 @@ function parseEnvFile(contents: string) {
  }
 }

+function formatEnvValue(value: string): string {
+  if (/^[A-Za-z0-9_./:@-]+$/.test(value)) {
+    return value;
+  }
+  return JSON.stringify(value);
+}
+
 function renderEnvFile(entries: Record<string, string>) {
  const lines = [
    "# Paperclip environment variables",
-    "# Generated by `paperclipai onboard`",
-    ...Object.entries(entries).map(([key, value]) => `${key}=${value}`),
+    "# Generated by Paperclip CLI commands",
+    ...Object.entries(entries).map(([key, value]) => `${key}=${formatEnvValue(value)}`),
    "",
  ];
  return lines.join("\n");
 }

+export function resolvePaperclipEnvFile(configPath?: string): string {
+  return resolveEnvFilePath(configPath);
+}
+
 export function resolveAgentJwtEnvFile(configPath?: string): string {
  return resolveEnvFilePath(configPath);
 }

+export function loadPaperclipEnvFile(configPath?: string): void {
+  loadAgentJwtEnvFile(resolveEnvFilePath(configPath));
+}
+
 export function loadAgentJwtEnvFile(filePath = resolveEnvFilePath()): void {
  if (loadedEnvFiles.has(filePath)) return;

@@ -78,13 +93,33 @@ export function ensureAgentJwtSecret(configPath?: string): { secret: string; cre
 }

 export function writeAgentJwtEnv(secret: string, filePath = resolveEnvFilePath()): void {
+  mergePaperclipEnvEntries({ [JWT_SECRET_ENV_KEY]: secret }, filePath);
+}
+
+export function readPaperclipEnvEntries(filePath = resolveEnvFilePath()): Record<string, string> {
+  if (!fs.existsSync(filePath)) return {};
+  return parseEnvFile(fs.readFileSync(filePath, "utf-8"));
+}
+
+export function writePaperclipEnvEntries(entries: Record<string, string>, filePath = resolveEnvFilePath()): void {
  const dir = path.dirname(filePath);
  fs.mkdirSync(dir, { recursive: true });
-
-  const current = fs.existsSync(filePath) ? parseEnvFile(fs.readFileSync(filePath, "utf-8")) : {};
-  current[JWT_SECRET_ENV_KEY] = secret;
-
-  fs.writeFileSync(filePath, renderEnvFile(current), {
+  fs.writeFileSync(filePath, renderEnvFile(entries), {
    mode: 0o600,
  });
 }
+
+export function mergePaperclipEnvEntries(
+  entries: Record<string, string>,
+  filePath = resolveEnvFilePath(),
+): Record<string, string> {
+  const current = readPaperclipEnvEntries(filePath);
+  const next = {
+    ...current,
+    ...Object.fromEntries(
+      Object.entries(entries).filter(([, value]) => typeof value === "string" && value.trim().length > 0),
+    ),
+  };
+  writePaperclipEnvEntries(next, filePath);
+  return next;
+}
--- a/cli/src/index.ts
+++ b/cli/src/index.ts
@@ -16,6 +16,9 @@ import { registerApprovalCommands } from "./commands/client/approval.js";
 import { registerActivityCommands } from "./commands/client/activity.js";
 import { registerDashboardCommands } from "./commands/client/dashboard.js";
 import { applyDataDirOverride, type DataDirOptionLike } from "./config/data-dir.js";
+import { loadPaperclipEnvFile } from "./config/env.js";
+import { registerWorktreeCommands } from "./commands/worktree.js";
+import { registerPluginCommands } from "./commands/client/plugin.js";

 const program = new Command();
 const DATA_DIR_OPTION_HELP =
@@ -33,6 +36,7 @@ program.hook("preAction", (_thisCommand, actionCommand) => {
    hasConfigOption: optionNames.has("config"),
    hasContextOption: optionNames.has("context"),
  });
+  loadPaperclipEnvFile(options.config);
 });

 program
@@ -132,6 +136,8 @@ registerAgentCommands(program);
 registerApprovalCommands(program);
 registerActivityCommands(program);
 registerDashboardCommands(program);
+registerWorktreeCommands(program);
+registerPluginCommands(program);

 const auth = program.command("auth").description("Authentication and bootstrap utilities");

--- a/cli/src/prompts/server.ts
+++ b/cli/src/prompts/server.ts
@@ -113,7 +113,7 @@ export async function promptServer(opts?: {
  }

  const port = Number(portStr) || 3100;
-  let auth: AuthConfig = { baseUrlMode: "auto" };
+  let auth: AuthConfig = { baseUrlMode: "auto", disableSignUp: false };
  if (deploymentMode === "authenticated" && exposure === "public") {
    const urlInput = await p.text({
      message: "Public base URL",
@@ -139,11 +139,13 @@ export async function promptServer(opts?: {
    }
    auth = {
      baseUrlMode: "explicit",
+      disableSignUp: false,
      publicBaseUrl: urlInput.trim().replace(/\/+$/, ""),
    };
  } else if (currentAuth?.baseUrlMode === "explicit" && currentAuth.publicBaseUrl) {
    auth = {
      baseUrlMode: "explicit",
+      disableSignUp: false,
      publicBaseUrl: currentAuth.publicBaseUrl,
    };
  }
@@ -160,4 +162,3 @@ export async function promptServer(opts?: {
    auth,
  };
 }
-
--- a/cli/tsconfig.json
+++ b/cli/tsconfig.json
@@ -1,5 +1,5 @@
 {
-  "extends": "../tsconfig.json",
+  "extends": "../tsconfig.base.json",
  "compilerOptions": {
    "outDir": "dist",
    "rootDir": "src"