paperclip/cli/src/commands/worktree.ts

import {
  chmodSync,
  copyFileSync,
  existsSync,
  mkdirSync,
  readdirSync,
  readFileSync,
  readlinkSync,
  rmSync,
  statSync,
  symlinkSync,
  writeFileSync,
} from "node:fs";
import os from "node:os";
import path from "node:path";
import { execFileSync } from "node:child_process";
import { createServer } from "node:net";
import * as p from "@clack/prompts";
import pc from "picocolors";
import { and, eq, inArray, sql } from "drizzle-orm";
import {
  applyPendingMigrations,
  agents,
  companies,
  createDb,
  ensurePostgresDatabase,
  formatDatabaseBackupResult,
  goals,
  heartbeatRuns,
  issueComments,
  issueDocuments,
  issues,
  projectWorkspaces,
  projects,
  runDatabaseBackup,
  runDatabaseRestore,
} from "@paperclipai/db";
import type { Command } from "commander";
import { ensureAgentJwtSecret, loadPaperclipEnvFile, mergePaperclipEnvEntries, readPaperclipEnvEntries, resolvePaperclipEnvFile } from "../config/env.js";
import { expandHomePrefix } from "../config/home.js";
import type { PaperclipConfig } from "../config/schema.js";
import { readConfig, resolveConfigPath, writeConfig } from "../config/store.js";
import { printPaperclipCliBanner } from "../utils/banner.js";
import { resolveRuntimeLikePath } from "../utils/path-resolver.js";
import {
  buildWorktreeConfig,
  buildWorktreeEnvEntries,
  DEFAULT_WORKTREE_HOME,
  formatShellExports,
  generateWorktreeColor,
  isWorktreeSeedMode,
  resolveSuggestedWorktreeName,
  resolveWorktreeSeedPlan,
  resolveWorktreeLocalPaths,
  sanitizeWorktreeInstanceId,
  type WorktreeSeedMode,
  type WorktreeLocalPaths,
} from "./worktree-lib.js";
import {
  buildWorktreeMergePlan,
  parseWorktreeMergeScopes,
  type PlannedCommentInsert,
  type PlannedIssueInsert,
} from "./worktree-merge-history-lib.js";

type WorktreeInitOptions = {
  name?: string;
  instance?: string;
  home?: string;
  fromConfig?: string;
  fromDataDir?: string;
  fromInstance?: string;
  sourceConfigPathOverride?: string;
  serverPort?: number;
  dbPort?: number;
  seed?: boolean;
  seedMode?: string;
  force?: boolean;
};

type WorktreeMakeOptions = WorktreeInitOptions & {
  startPoint?: string;
};

type WorktreeEnvOptions = {
  config?: string;
  json?: boolean;
};

type WorktreeMergeHistoryOptions = {
  company?: string;
  scope?: string;
  apply?: boolean;
  dry?: boolean;
  yes?: boolean;
};

type EmbeddedPostgresInstance = {
  initialise(): Promise<void>;
  start(): Promise<void>;
  stop(): Promise<void>;
};

type EmbeddedPostgresCtor = new (opts: {
  databaseDir: string;
  user: string;
  password: string;
  port: number;
  persistent: boolean;
  initdbFlags?: string[];
  onLog?: (message: unknown) => void;
  onError?: (message: unknown) => void;
}) => EmbeddedPostgresInstance;

type EmbeddedPostgresHandle = {
  port: number;
  startedByThisProcess: boolean;
  stop: () => Promise<void>;
};

type GitWorkspaceInfo = {
  root: string;
  commonDir: string;
  gitDir: string;
  hooksPath: string;
};

type CopiedGitHooksResult = {
  sourceHooksPath: string;
  targetHooksPath: string;
  copied: boolean;
};

type SeedWorktreeDatabaseResult = {
  backupSummary: string;
  reboundWorkspaces: Array<{
    name: string;
    fromCwd: string;
    toCwd: string;
  }>;
};

function nonEmpty(value: string | null | undefined): string | null {
  return typeof value === "string" && value.trim().length > 0 ? value.trim() : null;
}

function isCurrentSourceConfigPath(sourceConfigPath: string): boolean {
  const currentConfigPath = process.env.PAPERCLIP_CONFIG;
  if (!currentConfigPath || currentConfigPath.trim().length === 0) {
    return false;
  }
  return path.resolve(currentConfigPath) === path.resolve(sourceConfigPath);
}

const WORKTREE_NAME_PREFIX = "paperclip-";

function resolveWorktreeMakeName(name: string): string {
  const value = nonEmpty(name);
  if (!value) {
    throw new Error("Worktree name is required.");
  }
  if (!/^[A-Za-z0-9._-]+$/.test(value)) {
    throw new Error(
      "Worktree name must contain only letters, numbers, dots, underscores, or dashes.",
    );
  }
  return value.startsWith(WORKTREE_NAME_PREFIX) ? value : `${WORKTREE_NAME_PREFIX}${value}`;
}

function resolveWorktreeHome(explicit?: string): string {
  return explicit ?? process.env.PAPERCLIP_WORKTREES_DIR ?? DEFAULT_WORKTREE_HOME;
}

function resolveWorktreeStartPoint(explicit?: string): string | undefined {
  return explicit ?? nonEmpty(process.env.PAPERCLIP_WORKTREE_START_POINT) ?? undefined;
}

export function resolveWorktreeMakeTargetPath(name: string): string {
  return path.resolve(os.homedir(), resolveWorktreeMakeName(name));
}

function extractExecSyncErrorMessage(error: unknown): string | null {
  if (!error || typeof error !== "object") {
    return error instanceof Error ? error.message : null;
  }

  const stderr = "stderr" in error ? error.stderr : null;
  if (typeof stderr === "string") {
    return nonEmpty(stderr);
  }
  if (stderr instanceof Buffer) {
    return nonEmpty(stderr.toString("utf8"));
  }

  return error instanceof Error ? nonEmpty(error.message) : null;
}

function localBranchExists(cwd: string, branchName: string): boolean {
  try {
    execFileSync("git", ["show-ref", "--verify", "--quiet", `refs/heads/${branchName}`], {
      cwd,
      stdio: "ignore",
    });
    return true;
  } catch {
    return false;
  }
}

export function resolveGitWorktreeAddArgs(input: {
  branchName: string;
  targetPath: string;
  branchExists: boolean;
  startPoint?: string;
}): string[] {
  if (input.branchExists && !input.startPoint) {
    return ["worktree", "add", input.targetPath, input.branchName];
  }
  const commitish = input.startPoint ?? "HEAD";
  return ["worktree", "add", "-b", input.branchName, input.targetPath, commitish];
}

function readPidFilePort(postmasterPidFile: string): number | null {
  if (!existsSync(postmasterPidFile)) return null;
  try {
    const lines = readFileSync(postmasterPidFile, "utf8").split("\n");
    const port = Number(lines[3]?.trim());
    return Number.isInteger(port) && port > 0 ? port : null;
  } catch {
    return null;
  }
}

function readRunningPostmasterPid(postmasterPidFile: string): number | null {
  if (!existsSync(postmasterPidFile)) return null;
  try {
    const pid = Number(readFileSync(postmasterPidFile, "utf8").split("\n")[0]?.trim());
    if (!Number.isInteger(pid) || pid <= 0) return null;
    process.kill(pid, 0);
    return pid;
  } catch {
    return null;
  }
}

async function isPortAvailable(port: number): Promise<boolean> {
  return await new Promise<boolean>((resolve) => {
    const server = createServer();
    server.unref();
    server.once("error", () => resolve(false));
    server.listen(port, "127.0.0.1", () => {
      server.close(() => resolve(true));
    });
  });
}

async function findAvailablePort(preferredPort: number, reserved = new Set<number>()): Promise<number> {
  let port = Math.max(1, Math.trunc(preferredPort));
  while (reserved.has(port) || !(await isPortAvailable(port))) {
    port += 1;
  }
  return port;
}

function detectGitBranchName(cwd: string): string | null {
  try {
    const value = execFileSync("git", ["branch", "--show-current"], {
      cwd,
      encoding: "utf8",
      stdio: ["ignore", "pipe", "ignore"],
    }).trim();
    return nonEmpty(value);
  } catch {
    return null;
  }
}

function detectGitWorkspaceInfo(cwd: string): GitWorkspaceInfo | null {
  try {
    const root = execFileSync("git", ["rev-parse", "--show-toplevel"], {
      cwd,
      encoding: "utf8",
      stdio: ["ignore", "pipe", "ignore"],
    }).trim();
    const commonDirRaw = execFileSync("git", ["rev-parse", "--git-common-dir"], {
      cwd: root,
      encoding: "utf8",
      stdio: ["ignore", "pipe", "ignore"],
    }).trim();
    const gitDirRaw = execFileSync("git", ["rev-parse", "--git-dir"], {
      cwd: root,
      encoding: "utf8",
      stdio: ["ignore", "pipe", "ignore"],
    }).trim();
    const hooksPathRaw = execFileSync("git", ["rev-parse", "--git-path", "hooks"], {
      cwd: root,
      encoding: "utf8",
      stdio: ["ignore", "pipe", "ignore"],
    }).trim();
    return {
      root: path.resolve(root),
      commonDir: path.resolve(root, commonDirRaw),
      gitDir: path.resolve(root, gitDirRaw),
      hooksPath: path.resolve(root, hooksPathRaw),
    };
  } catch {
    return null;
  }
}

function copyDirectoryContents(sourceDir: string, targetDir: string): boolean {
  if (!existsSync(sourceDir)) return false;

  const entries = readdirSync(sourceDir, { withFileTypes: true });
  if (entries.length === 0) return false;

  mkdirSync(targetDir, { recursive: true });

  let copied = false;
  for (const entry of entries) {
    const sourcePath = path.resolve(sourceDir, entry.name);
    const targetPath = path.resolve(targetDir, entry.name);

    if (entry.isDirectory()) {
      mkdirSync(targetPath, { recursive: true });
      copyDirectoryContents(sourcePath, targetPath);
      copied = true;
      continue;
    }

    if (entry.isSymbolicLink()) {
      rmSync(targetPath, { recursive: true, force: true });
      symlinkSync(readlinkSync(sourcePath), targetPath);
      copied = true;
      continue;
    }

    copyFileSync(sourcePath, targetPath);
    try {
      chmodSync(targetPath, statSync(sourcePath).mode & 0o777);
    } catch {
      // best effort
    }
    copied = true;
  }

  return copied;
}

export function copyGitHooksToWorktreeGitDir(cwd: string): CopiedGitHooksResult | null {
  const workspace = detectGitWorkspaceInfo(cwd);
  if (!workspace) return null;

  const sourceHooksPath = workspace.hooksPath;
  const targetHooksPath = path.resolve(workspace.gitDir, "hooks");

  if (sourceHooksPath === targetHooksPath) {
    return {
      sourceHooksPath,
      targetHooksPath,
      copied: false,
    };
  }

  return {
    sourceHooksPath,
    targetHooksPath,
    copied: copyDirectoryContents(sourceHooksPath, targetHooksPath),
  };
}

export function rebindWorkspaceCwd(input: {
  sourceRepoRoot: string;
  targetRepoRoot: string;
  workspaceCwd: string;
}): string | null {
  const sourceRepoRoot = path.resolve(input.sourceRepoRoot);
  const targetRepoRoot = path.resolve(input.targetRepoRoot);
  const workspaceCwd = path.resolve(input.workspaceCwd);
  const relative = path.relative(sourceRepoRoot, workspaceCwd);
  if (!relative || relative === "") {
    return targetRepoRoot;
  }
  if (relative.startsWith("..") || path.isAbsolute(relative)) {
    return null;
  }
  return path.resolve(targetRepoRoot, relative);
}

async function rebindSeededProjectWorkspaces(input: {
  targetConnectionString: string;
  currentCwd: string;
}): Promise<SeedWorktreeDatabaseResult["reboundWorkspaces"]> {
  const targetRepo = detectGitWorkspaceInfo(input.currentCwd);
  if (!targetRepo) return [];

  const db = createDb(input.targetConnectionString);
  const closableDb = db as typeof db & {
    $client?: { end?: (opts?: { timeout?: number }) => Promise<void> };
  };

  try {
    const rows = await db
      .select({
        id: projectWorkspaces.id,
        name: projectWorkspaces.name,
        cwd: projectWorkspaces.cwd,
      })
      .from(projectWorkspaces);

    const rebound: SeedWorktreeDatabaseResult["reboundWorkspaces"] = [];
    for (const row of rows) {
      const workspaceCwd = nonEmpty(row.cwd);
      if (!workspaceCwd) continue;

      const sourceRepo = detectGitWorkspaceInfo(workspaceCwd);
      if (!sourceRepo) continue;
      if (sourceRepo.commonDir !== targetRepo.commonDir) continue;

      const reboundCwd = rebindWorkspaceCwd({
        sourceRepoRoot: sourceRepo.root,
        targetRepoRoot: targetRepo.root,
        workspaceCwd,
      });
      if (!reboundCwd) continue;

      const normalizedCurrent = path.resolve(workspaceCwd);
      if (reboundCwd === normalizedCurrent) continue;
      if (!existsSync(reboundCwd)) continue;

      await db
        .update(projectWorkspaces)
        .set({
          cwd: reboundCwd,
          updatedAt: new Date(),
        })
        .where(eq(projectWorkspaces.id, row.id));

      rebound.push({
        name: row.name,
        fromCwd: normalizedCurrent,
        toCwd: reboundCwd,
      });
    }

    return rebound;
  } finally {
    await closableDb.$client?.end?.({ timeout: 5 }).catch(() => undefined);
  }
}

export function resolveSourceConfigPath(opts: WorktreeInitOptions): string {
  if (opts.sourceConfigPathOverride) return path.resolve(opts.sourceConfigPathOverride);
  if (opts.fromConfig) return path.resolve(opts.fromConfig);
  if (!opts.fromDataDir && !opts.fromInstance) {
    return resolveConfigPath();
  }
  const sourceHome = path.resolve(expandHomePrefix(opts.fromDataDir ?? "~/.paperclip"));
  const sourceInstanceId = sanitizeWorktreeInstanceId(opts.fromInstance ?? "default");
  return path.resolve(sourceHome, "instances", sourceInstanceId, "config.json");
}

function resolveSourceConnectionString(config: PaperclipConfig, envEntries: Record<string, string>, portOverride?: number): string {
  if (config.database.mode === "postgres") {
    const connectionString = nonEmpty(envEntries.DATABASE_URL) ?? nonEmpty(config.database.connectionString);
    if (!connectionString) {
      throw new Error(
        "Source instance uses postgres mode but has no connection string in config or adjacent .env.",
      );
    }
    return connectionString;
  }

  const port = portOverride ?? config.database.embeddedPostgresPort;
  return `postgres://paperclip:paperclip@127.0.0.1:${port}/paperclip`;
}

export function copySeededSecretsKey(input: {
  sourceConfigPath: string;
  sourceConfig: PaperclipConfig;
  sourceEnvEntries: Record<string, string>;
  targetKeyFilePath: string;
}): void {
  if (input.sourceConfig.secrets.provider !== "local_encrypted") {
    return;
  }

  mkdirSync(path.dirname(input.targetKeyFilePath), { recursive: true });

  const allowProcessEnvFallback = isCurrentSourceConfigPath(input.sourceConfigPath);
  const sourceInlineMasterKey =
    nonEmpty(input.sourceEnvEntries.PAPERCLIP_SECRETS_MASTER_KEY) ??
    (allowProcessEnvFallback ? nonEmpty(process.env.PAPERCLIP_SECRETS_MASTER_KEY) : null);
  if (sourceInlineMasterKey) {
    writeFileSync(input.targetKeyFilePath, sourceInlineMasterKey, {
      encoding: "utf8",
      mode: 0o600,
    });
    try {
      chmodSync(input.targetKeyFilePath, 0o600);
    } catch {
      // best effort
    }
    return;
  }

  const sourceKeyFileOverride =
    nonEmpty(input.sourceEnvEntries.PAPERCLIP_SECRETS_MASTER_KEY_FILE) ??
    (allowProcessEnvFallback ? nonEmpty(process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE) : null);
  const sourceConfiguredKeyPath = sourceKeyFileOverride ?? input.sourceConfig.secrets.localEncrypted.keyFilePath;
  const sourceKeyFilePath = resolveRuntimeLikePath(sourceConfiguredKeyPath, input.sourceConfigPath);

  if (!existsSync(sourceKeyFilePath)) {
    throw new Error(
      `Cannot seed worktree database because source local_encrypted secrets key was not found at ${sourceKeyFilePath}.`,
    );
  }

  copyFileSync(sourceKeyFilePath, input.targetKeyFilePath);
  try {
    chmodSync(input.targetKeyFilePath, 0o600);
  } catch {
    // best effort
  }
}

async function ensureEmbeddedPostgres(dataDir: string, preferredPort: number): Promise<EmbeddedPostgresHandle> {
  const moduleName = "embedded-postgres";
  let EmbeddedPostgres: EmbeddedPostgresCtor;
  try {
    const mod = await import(moduleName);
    EmbeddedPostgres = mod.default as EmbeddedPostgresCtor;
  } catch {
    throw new Error(
      "Embedded PostgreSQL support requires dependency `embedded-postgres`. Reinstall dependencies and try again.",
    );
  }

  const postmasterPidFile = path.resolve(dataDir, "postmaster.pid");
  const runningPid = readRunningPostmasterPid(postmasterPidFile);
  if (runningPid) {
    return {
      port: readPidFilePort(postmasterPidFile) ?? preferredPort,
      startedByThisProcess: false,
      stop: async () => {},
    };
  }

  const port = await findAvailablePort(preferredPort);
  const instance = new EmbeddedPostgres({
    databaseDir: dataDir,
    user: "paperclip",
    password: "paperclip",
    port,
    persistent: true,
    initdbFlags: ["--encoding=UTF8", "--locale=C"],
    onLog: () => {},
    onError: () => {},
  });

  if (!existsSync(path.resolve(dataDir, "PG_VERSION"))) {
    await instance.initialise();
  }
  if (existsSync(postmasterPidFile)) {
    rmSync(postmasterPidFile, { force: true });
  }
  await instance.start();

  return {
    port,
    startedByThisProcess: true,
    stop: async () => {
      await instance.stop();
    },
  };
}

async function seedWorktreeDatabase(input: {
  sourceConfigPath: string;
  sourceConfig: PaperclipConfig;
  targetConfig: PaperclipConfig;
  targetPaths: WorktreeLocalPaths;
  instanceId: string;
  seedMode: WorktreeSeedMode;
}): Promise<SeedWorktreeDatabaseResult> {
  const seedPlan = resolveWorktreeSeedPlan(input.seedMode);
  const sourceEnvFile = resolvePaperclipEnvFile(input.sourceConfigPath);
  const sourceEnvEntries = readPaperclipEnvEntries(sourceEnvFile);
  copySeededSecretsKey({
    sourceConfigPath: input.sourceConfigPath,
    sourceConfig: input.sourceConfig,
    sourceEnvEntries,
    targetKeyFilePath: input.targetPaths.secretsKeyFilePath,
  });
  let sourceHandle: EmbeddedPostgresHandle | null = null;
  let targetHandle: EmbeddedPostgresHandle | null = null;

  try {
    if (input.sourceConfig.database.mode === "embedded-postgres") {
      sourceHandle = await ensureEmbeddedPostgres(
        input.sourceConfig.database.embeddedPostgresDataDir,
        input.sourceConfig.database.embeddedPostgresPort,
      );
    }
    const sourceConnectionString = resolveSourceConnectionString(
      input.sourceConfig,
      sourceEnvEntries,
      sourceHandle?.port,
    );
    const backup = await runDatabaseBackup({
      connectionString: sourceConnectionString,
      backupDir: path.resolve(input.targetPaths.backupDir, "seed"),
      retentionDays: 7,
      filenamePrefix: `${input.instanceId}-seed`,
      includeMigrationJournal: true,
      excludeTables: seedPlan.excludedTables,
      nullifyColumns: seedPlan.nullifyColumns,
    });

    targetHandle = await ensureEmbeddedPostgres(
      input.targetConfig.database.embeddedPostgresDataDir,
      input.targetConfig.database.embeddedPostgresPort,
    );

    const adminConnectionString = `postgres://paperclip:paperclip@127.0.0.1:${targetHandle.port}/postgres`;
    await ensurePostgresDatabase(adminConnectionString, "paperclip");
    const targetConnectionString = `postgres://paperclip:paperclip@127.0.0.1:${targetHandle.port}/paperclip`;
    await runDatabaseRestore({
      connectionString: targetConnectionString,
      backupFile: backup.backupFile,
    });
    await applyPendingMigrations(targetConnectionString);
    const reboundWorkspaces = await rebindSeededProjectWorkspaces({
      targetConnectionString,
      currentCwd: input.targetPaths.cwd,
    });

    return {
      backupSummary: formatDatabaseBackupResult(backup),
      reboundWorkspaces,
    };
  } finally {
    if (targetHandle?.startedByThisProcess) {
      await targetHandle.stop();
    }
    if (sourceHandle?.startedByThisProcess) {
      await sourceHandle.stop();
    }
  }
}

async function runWorktreeInit(opts: WorktreeInitOptions): Promise<void> {
  const cwd = process.cwd();
  const worktreeName = resolveSuggestedWorktreeName(
    cwd,
    opts.name ?? detectGitBranchName(cwd) ?? undefined,
  );
  const seedMode = opts.seedMode ?? "minimal";
  if (!isWorktreeSeedMode(seedMode)) {
    throw new Error(`Unsupported seed mode "${seedMode}". Expected one of: minimal, full.`);
  }
  const instanceId = sanitizeWorktreeInstanceId(opts.instance ?? worktreeName);
  const paths = resolveWorktreeLocalPaths({
    cwd,
    homeDir: resolveWorktreeHome(opts.home),
    instanceId,
  });
  const branding = {
    name: worktreeName,
    color: generateWorktreeColor(),
  };
  const sourceConfigPath = resolveSourceConfigPath(opts);
  const sourceConfig = existsSync(sourceConfigPath) ? readConfig(sourceConfigPath) : null;

  if ((existsSync(paths.configPath) || existsSync(paths.instanceRoot)) && !opts.force) {
    throw new Error(
      `Worktree config already exists at ${paths.configPath} or instance data exists at ${paths.instanceRoot}. Re-run with --force to replace it.`,
    );
  }

  if (opts.force) {
    rmSync(paths.repoConfigDir, { recursive: true, force: true });
    rmSync(paths.instanceRoot, { recursive: true, force: true });
  }

  const preferredServerPort = opts.serverPort ?? ((sourceConfig?.server.port ?? 3100) + 1);
  const serverPort = await findAvailablePort(preferredServerPort);
  const preferredDbPort = opts.dbPort ?? ((sourceConfig?.database.embeddedPostgresPort ?? 54329) + 1);
  const databasePort = await findAvailablePort(preferredDbPort, new Set([serverPort]));
  const targetConfig = buildWorktreeConfig({
    sourceConfig,
    paths,
    serverPort,
    databasePort,
  });

  writeConfig(targetConfig, paths.configPath);
  const sourceEnvEntries = readPaperclipEnvEntries(resolvePaperclipEnvFile(sourceConfigPath));
  const existingAgentJwtSecret =
    nonEmpty(sourceEnvEntries.PAPERCLIP_AGENT_JWT_SECRET) ??
    nonEmpty(process.env.PAPERCLIP_AGENT_JWT_SECRET);
  mergePaperclipEnvEntries(
    {
      ...buildWorktreeEnvEntries(paths, branding),
      ...(existingAgentJwtSecret ? { PAPERCLIP_AGENT_JWT_SECRET: existingAgentJwtSecret } : {}),
    },
    paths.envPath,
  );
  ensureAgentJwtSecret(paths.configPath);
  loadPaperclipEnvFile(paths.configPath);
  const copiedGitHooks = copyGitHooksToWorktreeGitDir(cwd);

  let seedSummary: string | null = null;
  let reboundWorkspaceSummary: SeedWorktreeDatabaseResult["reboundWorkspaces"] = [];
  if (opts.seed !== false) {
    if (!sourceConfig) {
      throw new Error(
        `Cannot seed worktree database because source config was not found at ${sourceConfigPath}. Use --no-seed or provide --from-config.`,
      );
    }
    const spinner = p.spinner();
    spinner.start(`Seeding isolated worktree database from source instance (${seedMode})...`);
    try {
      const seeded = await seedWorktreeDatabase({
        sourceConfigPath,
        sourceConfig,
        targetConfig,
        targetPaths: paths,
        instanceId,
        seedMode,
      });
      seedSummary = seeded.backupSummary;
      reboundWorkspaceSummary = seeded.reboundWorkspaces;
      spinner.stop(`Seeded isolated worktree database (${seedMode}).`);
    } catch (error) {
      spinner.stop(pc.red("Failed to seed worktree database."));
      throw error;
    }
  }

  p.log.message(pc.dim(`Repo config: ${paths.configPath}`));
  p.log.message(pc.dim(`Repo env: ${paths.envPath}`));
  p.log.message(pc.dim(`Isolated home: ${paths.homeDir}`));
  p.log.message(pc.dim(`Instance: ${paths.instanceId}`));
  p.log.message(pc.dim(`Worktree badge: ${branding.name} (${branding.color})`));
  p.log.message(pc.dim(`Server port: ${serverPort} | DB port: ${databasePort}`));
  if (copiedGitHooks?.copied) {
    p.log.message(
      pc.dim(`Mirrored git hooks: ${copiedGitHooks.sourceHooksPath} -> ${copiedGitHooks.targetHooksPath}`),
    );
  }
  if (seedSummary) {
    p.log.message(pc.dim(`Seed mode: ${seedMode}`));
    p.log.message(pc.dim(`Seed snapshot: ${seedSummary}`));
    for (const rebound of reboundWorkspaceSummary) {
      p.log.message(
        pc.dim(`Rebound workspace ${rebound.name}: ${rebound.fromCwd} -> ${rebound.toCwd}`),
      );
    }
  }
  p.outro(
    pc.green(
      `Worktree ready. Run Paperclip inside this repo and the CLI/server will use ${paths.instanceId} automatically.`,
    ),
  );
}

export async function worktreeInitCommand(opts: WorktreeInitOptions): Promise<void> {
  printPaperclipCliBanner();
  p.intro(pc.bgCyan(pc.black(" paperclipai worktree init ")));
  await runWorktreeInit(opts);
}

export async function worktreeMakeCommand(nameArg: string, opts: WorktreeMakeOptions): Promise<void> {
  printPaperclipCliBanner();
  p.intro(pc.bgCyan(pc.black(" paperclipai worktree:make ")));

  const name = resolveWorktreeMakeName(nameArg);
  const startPoint = resolveWorktreeStartPoint(opts.startPoint);
  const sourceCwd = process.cwd();
  const sourceConfigPath = resolveSourceConfigPath(opts);
  const targetPath = resolveWorktreeMakeTargetPath(name);
  if (existsSync(targetPath)) {
    throw new Error(`Target path already exists: ${targetPath}`);
  }

  mkdirSync(path.dirname(targetPath), { recursive: true });
  if (startPoint) {
    const [remote] = startPoint.split("/", 1);
    try {
      execFileSync("git", ["fetch", remote], {
        cwd: sourceCwd,
        stdio: ["ignore", "pipe", "pipe"],
      });
    } catch (error) {
      throw new Error(
        `Failed to fetch from remote "${remote}": ${extractExecSyncErrorMessage(error) ?? String(error)}`,
      );
    }
  }

  const worktreeArgs = resolveGitWorktreeAddArgs({
    branchName: name,
    targetPath,
    branchExists: !startPoint && localBranchExists(sourceCwd, name),
    startPoint,
  });

  const spinner = p.spinner();
  spinner.start(`Creating git worktree at ${targetPath}...`);
  try {
    execFileSync("git", worktreeArgs, {
      cwd: sourceCwd,
      stdio: ["ignore", "pipe", "pipe"],
    });
    spinner.stop(`Created git worktree at ${targetPath}.`);
  } catch (error) {
    spinner.stop(pc.red("Failed to create git worktree."));
    throw new Error(extractExecSyncErrorMessage(error) ?? String(error));
  }

  const installSpinner = p.spinner();
  installSpinner.start("Installing dependencies...");
  try {
    execFileSync("pnpm", ["install"], {
      cwd: targetPath,
      stdio: ["ignore", "pipe", "pipe"],
    });
    installSpinner.stop("Installed dependencies.");
  } catch (error) {
    installSpinner.stop(pc.yellow("Failed to install dependencies (continuing anyway)."));
    p.log.warning(extractExecSyncErrorMessage(error) ?? String(error));
  }

  const originalCwd = process.cwd();
  try {
    process.chdir(targetPath);
    await runWorktreeInit({
      ...opts,
      name,
      sourceConfigPathOverride: sourceConfigPath,
    });
  } catch (error) {
    throw error;
  } finally {
    process.chdir(originalCwd);
  }
}

type WorktreeCleanupOptions = {
  instance?: string;
  home?: string;
  force?: boolean;
};

type GitWorktreeListEntry = {
  worktree: string;
  branch: string | null;
  bare: boolean;
  detached: boolean;
};

function parseGitWorktreeList(cwd: string): GitWorktreeListEntry[] {
  const raw = execFileSync("git", ["worktree", "list", "--porcelain"], {
    cwd,
    encoding: "utf8",
    stdio: ["ignore", "pipe", "pipe"],
  });
  const entries: GitWorktreeListEntry[] = [];
  let current: Partial<GitWorktreeListEntry> = {};
  for (const line of raw.split("\n")) {
    if (line.startsWith("worktree ")) {
      current = { worktree: line.slice("worktree ".length) };
    } else if (line.startsWith("branch ")) {
      current.branch = line.slice("branch ".length);
    } else if (line === "bare") {
      current.bare = true;
    } else if (line === "detached") {
      current.detached = true;
    } else if (line === "" && current.worktree) {
      entries.push({
        worktree: current.worktree,
        branch: current.branch ?? null,
        bare: current.bare ?? false,
        detached: current.detached ?? false,
      });
      current = {};
    }
  }
  if (current.worktree) {
    entries.push({
      worktree: current.worktree,
      branch: current.branch ?? null,
      bare: current.bare ?? false,
      detached: current.detached ?? false,
    });
  }
  return entries;
}

function branchHasUniqueCommits(cwd: string, branchName: string): boolean {
  try {
    const output = execFileSync(
      "git",
      ["log", "--oneline", branchName, "--not", "--remotes", "--exclude", `refs/heads/${branchName}`, "--branches"],
      { cwd, encoding: "utf8", stdio: ["ignore", "pipe", "pipe"] },
    ).trim();
    return output.length > 0;
  } catch {
    return false;
  }
}

function branchExistsOnAnyRemote(cwd: string, branchName: string): boolean {
  try {
    const output = execFileSync(
      "git",
      ["branch", "-r", "--list", `*/${branchName}`],
      { cwd, encoding: "utf8", stdio: ["ignore", "pipe", "pipe"] },
    ).trim();
    return output.length > 0;
  } catch {
    return false;
  }
}

function worktreePathHasUncommittedChanges(worktreePath: string): boolean {
  try {
    const output = execFileSync(
      "git",
      ["status", "--porcelain"],
      { cwd: worktreePath, encoding: "utf8", stdio: ["ignore", "pipe", "pipe"] },
    ).trim();
    return output.length > 0;
  } catch {
    return false;
  }
}

export async function worktreeCleanupCommand(nameArg: string, opts: WorktreeCleanupOptions): Promise<void> {
  printPaperclipCliBanner();
  p.intro(pc.bgCyan(pc.black(" paperclipai worktree:cleanup ")));

  const name = resolveWorktreeMakeName(nameArg);
  const sourceCwd = process.cwd();
  const targetPath = resolveWorktreeMakeTargetPath(name);
  const instanceId = sanitizeWorktreeInstanceId(opts.instance ?? name);
  const homeDir = path.resolve(expandHomePrefix(resolveWorktreeHome(opts.home)));
  const instanceRoot = path.resolve(homeDir, "instances", instanceId);

  // ── 1. Assess current state ──────────────────────────────────────────

  const hasBranch = localBranchExists(sourceCwd, name);
  const hasTargetDir = existsSync(targetPath);
  const hasInstanceData = existsSync(instanceRoot);

  const worktrees = parseGitWorktreeList(sourceCwd);
  const linkedWorktree = worktrees.find(
    (wt) => wt.branch === `refs/heads/${name}` || path.resolve(wt.worktree) === path.resolve(targetPath),
  );

  if (!hasBranch && !hasTargetDir && !hasInstanceData && !linkedWorktree) {
    p.log.info("Nothing to clean up — no branch, worktree directory, or instance data found.");
    p.outro(pc.green("Already clean."));
    return;
  }

  // ── 2. Safety checks ────────────────────────────────────────────────

  const problems: string[] = [];

  if (hasBranch && branchHasUniqueCommits(sourceCwd, name)) {
    const onRemote = branchExistsOnAnyRemote(sourceCwd, name);
    if (onRemote) {
      p.log.info(
        `Branch "${name}" has unique local commits, but the branch also exists on a remote — safe to delete locally.`,
      );
    } else {
      problems.push(
        `Branch "${name}" has commits not found on any other branch or remote. ` +
          `Deleting it will lose work. Push it first, or use --force.`,
      );
    }
  }

  if (hasTargetDir && worktreePathHasUncommittedChanges(targetPath)) {
    problems.push(
      `Worktree directory ${targetPath} has uncommitted changes. Commit or stash first, or use --force.`,
    );
  }

  if (problems.length > 0 && !opts.force) {
    for (const problem of problems) {
      p.log.error(problem);
    }
    throw new Error("Safety checks failed. Resolve the issues above or re-run with --force.");
  }
  if (problems.length > 0 && opts.force) {
    for (const problem of problems) {
      p.log.warning(`Overridden by --force: ${problem}`);
    }
  }

  // ── 3. Clean up (idempotent steps) ──────────────────────────────────

  // 3a. Remove the git worktree registration
  if (linkedWorktree) {
    const worktreeDirExists = existsSync(linkedWorktree.worktree);
    const spinner = p.spinner();
    if (worktreeDirExists) {
      spinner.start(`Removing git worktree at ${linkedWorktree.worktree}...`);
      try {
        const removeArgs = ["worktree", "remove", linkedWorktree.worktree];
        if (opts.force) removeArgs.push("--force");
        execFileSync("git", removeArgs, {
          cwd: sourceCwd,
          stdio: ["ignore", "pipe", "pipe"],
        });
        spinner.stop(`Removed git worktree at ${linkedWorktree.worktree}.`);
      } catch (error) {
        spinner.stop(pc.yellow(`Could not remove worktree cleanly, will prune instead.`));
        p.log.warning(extractExecSyncErrorMessage(error) ?? String(error));
      }
    } else {
      spinner.start("Pruning stale worktree entry...");
      execFileSync("git", ["worktree", "prune"], {
        cwd: sourceCwd,
        stdio: ["ignore", "pipe", "pipe"],
      });
      spinner.stop("Pruned stale worktree entry.");
    }
  } else {
    // Even without a linked worktree, prune to clean up any orphaned entries
    execFileSync("git", ["worktree", "prune"], {
      cwd: sourceCwd,
      stdio: ["ignore", "pipe", "pipe"],
    });
  }

  // 3b. Remove the worktree directory if it still exists (e.g. partial creation)
  if (existsSync(targetPath)) {
    const spinner = p.spinner();
    spinner.start(`Removing worktree directory ${targetPath}...`);
    rmSync(targetPath, { recursive: true, force: true });
    spinner.stop(`Removed worktree directory ${targetPath}.`);
  }

  // 3c. Delete the local branch (now safe — worktree is gone)
  if (localBranchExists(sourceCwd, name)) {
    const spinner = p.spinner();
    spinner.start(`Deleting local branch "${name}"...`);
    try {
      const deleteFlag = opts.force ? "-D" : "-d";
      execFileSync("git", ["branch", deleteFlag, name], {
        cwd: sourceCwd,
        stdio: ["ignore", "pipe", "pipe"],
      });
      spinner.stop(`Deleted local branch "${name}".`);
    } catch (error) {
      spinner.stop(pc.yellow(`Could not delete branch "${name}".`));
      p.log.warning(extractExecSyncErrorMessage(error) ?? String(error));
    }
  }

  // 3d. Remove instance data
  if (existsSync(instanceRoot)) {
    const spinner = p.spinner();
    spinner.start(`Removing instance data at ${instanceRoot}...`);
    rmSync(instanceRoot, { recursive: true, force: true });
    spinner.stop(`Removed instance data at ${instanceRoot}.`);
  }

  p.outro(pc.green("Cleanup complete."));
}

export async function worktreeEnvCommand(opts: WorktreeEnvOptions): Promise<void> {
  const configPath = resolveConfigPath(opts.config);
  const envPath = resolvePaperclipEnvFile(configPath);
  const envEntries = readPaperclipEnvEntries(envPath);
  const out = {
    PAPERCLIP_CONFIG: configPath,
    ...(envEntries.PAPERCLIP_HOME ? { PAPERCLIP_HOME: envEntries.PAPERCLIP_HOME } : {}),
    ...(envEntries.PAPERCLIP_INSTANCE_ID ? { PAPERCLIP_INSTANCE_ID: envEntries.PAPERCLIP_INSTANCE_ID } : {}),
    ...(envEntries.PAPERCLIP_CONTEXT ? { PAPERCLIP_CONTEXT: envEntries.PAPERCLIP_CONTEXT } : {}),
    ...envEntries,
  };

  if (opts.json) {
    console.log(JSON.stringify(out, null, 2));
    return;
  }

  console.log(formatShellExports(out));
}

type ClosableDb = ReturnType<typeof createDb> & {
  $client?: { end?: (opts?: { timeout?: number }) => Promise<void> };
};

type OpenDbHandle = {
  db: ClosableDb;
  stop: () => Promise<void>;
};

type ResolvedMergeCompany = {
  id: string;
  name: string;
  issuePrefix: string;
};

function requirePathArgument(name: string, value: string | undefined): string {
  const trimmed = nonEmpty(value);
  if (!trimmed) {
    throw new Error(`${name} is required.`);
  }
  return path.resolve(trimmed);
}

async function closeDb(db: ClosableDb): Promise<void> {
  await db.$client?.end?.({ timeout: 5 }).catch(() => undefined);
}

async function openConfiguredDb(configPath: string): Promise<OpenDbHandle> {
  const config = readConfig(configPath);
  if (!config) {
    throw new Error(`Config not found at ${configPath}.`);
  }
  const envEntries = readPaperclipEnvEntries(resolvePaperclipEnvFile(configPath));
  let embeddedHandle: EmbeddedPostgresHandle | null = null;

  try {
    if (config.database.mode === "embedded-postgres") {
      embeddedHandle = await ensureEmbeddedPostgres(
        config.database.embeddedPostgresDataDir,
        config.database.embeddedPostgresPort,
      );
    }
    const connectionString = resolveSourceConnectionString(config, envEntries, embeddedHandle?.port);
    const db = createDb(connectionString) as ClosableDb;
    return {
      db,
      stop: async () => {
        await closeDb(db);
        if (embeddedHandle?.startedByThisProcess) {
          await embeddedHandle.stop();
        }
      },
    };
  } catch (error) {
    if (embeddedHandle?.startedByThisProcess) {
      await embeddedHandle.stop().catch(() => undefined);
    }
    throw error;
  }
}

async function resolveMergeCompany(input: {
  sourceDb: ClosableDb;
  targetDb: ClosableDb;
  selector?: string;
}): Promise<ResolvedMergeCompany> {
  const [sourceCompanies, targetCompanies] = await Promise.all([
    input.sourceDb
      .select({
        id: companies.id,
        name: companies.name,
        issuePrefix: companies.issuePrefix,
      })
      .from(companies),
    input.targetDb
      .select({
        id: companies.id,
        name: companies.name,
        issuePrefix: companies.issuePrefix,
      })
      .from(companies),
  ]);

  const targetById = new Map(targetCompanies.map((company) => [company.id, company]));
  const shared = sourceCompanies.filter((company) => targetById.has(company.id));
  const selector = nonEmpty(input.selector);
  if (selector) {
    const matched = shared.find(
      (company) => company.id === selector || company.issuePrefix.toLowerCase() === selector.toLowerCase(),
    );
    if (!matched) {
      throw new Error(`Could not resolve company "${selector}" in both source and target databases.`);
    }
    return matched;
  }

  if (shared.length === 1) {
    return shared[0];
  }

  if (shared.length === 0) {
    throw new Error("Source and target databases do not share a company id. Pass --company explicitly once both sides match.");
  }

  const options = shared
    .map((company) => `${company.issuePrefix} (${company.name})`)
    .join(", ");
  throw new Error(`Multiple shared companies found. Re-run with --company <id-or-prefix>. Options: ${options}`);
}

function renderMergePlan(plan: Awaited<ReturnType<typeof collectMergePlan>>["plan"], extras: {
  sourcePath: string;
  unsupportedRunCount: number;
  unsupportedDocumentCount: number;
}): string {
  const lines = [
    `Mode: preview`,
    `Source: ${extras.sourcePath}`,
    `Company: ${plan.companyName} (${plan.issuePrefix})`,
    "",
    "Issues",
    `- insert: ${plan.counts.issuesToInsert}`,
    `- already present: ${plan.counts.issuesExisting}`,
    `- shared/imported issues with drift: ${plan.counts.issueDrift}`,
  ];

  const issueInserts = plan.issuePlans.filter((item): item is PlannedIssueInsert => item.action === "insert");
  if (issueInserts.length > 0) {
    lines.push("");
    lines.push("Planned issue imports");
    for (const issue of issueInserts) {
      const projectNote =
        issue.projectResolution === "mapped" && issue.mappedProjectName
          ? ` project->${issue.mappedProjectName}`
          : "";
      const adjustments = issue.adjustments.length > 0 ? ` [${issue.adjustments.join(", ")}]` : "";
      lines.push(
        `- ${issue.source.identifier ?? issue.source.id} -> ${issue.previewIdentifier} (${issue.targetStatus}${projectNote})${adjustments}`,
      );
    }
  }

  if (plan.scopes.includes("comments")) {
    lines.push("");
    lines.push("Comments");
    lines.push(`- insert: ${plan.counts.commentsToInsert}`);
    lines.push(`- already present: ${plan.counts.commentsExisting}`);
    lines.push(`- skipped (missing parent): ${plan.counts.commentsMissingParent}`);
  }

  lines.push("");
  lines.push("Adjustments");
  lines.push(`- cleared assignee agents: ${plan.adjustments.clear_assignee_agent}`);
  lines.push(`- cleared projects: ${plan.adjustments.clear_project}`);
  lines.push(`- cleared project workspaces: ${plan.adjustments.clear_project_workspace}`);
  lines.push(`- cleared goals: ${plan.adjustments.clear_goal}`);
  lines.push(`- cleared comment author agents: ${plan.adjustments.clear_author_agent}`);
  lines.push(`- coerced in_progress to todo: ${plan.adjustments.coerce_in_progress_to_todo}`);

  lines.push("");
  lines.push("Not imported in this phase");
  lines.push(`- heartbeat runs: ${extras.unsupportedRunCount}`);
  lines.push(`- issue documents: ${extras.unsupportedDocumentCount}`);
  lines.push("");
  lines.push("Identifiers shown above are provisional preview values. `--apply` reserves fresh issue numbers at write time.");

  return lines.join("\n");
}

async function collectMergePlan(input: {
  sourceDb: ClosableDb;
  targetDb: ClosableDb;
  company: ResolvedMergeCompany;
  scopes: ReturnType<typeof parseWorktreeMergeScopes>;
  projectIdOverrides?: Record<string, string | null | undefined>;
}) {
  const companyId = input.company.id;
  const [targetCompanyRow, sourceIssuesRows, targetIssuesRows, sourceCommentsRows, targetCommentsRows, sourceProjectsRows, targetProjectsRows, targetAgentsRows, targetProjectWorkspaceRows, targetGoalsRows, runCountRows, documentCountRows] = await Promise.all([
    input.targetDb
      .select({
        issueCounter: companies.issueCounter,
      })
      .from(companies)
      .where(eq(companies.id, companyId))
      .then((rows) => rows[0] ?? null),
    input.sourceDb
      .select()
      .from(issues)
      .where(eq(issues.companyId, companyId)),
    input.targetDb
      .select()
      .from(issues)
      .where(eq(issues.companyId, companyId)),
    input.scopes.includes("comments")
      ? input.sourceDb
        .select()
        .from(issueComments)
        .where(eq(issueComments.companyId, companyId))
      : Promise.resolve([]),
    input.scopes.includes("comments")
      ? input.targetDb
        .select()
        .from(issueComments)
        .where(eq(issueComments.companyId, companyId))
      : Promise.resolve([]),
    input.sourceDb
      .select()
      .from(projects)
      .where(eq(projects.companyId, companyId)),
    input.targetDb
      .select()
      .from(projects)
      .where(eq(projects.companyId, companyId)),
    input.targetDb
      .select()
      .from(agents)
      .where(eq(agents.companyId, companyId)),
    input.targetDb
      .select()
      .from(projectWorkspaces)
      .where(eq(projectWorkspaces.companyId, companyId)),
    input.targetDb
      .select()
      .from(goals)
      .where(eq(goals.companyId, companyId)),
    input.sourceDb
      .select({ count: sql<number>`count(*)::int` })
      .from(heartbeatRuns)
      .where(eq(heartbeatRuns.companyId, companyId)),
    input.sourceDb
      .select({ count: sql<number>`count(*)::int` })
      .from(issueDocuments)
      .innerJoin(issues, eq(issueDocuments.issueId, issues.id))
      .where(eq(issues.companyId, companyId)),
  ]);

  if (!targetCompanyRow) {
    throw new Error(`Target company ${companyId} was not found.`);
  }

  const plan = buildWorktreeMergePlan({
    companyId,
    companyName: input.company.name,
    issuePrefix: input.company.issuePrefix,
    previewIssueCounterStart: targetCompanyRow.issueCounter,
    scopes: input.scopes,
    sourceIssues: sourceIssuesRows,
    targetIssues: targetIssuesRows,
    sourceComments: sourceCommentsRows,
    targetComments: targetCommentsRows,
    targetAgents: targetAgentsRows,
    targetProjects: targetProjectsRows,
    targetProjectWorkspaces: targetProjectWorkspaceRows,
    targetGoals: targetGoalsRows,
    projectIdOverrides: input.projectIdOverrides,
  });

  return {
    plan,
    sourceProjects: sourceProjectsRows,
    targetProjects: targetProjectsRows,
    unsupportedRunCount: runCountRows[0]?.count ?? 0,
    unsupportedDocumentCount: documentCountRows[0]?.count ?? 0,
  };
}

async function promptForProjectMappings(input: {
  plan: Awaited<ReturnType<typeof collectMergePlan>>["plan"];
  sourceProjects: Awaited<ReturnType<typeof collectMergePlan>>["sourceProjects"];
  targetProjects: Awaited<ReturnType<typeof collectMergePlan>>["targetProjects"];
}): Promise<Record<string, string | null>> {
  const missingProjectIds = [
    ...new Set(
      input.plan.issuePlans
        .filter((plan): plan is PlannedIssueInsert => plan.action === "insert")
        .filter((plan) => !!plan.source.projectId && plan.projectResolution === "cleared")
        .map((plan) => plan.source.projectId as string),
    ),
  ];
  if (missingProjectIds.length === 0 || input.targetProjects.length === 0) {
    return {};
  }

  const sourceProjectsById = new Map(input.sourceProjects.map((project) => [project.id, project]));
  const targetChoices = [...input.targetProjects]
    .sort((left, right) => left.name.localeCompare(right.name))
    .map((project) => ({
      value: project.id,
      label: project.name,
      hint: project.status,
    }));

  const mappings: Record<string, string | null> = {};
  for (const sourceProjectId of missingProjectIds) {
    const sourceProject = sourceProjectsById.get(sourceProjectId);
    if (!sourceProject) continue;
    const nameMatch = input.targetProjects.find(
      (project) => project.name.trim().toLowerCase() === sourceProject.name.trim().toLowerCase(),
    );
    const selection = await p.select<string | null>({
      message: `Project "${sourceProject.name}" is missing in target. How should ${input.plan.issuePrefix} imports handle it?`,
      options: [
        ...(nameMatch
          ? [{
              value: nameMatch.id,
              label: `Map to ${nameMatch.name}`,
              hint: "Recommended: exact name match",
            }]
          : []),
        {
          value: null,
          label: "Leave unset",
          hint: "Keep imported issues without a project",
        },
        ...targetChoices.filter((choice) => choice.value !== nameMatch?.id),
      ],
      initialValue: nameMatch?.id ?? null,
    });
    if (p.isCancel(selection)) {
      throw new Error("Project mapping cancelled.");
    }
    mappings[sourceProjectId] = selection;
  }

  return mappings;
}

async function applyMergePlan(input: {
  targetDb: ClosableDb;
  company: ResolvedMergeCompany;
  plan: Awaited<ReturnType<typeof collectMergePlan>>["plan"];
}) {
  const companyId = input.company.id;

  return await input.targetDb.transaction(async (tx) => {
    const issueCandidates = input.plan.issuePlans.filter(
      (plan): plan is PlannedIssueInsert => plan.action === "insert",
    );
    const issueCandidateIds = issueCandidates.map((issue) => issue.source.id);
    const existingIssueIds = issueCandidateIds.length > 0
      ? new Set(
        (await tx
          .select({ id: issues.id })
          .from(issues)
          .where(inArray(issues.id, issueCandidateIds)))
          .map((row) => row.id),
      )
      : new Set<string>();
    const issueInserts = issueCandidates.filter((issue) => !existingIssueIds.has(issue.source.id));

    let nextIssueNumber = 0;
    if (issueInserts.length > 0) {
      const [companyRow] = await tx
        .update(companies)
        .set({ issueCounter: sql`${companies.issueCounter} + ${issueInserts.length}` })
        .where(eq(companies.id, companyId))
        .returning({ issueCounter: companies.issueCounter });
      nextIssueNumber = companyRow.issueCounter - issueInserts.length + 1;
    }

    const insertedIssueIdentifiers = new Map<string, string>();
    for (const issue of issueInserts) {
      const issueNumber = nextIssueNumber;
      nextIssueNumber += 1;
      const identifier = `${input.company.issuePrefix}-${issueNumber}`;
      insertedIssueIdentifiers.set(issue.source.id, identifier);
      await tx.insert(issues).values({
        id: issue.source.id,
        companyId,
        projectId: issue.targetProjectId,
        projectWorkspaceId: issue.targetProjectWorkspaceId,
        goalId: issue.targetGoalId,
        parentId: issue.source.parentId,
        title: issue.source.title,
        description: issue.source.description,
        status: issue.targetStatus,
        priority: issue.source.priority,
        assigneeAgentId: issue.targetAssigneeAgentId,
        assigneeUserId: issue.source.assigneeUserId,
        checkoutRunId: null,
        executionRunId: null,
        executionAgentNameKey: null,
        executionLockedAt: null,
        createdByAgentId: issue.targetCreatedByAgentId,
        createdByUserId: issue.source.createdByUserId,
        issueNumber,
        identifier,
        requestDepth: issue.source.requestDepth,
        billingCode: issue.source.billingCode,
        assigneeAdapterOverrides: issue.targetAssigneeAgentId ? issue.source.assigneeAdapterOverrides : null,
        executionWorkspaceId: null,
        executionWorkspacePreference: null,
        executionWorkspaceSettings: null,
        startedAt: issue.source.startedAt,
        completedAt: issue.source.completedAt,
        cancelledAt: issue.source.cancelledAt,
        hiddenAt: issue.source.hiddenAt,
        createdAt: issue.source.createdAt,
        updatedAt: issue.source.updatedAt,
      });
    }

    const commentCandidates = input.plan.commentPlans.filter(
      (plan): plan is PlannedCommentInsert => plan.action === "insert",
    );
    const commentCandidateIds = commentCandidates.map((comment) => comment.source.id);
    const existingCommentIds = commentCandidateIds.length > 0
      ? new Set(
        (await tx
          .select({ id: issueComments.id })
          .from(issueComments)
          .where(inArray(issueComments.id, commentCandidateIds)))
          .map((row) => row.id),
      )
      : new Set<string>();

    for (const comment of commentCandidates) {
      if (existingCommentIds.has(comment.source.id)) continue;
      const parentExists = await tx
        .select({ id: issues.id })
        .from(issues)
        .where(and(eq(issues.id, comment.source.issueId), eq(issues.companyId, companyId)))
        .then((rows) => rows[0] ?? null);
      if (!parentExists) continue;
      await tx.insert(issueComments).values({
        id: comment.source.id,
        companyId,
        issueId: comment.source.issueId,
        authorAgentId: comment.targetAuthorAgentId,
        authorUserId: comment.source.authorUserId,
        body: comment.source.body,
        createdAt: comment.source.createdAt,
        updatedAt: comment.source.updatedAt,
      });
    }

    return {
      insertedIssues: issueInserts.length,
      insertedComments: commentCandidates.filter((comment) => !existingCommentIds.has(comment.source.id)).length,
      insertedIssueIdentifiers,
    };
  });
}

export async function worktreeMergeHistoryCommand(sourceArg: string, opts: WorktreeMergeHistoryOptions): Promise<void> {
  if (opts.apply && opts.dry) {
    throw new Error("Use either --apply or --dry, not both.");
  }

  const sourceRoot = requirePathArgument("Source worktree path", sourceArg);
  const sourceConfigPath = path.resolve(sourceRoot, ".paperclip", "config.json");
  if (!existsSync(sourceConfigPath)) {
    throw new Error(`Source worktree config not found at ${sourceConfigPath}.`);
  }

  const targetConfigPath = resolveConfigPath();
  if (path.resolve(sourceConfigPath) === path.resolve(targetConfigPath)) {
    throw new Error("Source and target Paperclip configs are the same. Point --source at a different worktree.");
  }

  const scopes = parseWorktreeMergeScopes(opts.scope);
  const sourceHandle = await openConfiguredDb(sourceConfigPath);
  const targetHandle = await openConfiguredDb(targetConfigPath);

  try {
    const company = await resolveMergeCompany({
      sourceDb: sourceHandle.db,
      targetDb: targetHandle.db,
      selector: opts.company,
    });
    let collected = await collectMergePlan({
      sourceDb: sourceHandle.db,
      targetDb: targetHandle.db,
      company,
      scopes,
    });
    if (!opts.yes) {
      const projectIdOverrides = await promptForProjectMappings({
        plan: collected.plan,
        sourceProjects: collected.sourceProjects,
        targetProjects: collected.targetProjects,
      });
      if (Object.keys(projectIdOverrides).length > 0) {
        collected = await collectMergePlan({
          sourceDb: sourceHandle.db,
          targetDb: targetHandle.db,
          company,
          scopes,
          projectIdOverrides,
        });
      }
    }

    console.log(renderMergePlan(collected.plan, {
      sourcePath: sourceRoot,
      unsupportedRunCount: collected.unsupportedRunCount,
      unsupportedDocumentCount: collected.unsupportedDocumentCount,
    }));

    if (!opts.apply) {
      return;
    }

    const confirmed = opts.yes
      ? true
      : await p.confirm({
        message: `Import ${collected.plan.counts.issuesToInsert} issues and ${collected.plan.counts.commentsToInsert} comments from ${path.basename(sourceRoot)}?`,
        initialValue: false,
      });
    if (p.isCancel(confirmed) || !confirmed) {
      p.log.warn("Import cancelled.");
      return;
    }

    const applied = await applyMergePlan({
      targetDb: targetHandle.db,
      company,
      plan: collected.plan,
    });
    p.outro(
      pc.green(
        `Imported ${applied.insertedIssues} issues and ${applied.insertedComments} comments into ${company.issuePrefix}.`,
      ),
    );
  } finally {
    await targetHandle.stop();
    await sourceHandle.stop();
  }
}

export function registerWorktreeCommands(program: Command): void {
  const worktree = program.command("worktree").description("Worktree-local Paperclip instance helpers");

  program
    .command("worktree:make")
    .description("Create ~/NAME as a git worktree, then initialize an isolated Paperclip instance inside it")
    .argument("<name>", "Worktree name — auto-prefixed with paperclip- if needed (created at ~/paperclip-NAME)")
    .option("--start-point <ref>", "Remote ref to base the new branch on (env: PAPERCLIP_WORKTREE_START_POINT)")
    .option("--instance <id>", "Explicit isolated instance id")
    .option("--home <path>", `Home root for worktree instances (env: PAPERCLIP_WORKTREES_DIR, default: ${DEFAULT_WORKTREE_HOME})`)
    .option("--from-config <path>", "Source config.json to seed from")
    .option("--from-data-dir <path>", "Source PAPERCLIP_HOME used when deriving the source config")
    .option("--from-instance <id>", "Source instance id when deriving the source config", "default")
    .option("--server-port <port>", "Preferred server port", (value) => Number(value))
    .option("--db-port <port>", "Preferred embedded Postgres port", (value) => Number(value))
    .option("--seed-mode <mode>", "Seed profile: minimal or full (default: minimal)", "minimal")
    .option("--no-seed", "Skip database seeding from the source instance")
    .option("--force", "Replace existing repo-local config and isolated instance data", false)
    .action(worktreeMakeCommand);

  worktree
    .command("init")
    .description("Create repo-local config/env and an isolated instance for this worktree")
    .option("--name <name>", "Display name used to derive the instance id")
    .option("--instance <id>", "Explicit isolated instance id")
    .option("--home <path>", `Home root for worktree instances (env: PAPERCLIP_WORKTREES_DIR, default: ${DEFAULT_WORKTREE_HOME})`)
    .option("--from-config <path>", "Source config.json to seed from")
    .option("--from-data-dir <path>", "Source PAPERCLIP_HOME used when deriving the source config")
    .option("--from-instance <id>", "Source instance id when deriving the source config", "default")
    .option("--server-port <port>", "Preferred server port", (value) => Number(value))
    .option("--db-port <port>", "Preferred embedded Postgres port", (value) => Number(value))
    .option("--seed-mode <mode>", "Seed profile: minimal or full (default: minimal)", "minimal")
    .option("--no-seed", "Skip database seeding from the source instance")
    .option("--force", "Replace existing repo-local config and isolated instance data", false)
    .action(worktreeInitCommand);

  worktree
    .command("env")
    .description("Print shell exports for the current worktree-local Paperclip instance")
    .option("-c, --config <path>", "Path to config file")
    .option("--json", "Print JSON instead of shell exports")
    .action(worktreeEnvCommand);

  program
    .command("worktree:merge-history")
    .description("Preview or import issue/comment history from another worktree into the current instance")
    .argument("<source>", "Path to the source worktree root")
    .option("--company <id-or-prefix>", "Company id or issue prefix to import")
    .option("--scope <items>", "Comma-separated scopes to import (issues, comments)", "issues,comments")
    .option("--apply", "Apply the import after previewing the plan", false)
    .option("--dry", "Preview only and do not import anything", false)
    .option("--yes", "Skip the interactive confirmation prompt when applying", false)
    .action(worktreeMergeHistoryCommand);

  program
    .command("worktree:cleanup")
    .description("Safely remove a worktree, its branch, and its isolated instance data")
    .argument("<name>", "Worktree name — auto-prefixed with paperclip- if needed")
    .option("--instance <id>", "Explicit instance id (if different from the worktree name)")
    .option("--home <path>", `Home root for worktree instances (env: PAPERCLIP_WORKTREES_DIR, default: ${DEFAULT_WORKTREE_HOME})`)
    .option("--force", "Bypass safety checks (uncommitted changes, unique commits)", false)
    .action(worktreeCleanupCommand);
}