cli/src/__tests__/worktree.test.ts

import fs from "node:fs";
import os from "node:os";
import path from "node:path";
import { execFileSync } from "node:child_process";
import { randomUUID } from "node:crypto";
import { eq } from "drizzle-orm";
import { afterEach, describe, expect, it, vi } from "vitest";
import {
  agents,
  authUsers,
  companies,
  createDb,
  issueComments,
  issues,
  projects,
  routines,
  routineTriggers,
} from "@penclipai/db";
import {
  copyGitHooksToWorktreeGitDir,
  copySeededSecretsKey,
  pauseSeededScheduledRoutines,
  quarantineSeededWorktreeExecutionState,
  readSourceAttachmentBody,
  rebindWorkspaceCwd,
  resolveSourceConfigPath,
  resolveWorktreeReseedSource,
  resolveWorktreeReseedTargetPaths,
  resolveGitWorktreeAddArgs,
  resolveWorktreeMakeTargetPath,
  worktreeRepairCommand,
  worktreeInitCommand,
  worktreeMakeCommand,
  worktreeReseedCommand,
} 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";
import {
  getEmbeddedPostgresTestSupport,
  startEmbeddedPostgresTestDatabase,
} from "./helpers/embedded-postgres.js";

const ORIGINAL_CWD = process.cwd();
const ORIGINAL_ENV = { ...process.env };
const embeddedPostgresSupport = await getEmbeddedPostgresTestSupport();
const itEmbeddedPostgres = embeddedPostgresSupport.supported ? it : it.skip;
const describeEmbeddedPostgres = embeddedPostgresSupport.supported ? describe : describe.skip;

if (!embeddedPostgresSupport.supported) {
  console.warn(
    `Skipping embedded Postgres worktree CLI tests on this host: ${embeddedPostgresSupport.reason ?? "unsupported environment"}`,
  );
}

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,
    },
    telemetry: {
      enabled: true,
    },
    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("falls back across storage roots before skipping a missing attachment object", async () => {
    const missingErr = Object.assign(new Error("missing"), { code: "ENOENT" });
    const expected = Buffer.from("image-bytes");
    await expect(
      readSourceAttachmentBody(
        [
          {
            getObject: vi.fn().mockRejectedValue(missingErr),
          },
          {
            getObject: vi.fn().mockResolvedValue(expected),
          },
        ],
        "company-1",
        "company-1/issues/issue-1/missing.png",
      ),
    ).resolves.toEqual(expected);
  });

  it("returns null when an attachment object is missing from every lookup storage", async () => {
    const missingErr = Object.assign(new Error("missing"), { code: "ENOENT" });
    await expect(
      readSourceAttachmentBody(
        [
          {
            getObject: vi.fn().mockRejectedValue(missingErr),
          },
          {
            getObject: vi.fn().mockRejectedValue(Object.assign(new Error("missing"), { status: 404 })),
          },
        ],
        "company-1",
        "company-1/issues/issue-1/missing.png",
      ),
    ).resolves.toBeNull();
  });

  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({});
  });

  itEmbeddedPostgres("quarantines copied live execution state in seeded worktree databases", async () => {
    const tempDb = await startEmbeddedPostgresTestDatabase("paperclip-worktree-quarantine-");
    const db = createDb(tempDb.connectionString);
    const companyId = randomUUID();
    const agentId = randomUUID();
    const idleAgentId = randomUUID();
    const inProgressIssueId = randomUUID();
    const todoIssueId = randomUUID();
    const reviewIssueId = randomUUID();
    const userIssueId = randomUUID();

    try {
      await db.insert(companies).values({
        id: companyId,
        name: "Paperclip",
        issuePrefix: "WTQ",
        requireBoardApprovalForNewAgents: false,
      });
      await db.insert(agents).values([
        {
          id: agentId,
          companyId,
          name: "CodexCoder",
          role: "engineer",
          status: "running",
          adapterType: "codex_local",
          adapterConfig: {},
          runtimeConfig: {
            heartbeat: { enabled: true, intervalSec: 60 },
            wakeOnDemand: true,
          },
          permissions: {},
        },
        {
          id: idleAgentId,
          companyId,
          name: "Reviewer",
          role: "reviewer",
          status: "idle",
          adapterType: "codex_local",
          adapterConfig: {},
          runtimeConfig: { heartbeat: { enabled: false, intervalSec: 300 } },
          permissions: {},
        },
      ]);
      await db.insert(issues).values([
        {
          id: inProgressIssueId,
          companyId,
          title: "Copied in-flight issue",
          status: "in_progress",
          priority: "medium",
          assigneeAgentId: agentId,
          issueNumber: 1,
          identifier: "WTQ-1",
          executionAgentNameKey: "codexcoder",
          executionLockedAt: new Date("2026-04-18T00:00:00.000Z"),
        },
        {
          id: todoIssueId,
          companyId,
          title: "Copied assigned todo issue",
          status: "todo",
          priority: "medium",
          assigneeAgentId: agentId,
          issueNumber: 2,
          identifier: "WTQ-2",
        },
        {
          id: reviewIssueId,
          companyId,
          title: "Copied assigned review issue",
          status: "in_review",
          priority: "medium",
          assigneeAgentId: idleAgentId,
          issueNumber: 3,
          identifier: "WTQ-3",
        },
        {
          id: userIssueId,
          companyId,
          title: "Copied user issue",
          status: "todo",
          priority: "medium",
          assigneeUserId: "user-1",
          issueNumber: 4,
          identifier: "WTQ-4",
        },
      ]);

      await expect(quarantineSeededWorktreeExecutionState(tempDb.connectionString)).resolves.toEqual({
        disabledTimerHeartbeats: 1,
        resetRunningAgents: 1,
        quarantinedInProgressIssues: 1,
        unassignedTodoIssues: 1,
        unassignedReviewIssues: 1,
      });

      const [quarantinedAgent] = await db.select().from(agents).where(eq(agents.id, agentId));
      expect(quarantinedAgent?.status).toBe("idle");
      expect(quarantinedAgent?.runtimeConfig).toMatchObject({
        heartbeat: { enabled: false, intervalSec: 60 },
        wakeOnDemand: true,
      });

      const [inProgressIssue] = await db.select().from(issues).where(eq(issues.id, inProgressIssueId));
      expect(inProgressIssue?.status).toBe("blocked");
      expect(inProgressIssue?.assigneeAgentId).toBeNull();
      expect(inProgressIssue?.executionAgentNameKey).toBeNull();
      expect(inProgressIssue?.executionLockedAt).toBeNull();

      const [todoIssue] = await db.select().from(issues).where(eq(issues.id, todoIssueId));
      expect(todoIssue?.status).toBe("todo");
      expect(todoIssue?.assigneeAgentId).toBeNull();

      const [reviewIssue] = await db.select().from(issues).where(eq(issues.id, reviewIssueId));
      expect(reviewIssue?.status).toBe("in_review");
      expect(reviewIssue?.assigneeAgentId).toBeNull();

      const [userIssue] = await db.select().from(issues).where(eq(issues.id, userIssueId));
      expect(userIssue?.status).toBe("todo");
      expect(userIssue?.assigneeUserId).toBe("user-1");

      const comments = await db.select().from(issueComments).where(eq(issueComments.issueId, inProgressIssueId));
      expect(comments).toHaveLength(1);
      expect(comments[0]?.body).toContain("Quarantined during worktree seed");
    } finally {
      await db.$client?.end?.({ timeout: 5 }).catch(() => undefined);
      await tempDb.cleanup();
    }
  }, 20_000);

  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 });
    }
  }, 15_000);

  itEmbeddedPostgres(
    "seeds authenticated users into minimally cloned worktree instances",
    async () => {
      const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-auth-seed-"));
      const worktreeRoot = path.join(tempRoot, "PAP-999-auth-seed");
      const sourceHome = path.join(tempRoot, "source-home");
      const sourceConfigDir = path.join(sourceHome, "instances", "source");
      const sourceConfigPath = path.join(sourceConfigDir, "config.json");
      const sourceEnvPath = path.join(sourceConfigDir, ".env");
      const sourceKeyPath = path.join(sourceConfigDir, "secrets", "master.key");
      const worktreeHome = path.join(tempRoot, ".paperclip-worktrees");
      const originalCwd = process.cwd();
      const sourceDb = await startEmbeddedPostgresTestDatabase("paperclip-worktree-auth-source-");

      try {
        const sourceDbClient = createDb(sourceDb.connectionString);
        await sourceDbClient.insert(authUsers).values({
          id: "user-existing",
          email: "existing@paperclip.ing",
          name: "Existing User",
          emailVerified: true,
          createdAt: new Date(),
          updatedAt: new Date(),
        });

        fs.mkdirSync(path.dirname(sourceKeyPath), { recursive: true });
        fs.mkdirSync(worktreeRoot, { recursive: true });

        const sourceConfig = buildSourceConfig();
        sourceConfig.database = {
          mode: "postgres",
          embeddedPostgresDataDir: path.join(sourceConfigDir, "db"),
          embeddedPostgresPort: 54329,
          backup: {
            enabled: true,
            intervalMinutes: 60,
            retentionDays: 30,
            dir: path.join(sourceConfigDir, "backups"),
          },
          connectionString: sourceDb.connectionString,
        };
        sourceConfig.logging.logDir = path.join(sourceConfigDir, "logs");
        sourceConfig.storage.localDisk.baseDir = path.join(sourceConfigDir, "storage");
        sourceConfig.secrets.localEncrypted.keyFilePath = sourceKeyPath;

        fs.writeFileSync(sourceConfigPath, JSON.stringify(sourceConfig, null, 2) + "\n", "utf8");
        fs.writeFileSync(sourceEnvPath, "", "utf8");
        fs.writeFileSync(sourceKeyPath, "source-master-key", "utf8");

        process.chdir(worktreeRoot);
        await worktreeInitCommand({
          name: "PAP-999-auth-seed",
          home: worktreeHome,
          fromConfig: sourceConfigPath,
          force: true,
        });

        const targetConfig = JSON.parse(
          fs.readFileSync(path.join(worktreeRoot, ".paperclip", "config.json"), "utf8"),
        ) as PaperclipConfig;
        const { default: EmbeddedPostgres } = await import("embedded-postgres");
        const targetPg = new EmbeddedPostgres({
          databaseDir: targetConfig.database.embeddedPostgresDataDir,
          user: "paperclip",
          password: "paperclip",
          port: targetConfig.database.embeddedPostgresPort,
          persistent: true,
          initdbFlags: ["--encoding=UTF8", "--locale=C", "--lc-messages=C"],
          onLog: () => {},
          onError: () => {},
        });

        await targetPg.start();
        try {
          const targetDb = createDb(
            `postgres://paperclip:paperclip@127.0.0.1:${targetConfig.database.embeddedPostgresPort}/paperclip`,
          );
          const seededUsers = await targetDb.select().from(authUsers);
          expect(seededUsers.some((row) => row.email === "existing@paperclip.ing")).toBe(true);
        } finally {
          await targetPg.stop();
        }
      } finally {
        process.chdir(originalCwd);
        await sourceDb.cleanup();
        fs.rmSync(tempRoot, { recursive: true, force: true });
      }
    },
    60_000,
  );

  it("avoids ports already claimed by sibling worktree instance configs", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-claimed-ports-"));
    const repoRoot = path.join(tempRoot, "repo");
    const homeDir = path.join(tempRoot, ".paperclip-worktrees");
    const siblingInstanceRoot = path.join(homeDir, "instances", "existing-worktree");
    const originalCwd = process.cwd();

    try {
      fs.mkdirSync(repoRoot, { recursive: true });
      fs.mkdirSync(siblingInstanceRoot, { recursive: true });
      fs.writeFileSync(
        path.join(siblingInstanceRoot, "config.json"),
        JSON.stringify(
          {
            ...buildSourceConfig(),
            database: {
              mode: "embedded-postgres",
              embeddedPostgresDataDir: path.join(siblingInstanceRoot, "db"),
              embeddedPostgresPort: 54330,
              backup: {
                enabled: true,
                intervalMinutes: 60,
                retentionDays: 30,
                dir: path.join(siblingInstanceRoot, "backups"),
              },
            },
            logging: {
              mode: "file",
              logDir: path.join(siblingInstanceRoot, "logs"),
            },
            server: {
              deploymentMode: "authenticated",
              exposure: "private",
              host: "127.0.0.1",
              port: 3101,
              allowedHostnames: ["localhost"],
              serveUi: true,
            },
            storage: {
              provider: "local_disk",
              localDisk: {
                baseDir: path.join(siblingInstanceRoot, "storage"),
              },
              s3: {
                bucket: "paperclip",
                region: "us-east-1",
                prefix: "",
                forcePathStyle: false,
              },
            },
            secrets: {
              provider: "local_encrypted",
              strictMode: false,
              localEncrypted: {
                keyFilePath: path.join(siblingInstanceRoot, "secrets", "master.key"),
              },
            },
          },
          null,
          2,
        ) + "\n",
      );

      process.chdir(repoRoot);
      await worktreeInitCommand({
        seed: false,
        fromConfig: path.join(tempRoot, "missing", "config.json"),
        home: homeDir,
      });

      const config = JSON.parse(fs.readFileSync(path.join(repoRoot, ".paperclip", "config.json"), "utf8"));
      expect(config.server.port).toBeGreaterThan(3101);
      expect(config.database.embeddedPostgresPort).not.toBe(54330);
      expect(config.database.embeddedPostgresPort).not.toBe(config.server.port);
      expect(config.database.embeddedPostgresPort).toBeGreaterThan(54330);
    } finally {
      process.chdir(originalCwd);
      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("requires an explicit reseed source", () => {
    expect(() => resolveWorktreeReseedSource({})).toThrow(
      "Pass --from <worktree> or --from-config/--from-instance explicitly so the reseed source is unambiguous.",
    );
  });

  it("rejects mixed reseed source selectors", () => {
    expect(() => resolveWorktreeReseedSource({
      from: "current",
      fromInstance: "default",
    })).toThrow(
      "Use either --from <worktree> or --from-config/--from-data-dir/--from-instance, not both.",
    );
  });

  it("derives worktree reseed target paths from the adjacent env file", () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-target-"));
    const worktreeRoot = path.join(tempRoot, "repo");
    const configPath = path.join(worktreeRoot, ".paperclip", "config.json");
    const envPath = path.join(worktreeRoot, ".paperclip", ".env");

    try {
      fs.mkdirSync(path.dirname(configPath), { recursive: true });
      fs.writeFileSync(configPath, JSON.stringify(buildSourceConfig()), "utf8");
      fs.writeFileSync(
        envPath,
        [
          "PAPERCLIP_HOME=/tmp/paperclip-worktrees",
          "PAPERCLIP_INSTANCE_ID=pap-1132-chat",
        ].join("\n"),
        "utf8",
      );
      expect(
        resolveWorktreeReseedTargetPaths({
          configPath,
          rootPath: worktreeRoot,
        }),
      ).toMatchObject({
        cwd: worktreeRoot,
        homeDir: path.resolve("/tmp/paperclip-worktrees"),
        instanceId: "pap-1132-chat",
      });
    } finally {
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  });

  it("rejects reseed targets without worktree env metadata", () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-target-missing-"));
    const worktreeRoot = path.join(tempRoot, "repo");
    const configPath = path.join(worktreeRoot, ".paperclip", "config.json");

    try {
      fs.mkdirSync(path.dirname(configPath), { recursive: true });
      fs.writeFileSync(configPath, JSON.stringify(buildSourceConfig()), "utf8");
      fs.writeFileSync(path.join(worktreeRoot, ".paperclip", ".env"), "", "utf8");

      expect(() =>
        resolveWorktreeReseedTargetPaths({
          configPath,
          rootPath: worktreeRoot,
        })).toThrow("does not look like a worktree-local Paperclip instance");
    } finally {
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  });

  it("fails loudly when an explicit embedded-postgres reseed source has no data directory", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-missing-source-"));
    const repoRoot = path.join(tempRoot, "repo");
    const sourceRoot = path.join(tempRoot, "source");
    const homeDir = path.join(tempRoot, ".paperclip-worktrees");
    const currentInstanceId = "existing-worktree";
    const currentPaths = resolveWorktreeLocalPaths({
      cwd: repoRoot,
      homeDir,
      instanceId: currentInstanceId,
    });
    const sourcePaths = resolveWorktreeLocalPaths({
      cwd: sourceRoot,
      homeDir: path.join(tempRoot, ".paperclip-source"),
      instanceId: "default",
    });
    const originalCwd = process.cwd();
    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;

    try {
      fs.mkdirSync(path.dirname(currentPaths.configPath), { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.configPath), { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.secretsKeyFilePath), { recursive: true });
      fs.mkdirSync(repoRoot, { recursive: true });
      fs.mkdirSync(sourceRoot, { recursive: true });

      const currentConfig = buildWorktreeConfig({
        sourceConfig: buildSourceConfig(),
        paths: currentPaths,
        serverPort: 3114,
        databasePort: 54341,
      });
      const sourceConfig = buildWorktreeConfig({
        sourceConfig: buildSourceConfig(),
        paths: sourcePaths,
        serverPort: 3200,
        databasePort: 54400,
      });
      fs.writeFileSync(currentPaths.configPath, JSON.stringify(currentConfig, null, 2), "utf8");
      fs.writeFileSync(
        currentPaths.envPath,
        [
          `PAPERCLIP_HOME=${homeDir}`,
          `PAPERCLIP_INSTANCE_ID=${currentInstanceId}`,
        ].join("\n"),
        "utf8",
      );
      fs.writeFileSync(sourcePaths.configPath, JSON.stringify(sourceConfig, null, 2), "utf8");
      fs.writeFileSync(sourcePaths.secretsKeyFilePath, "source-secret", "utf8");

      delete process.env.PAPERCLIP_CONFIG;
      process.chdir(repoRoot);

      await expect(worktreeReseedCommand({
        fromConfig: sourcePaths.configPath,
        yes: true,
      })).rejects.toThrow("has no data directory");
    } 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("worktree init with --no-seed preserves the current worktree identity and keeps or safely bumps the db port", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-"));
    const repoRoot = path.join(tempRoot, "repo");
    const sourceRoot = path.join(tempRoot, "source");
    const homeDir = path.join(tempRoot, ".paperclip-worktrees");
    const currentInstanceId = "existing-worktree";
    const currentPaths = resolveWorktreeLocalPaths({
      cwd: repoRoot,
      homeDir,
      instanceId: currentInstanceId,
    });
    const sourcePaths = resolveWorktreeLocalPaths({
      cwd: sourceRoot,
      homeDir: path.join(tempRoot, ".paperclip-source"),
      instanceId: "default",
    });
    const originalCwd = process.cwd();
    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;

    try {
      fs.mkdirSync(path.dirname(currentPaths.configPath), { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.configPath), { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.secretsKeyFilePath), { recursive: true });
      fs.mkdirSync(repoRoot, { recursive: true });
      fs.mkdirSync(sourceRoot, { recursive: true });

      const currentConfig = buildWorktreeConfig({
        sourceConfig: buildSourceConfig(),
        paths: currentPaths,
        serverPort: 3114,
        databasePort: 54341,
      });
      const sourceConfig = buildWorktreeConfig({
        sourceConfig: buildSourceConfig(),
        paths: sourcePaths,
        serverPort: 3200,
        databasePort: 54400,
      });
      fs.writeFileSync(currentPaths.configPath, JSON.stringify(currentConfig, null, 2), "utf8");
      fs.writeFileSync(sourcePaths.configPath, JSON.stringify(sourceConfig, null, 2), "utf8");
      fs.writeFileSync(sourcePaths.secretsKeyFilePath, "source-secret", "utf8");
      fs.writeFileSync(
        currentPaths.envPath,
        [
          `PAPERCLIP_HOME=${homeDir}`,
          `PAPERCLIP_INSTANCE_ID=${currentInstanceId}`,
          "PAPERCLIP_WORKTREE_NAME=existing-name",
          "PAPERCLIP_WORKTREE_COLOR=\"#112233\"",
        ].join("\n"),
        "utf8",
      );

      delete process.env.PAPERCLIP_CONFIG;
      process.chdir(repoRoot);

      await worktreeInitCommand({
        name: "existing-name",
        color: "#112233",
        instance: currentInstanceId,
        home: homeDir,
        fromConfig: sourcePaths.configPath,
        serverPort: 3114,
        dbPort: 54341,
        seed: false,
        force: true,
      });

      const rewrittenConfig = JSON.parse(fs.readFileSync(currentPaths.configPath, "utf8"));
      const rewrittenEnv = fs.readFileSync(currentPaths.envPath, "utf8");

      expect(rewrittenConfig.server.port).toBe(3114);
      expect(rewrittenConfig.database.embeddedPostgresPort).toBeGreaterThanOrEqual(54341);
      expect(rewrittenConfig.database.embeddedPostgresPort).not.toBe(rewrittenConfig.server.port);
      expect(rewrittenConfig.database.embeddedPostgresDataDir).toBe(currentPaths.embeddedPostgresDataDir);
      expect(rewrittenEnv).toContain(`PAPERCLIP_INSTANCE_ID=${currentInstanceId}`);
      expect(rewrittenEnv).toContain("PAPERCLIP_WORKTREE_NAME=existing-name");
      expect(rewrittenEnv).toContain("PAPERCLIP_WORKTREE_COLOR='#112233'");
    } 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 });
    }
  }, 30_000);

  it("restores the current worktree config and instance data if reseed fails", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-reseed-rollback-"));
    const repoRoot = path.join(tempRoot, "repo");
    const sourceRoot = path.join(tempRoot, "source");
    const homeDir = path.join(tempRoot, ".paperclip-worktrees");
    const currentInstanceId = "rollback-worktree";
    const currentPaths = resolveWorktreeLocalPaths({
      cwd: repoRoot,
      homeDir,
      instanceId: currentInstanceId,
    });
    const sourcePaths = resolveWorktreeLocalPaths({
      cwd: sourceRoot,
      homeDir: path.join(tempRoot, ".paperclip-source"),
      instanceId: "default",
    });
    const originalCwd = process.cwd();
    const originalPaperclipConfig = process.env.PAPERCLIP_CONFIG;

    try {
      fs.mkdirSync(path.dirname(currentPaths.configPath), { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.configPath), { recursive: true });
      fs.mkdirSync(currentPaths.instanceRoot, { recursive: true });
      fs.mkdirSync(path.dirname(sourcePaths.secretsKeyFilePath), { recursive: true });
      fs.mkdirSync(repoRoot, { recursive: true });
      fs.mkdirSync(sourceRoot, { recursive: true });

      const currentConfig = buildWorktreeConfig({
        sourceConfig: buildSourceConfig(),
        paths: currentPaths,
        serverPort: 3114,
        databasePort: 54341,
      });
      const sourceConfig = {
        ...buildSourceConfig(),
        database: {
          mode: "postgres",
          connectionString: "",
        },
        secrets: {
          provider: "local_encrypted",
          strictMode: false,
          localEncrypted: {
            keyFilePath: sourcePaths.secretsKeyFilePath,
          },
        },
      } as PaperclipConfig;

      fs.writeFileSync(currentPaths.configPath, JSON.stringify(currentConfig, null, 2), "utf8");
      fs.writeFileSync(currentPaths.envPath, `PAPERCLIP_HOME=${homeDir}\nPAPERCLIP_INSTANCE_ID=${currentInstanceId}\n`, "utf8");
      fs.writeFileSync(path.join(currentPaths.instanceRoot, "marker.txt"), "keep me", "utf8");
      fs.writeFileSync(sourcePaths.configPath, JSON.stringify(sourceConfig, null, 2), "utf8");
      fs.writeFileSync(sourcePaths.secretsKeyFilePath, "source-secret", "utf8");

      delete process.env.PAPERCLIP_CONFIG;
      process.chdir(repoRoot);

      await expect(worktreeReseedCommand({
        fromConfig: sourcePaths.configPath,
        yes: true,
      })).rejects.toThrow("Source instance uses postgres mode but has no connection string");

      const restoredConfig = JSON.parse(fs.readFileSync(currentPaths.configPath, "utf8"));
      const restoredEnv = fs.readFileSync(currentPaths.envPath, "utf8");
      const restoredMarker = fs.readFileSync(path.join(currentPaths.instanceRoot, "marker.txt"), "utf8");

      expect(restoredConfig.server.port).toBe(3114);
      expect(restoredConfig.database.embeddedPostgresPort).toBe(54341);
      expect(restoredEnv).toContain(`PAPERCLIP_INSTANCE_ID=${currentInstanceId}`);
      expect(restoredMarker).toBe("keep me");
    } 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", () => {
    const targetRepoRoot = path.resolve("/Users/example/paperclip-pr-432");
    expect(
      rebindWorkspaceCwd({
        sourceRepoRoot: "/Users/example/paperclip",
        targetRepoRoot,
        workspaceCwd: "/Users/example/paperclip",
      }),
    ).toBe(targetRepoRoot);

    expect(
      rebindWorkspaceCwd({
        sourceRepoRoot: "/Users/example/paperclip",
        targetRepoRoot,
        workspaceCwd: "/Users/example/paperclip/packages/db",
      }),
    ).toBe(path.resolve(targetRepoRoot, "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");
      const sourceSharedDir = path.join(tempRoot, "shared-hook-data");
      const sourceLinkedDirPath = path.join(sourceHooksDir, "shared-hook-data");
      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");
      fs.mkdirSync(sourceSharedDir, { recursive: true });
      fs.writeFileSync(path.join(sourceSharedDir, "config.txt"), "shared-hook-config\n", "utf8");
      fs.symlinkSync(
        sourceSharedDir,
        sourceLinkedDirPath,
        process.platform === "win32" ? "junction" : "dir",
      );

      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");
      const targetLinkedDirPath = path.join(resolvedTargetHooksDir, "shared-hook-data");

      expect(copied?.copied).toBe(true);
      expect(fs.existsSync(copied!.sourceHooksPath)).toBe(true);
      expect(path.basename(copied!.sourceHooksPath)).toBe("hooks");
      expect(fs.realpathSync(copied!.targetHooksPath)).toBe(resolvedTargetHooksDir);
      expect(fs.readFileSync(targetHookPath, "utf8")).toBe("#!/usr/bin/env bash\nexit 0\n");
      if (process.platform !== "win32") {
        expect(fs.statSync(targetHookPath).mode & 0o111).not.toBe(0);
      }
      expect(fs.readFileSync(targetTokensPath, "utf8")).toBe("secret-token\n");
      expect(fs.realpathSync(targetLinkedDirPath)).toBe(fs.realpathSync(sourceSharedDir));
      expect(fs.readFileSync(path.join(targetLinkedDirPath, "config.txt"), "utf8")).toBe("shared-hook-config\n");
    } finally {
      execFileSync("git", ["worktree", "remove", "--force", worktreePath], { cwd: repoRoot, stdio: "ignore" });
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  }, 15_000);

  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);

  it("no-ops on the primary checkout unless --branch is provided", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-repair-primary-"));
    const repoRoot = path.join(tempRoot, "repo");
    const originalCwd = process.cwd();

    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" });

      process.chdir(repoRoot);
      await worktreeRepairCommand({});

      expect(fs.existsSync(path.join(repoRoot, ".paperclip", "config.json"))).toBe(false);
      expect(fs.existsSync(path.join(repoRoot, ".paperclip", "worktrees"))).toBe(false);
    } finally {
      process.chdir(originalCwd);
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  });

  it("repairs the current linked worktree when Paperclip metadata is missing", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-repair-current-"));
    const repoRoot = path.join(tempRoot, "repo");
    const worktreePath = path.join(repoRoot, ".paperclip", "worktrees", "repair-me");
    const sourceConfigPath = path.join(tempRoot, "source-config.json");
    const worktreeHome = path.join(tempRoot, ".paperclip-worktrees");
    const worktreePaths = resolveWorktreeLocalPaths({
      cwd: worktreePath,
      homeDir: worktreeHome,
      instanceId: sanitizeWorktreeInstanceId(path.basename(worktreePath)),
    });
    const originalCwd = process.cwd();

    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" });
      fs.mkdirSync(path.dirname(worktreePath), { recursive: true });
      execFileSync("git", ["worktree", "add", "-b", "repair-me", worktreePath, "HEAD"], {
        cwd: repoRoot,
        stdio: "ignore",
      });

      fs.writeFileSync(sourceConfigPath, JSON.stringify(buildSourceConfig(), null, 2), "utf8");
      fs.mkdirSync(worktreePaths.instanceRoot, { recursive: true });
      fs.writeFileSync(path.join(worktreePaths.instanceRoot, "marker.txt"), "stale", "utf8");

      process.chdir(worktreePath);
      await worktreeRepairCommand({
        fromConfig: sourceConfigPath,
        home: worktreeHome,
        noSeed: true,
      });

      expect(fs.existsSync(path.join(worktreePath, ".paperclip", "config.json"))).toBe(true);
      expect(fs.existsSync(path.join(worktreePath, ".paperclip", ".env"))).toBe(true);
      expect(fs.existsSync(path.join(worktreePaths.instanceRoot, "marker.txt"))).toBe(false);
    } finally {
      process.chdir(originalCwd);
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  }, 20_000);

  it("creates and repairs a missing branch worktree when --branch is provided", async () => {
    const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-repair-branch-"));
    const repoRoot = path.join(tempRoot, "repo");
    const sourceConfigPath = path.join(tempRoot, "source-config.json");
    const worktreeHome = path.join(tempRoot, ".paperclip-worktrees");
    const originalCwd = process.cwd();
    const expectedWorktreePath = path.join(repoRoot, ".paperclip", "worktrees", "feature-repair-me");

    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" });
      fs.writeFileSync(sourceConfigPath, JSON.stringify(buildSourceConfig(), null, 2), "utf8");

      process.chdir(repoRoot);
      await worktreeRepairCommand({
        branch: "feature/repair-me",
        fromConfig: sourceConfigPath,
        home: worktreeHome,
        noSeed: true,
      });

      expect(fs.existsSync(path.join(expectedWorktreePath, ".git"))).toBe(true);
      expect(fs.existsSync(path.join(expectedWorktreePath, ".paperclip", "config.json"))).toBe(true);
      expect(fs.existsSync(path.join(expectedWorktreePath, ".paperclip", ".env"))).toBe(true);
    } finally {
      process.chdir(originalCwd);
      fs.rmSync(tempRoot, { recursive: true, force: true });
    }
  }, 20_000);
});

describeEmbeddedPostgres("pauseSeededScheduledRoutines", () => {
  it("pauses only routines with enabled schedule triggers", async () => {
    const tempDb = await startEmbeddedPostgresTestDatabase("paperclip-worktree-routines-");
    const db = createDb(tempDb.connectionString);
    const companyId = randomUUID();
    const projectId = randomUUID();
    const agentId = randomUUID();
    const activeScheduledRoutineId = randomUUID();
    const activeApiRoutineId = randomUUID();
    const pausedScheduledRoutineId = randomUUID();
    const archivedScheduledRoutineId = randomUUID();
    const disabledScheduleRoutineId = randomUUID();

    try {
      await db.insert(companies).values({
        id: companyId,
        name: "Paperclip",
        issuePrefix: `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`,
        requireBoardApprovalForNewAgents: false,
      });
      await db.insert(agents).values({
        id: agentId,
        companyId,
        name: "Coder",
        adapterType: "process",
        adapterConfig: {},
        runtimeConfig: {},
        permissions: {},
      });
      await db.insert(projects).values({
        id: projectId,
        companyId,
        name: "Project",
        status: "in_progress",
      });
      await db.insert(routines).values([
        {
          id: activeScheduledRoutineId,
          companyId,
          projectId,
          assigneeAgentId: agentId,
          title: "Active scheduled",
          status: "active",
        },
        {
          id: activeApiRoutineId,
          companyId,
          projectId,
          assigneeAgentId: agentId,
          title: "Active API",
          status: "active",
        },
        {
          id: pausedScheduledRoutineId,
          companyId,
          projectId,
          assigneeAgentId: agentId,
          title: "Paused scheduled",
          status: "paused",
        },
        {
          id: archivedScheduledRoutineId,
          companyId,
          projectId,
          assigneeAgentId: agentId,
          title: "Archived scheduled",
          status: "archived",
        },
        {
          id: disabledScheduleRoutineId,
          companyId,
          projectId,
          assigneeAgentId: agentId,
          title: "Disabled schedule",
          status: "active",
        },
      ]);
      await db.insert(routineTriggers).values([
        {
          companyId,
          routineId: activeScheduledRoutineId,
          kind: "schedule",
          enabled: true,
          cronExpression: "0 9 * * *",
          timezone: "UTC",
        },
        {
          companyId,
          routineId: activeApiRoutineId,
          kind: "api",
          enabled: true,
        },
        {
          companyId,
          routineId: pausedScheduledRoutineId,
          kind: "schedule",
          enabled: true,
          cronExpression: "0 10 * * *",
          timezone: "UTC",
        },
        {
          companyId,
          routineId: archivedScheduledRoutineId,
          kind: "schedule",
          enabled: true,
          cronExpression: "0 11 * * *",
          timezone: "UTC",
        },
        {
          companyId,
          routineId: disabledScheduleRoutineId,
          kind: "schedule",
          enabled: false,
          cronExpression: "0 12 * * *",
          timezone: "UTC",
        },
      ]);

      const pausedCount = await pauseSeededScheduledRoutines(tempDb.connectionString);
      expect(pausedCount).toBe(1);

      const rows = await db.select({ id: routines.id, status: routines.status }).from(routines);
      const statusById = new Map(rows.map((row: { id: string; status: string }) => [row.id, row.status]));
      expect(statusById.get(activeScheduledRoutineId)).toBe("paused");
      expect(statusById.get(activeApiRoutineId)).toBe("active");
      expect(statusById.get(pausedScheduledRoutineId)).toBe("paused");
      expect(statusById.get(archivedScheduledRoutineId)).toBe("archived");
      expect(statusById.get(disabledScheduleRoutineId)).toBe("active");
    } finally {
      await db.$client?.end?.({ timeout: 5 }).catch(() => undefined);
      await tempDb.cleanup();
    }
  }, 20_000);
});