fix(dev): copy linked metadata into independent seed files

docs/development.md

@@ -49,7 +49,7 @@ than downloading a published desktop release.
 - The **server itself** (e.g. when launched by the desktop app or `npm run start`) defaults to `~/.paseo` (see `packages/server/src/server/paseo-home.ts`).
 - **Repo dev scripts** default to `$ROOT/.dev/paseo-home`, where `$ROOT` is the current checkout or worktree root. This keeps all dev state scoped to the checkout instead of the packaged desktop app.
 - **`npm run cli -- ...`** runs through the same dev-home wrapper as the dev scripts, so the in-repo CLI automatically targets the current checkout's `.dev/paseo-home` and configured dev daemon endpoint.
-- **Paseo-created worktrees** seed `$PASEO_WORKTREE_PATH/.dev/paseo-home` from `$PASEO_SOURCE_CHECKOUT_PATH/.dev/paseo-home` by copying durable JSON metadata. Runtime files like pid files, sockets, and logs are not copied.
+- **Paseo-created worktrees** seed `$PASEO_WORKTREE_PATH/.dev/paseo-home` from `$PASEO_SOURCE_CHECKOUT_PATH/.dev/paseo-home` by copying agent and project JSON metadata and configuration. Both this setup and `PASEO_DEV_SEED_HOME` use the same seeder, which disables `agents.resumeOnStartup` in the copied config. Startup repairs copied running records without resuming agents or sending recovery prompts. Schedules and heartbeats (stored under `schedules/`), runtime files, identities, sockets, and logs are not copied. Existing nonempty homes are left unchanged unless explicitly reset. Copied agents still reference the original provider sessions and working directories: manually prompting one reaches that real session.
 - **This repo's worktree setup** also best-effort seeds `packages/app/ios` and the newest `.dev/ios-build` entry from the source checkout so iOS simulator services can reuse native project and Xcode cache state when it is safe enough to do so.
 
 Override knobs:

packages/server/src/server/agent/restart-recovery/index.test.ts

@@ -1,9 +1,12 @@
 import { expect, test } from "vitest";
-import { mkdtemp, rm } from "node:fs/promises";
+import { mkdtemp, rm, mkdir, writeFile, readdir, symlink } from "node:fs/promises";
 import { tmpdir } from "node:os";
+import { execFileSync, spawnSync } from "node:child_process";
+import { fileURLToPath } from "node:url";
 import { join } from "node:path";
 import { AgentStorage, parseStoredAgentRecord } from "../agent-storage.js";
 import { createTestLogger } from "../../../test-utils/test-logger.js";
+import { readPersistedConfig } from "../../persisted-config.js";
 import { createRestartRecovery } from "./index.js";
 
 test("recovery saves intent before normalization, clears before dispatch, and resumes each agent independently", async () => {
@@ -103,3 +106,130 @@ test("opt-out consumes pending recovery and excludes archived, private, owned an
     await rm(root, { recursive: true, force: true });
   }
 });
+
+const bashAvailable =
+  process.platform !== "win32" &&
+  spawnSync("bash", ["-c", "true"], { stdio: "ignore" }).status === 0;
+for (const seeder of ["setup", "shell", "setup-bom"] as const) {
+  test.skipIf(seeder === "shell" && !bashAvailable)(
+    `${seeder} seed never dispatches copied running or pending agents and excludes automation`,
+    async () => {
+      const root = await mkdtemp(join(tmpdir(), "inert-seed-"));
+      try {
+        const source = join(root, "source");
+        const targetRoot = join(root, "target");
+        const target = join(targetRoot, ".dev/paseo-home");
+        const storage = new AgentStorage(join(root, "source-records"), createTestLogger());
+        for (const [id, lastStatus, resumeOnStartup] of [
+          ["live", "running", false],
+          ["crashed", "running", true],
+          ["stopped", "closed", true],
+        ] as const) {
+          await storage.upsert(
+            parseStoredAgentRecord({
+              id,
+              lastStatus,
+              resumeOnStartup,
+              provider: "codex",
+              cwd: root,
+              createdAt: new Date().toISOString(),
+              updatedAt: new Date().toISOString(),
+            }),
+          );
+        }
+        await storage.flush();
+        await mkdir(source, { recursive: true });
+        await symlink(
+          join(root, "source-records"),
+          join(source, "agents"),
+          process.platform === "win32" ? "junction" : "dir",
+        );
+        await mkdir(join(source, "schedules"), { recursive: true });
+        await writeFile(join(source, "schedules", "schedule.json"), '{"kind":"scheduled"}');
+        await writeFile(join(source, "schedules", "heartbeat.json"), '{"kind":"heartbeat"}');
+        await writeFile(
+          join(source, "config.json"),
+          (seeder === "setup-bom" ? "\uFEFF" : "") +
+            JSON.stringify({
+              version: 1,
+              agents: { resumeOnStartup: true, resumePrompt: "Continue" },
+            }),
+        );
+        const repo = fileURLToPath(new URL("../../../../../../", import.meta.url));
+        const env = {
+          ...process.env,
+          PASEO_SOURCE_CHECKOUT_PATH: join(root, "checkout"),
+          PASEO_WORKTREE_PATH: targetRoot,
+          PASEO_DEV_SEED_HOME: source,
+          PASEO_HOME: target,
+        };
+        if (seeder !== "shell")
+          execFileSync(process.execPath, [join(repo, "scripts/seed-worktree-dev-state.mjs")], {
+            env,
+          });
+        else {
+          const linkedRepo = join(root, "linked-checkout");
+          await symlink(repo, linkedRepo, "dir");
+          execFileSync("bash", [join(linkedRepo, "scripts/dev-home.sh")], { env });
+        }
+        expect((await readdir(target)).sort()).toEqual(["agents", "config.json"]);
+        const config = readPersistedConfig(target);
+        const copied = new AgentStorage(join(target, "agents"), createTestLogger());
+        const dispatched: string[] = [];
+        const recovery = createRestartRecovery({
+          storage: copied,
+          settings: () => ({
+            enabled: config.agents?.resumeOnStartup === true,
+            prompt: "Continue",
+          }),
+          eligible: async () => true,
+          dispatch: async (id) => {
+            dispatched.push(id);
+          },
+          report: () => {},
+        });
+        await recovery.prepareStartup();
+        recovery.resumePending();
+        for (const record of await copied.listAll())
+          await recovery.waitForResume(record.id, new AbortController().signal);
+        expect(dispatched).toEqual([]);
+        expect((await copied.listAll()).map((r) => [r.lastStatus, r.resumeOnStartup])).toEqual([
+          ["closed", false],
+          ["closed", false],
+          ["closed", false],
+        ]);
+        expect(readPersistedConfig(source).agents?.resumeOnStartup).toBe(true);
+        const unchangedSource = new AgentStorage(join(root, "source-records"), createTestLogger());
+        expect((await unchangedSource.get("live"))?.lastStatus).toBe("running");
+      } finally {
+        await rm(root, { recursive: true, force: true });
+      }
+    },
+  );
+}
+
+test("seeding skips an existing home without reading invalid source config", async () => {
+  const root = await mkdtemp(join(tmpdir(), "seed-skip-"));
+  try {
+    const source = join(root, "source");
+    const targetRoot = join(root, "target");
+    const target = join(targetRoot, ".dev/paseo-home");
+    await mkdir(source, { recursive: true });
+    await mkdir(target, { recursive: true });
+    await writeFile(join(source, "config.json"), "invalid JSON");
+    await writeFile(join(target, "keep.json"), "{}");
+    const repo = fileURLToPath(new URL("../../../../../../", import.meta.url));
+    execFileSync(process.execPath, [join(repo, "scripts/seed-worktree-dev-state.mjs")], {
+      env: {
+        ...process.env,
+        PASEO_SOURCE_CHECKOUT_PATH: join(root, "checkout"),
+        PASEO_WORKTREE_PATH: targetRoot,
+        PASEO_DEV_SEED_HOME: source,
+        PASEO_DEV_RESET_HOME: "0",
+      },
+    });
+    expect(await readdir(target)).toEqual(["keep.json"]);
+  } finally {
+    await rm(root, { recursive: true, force: true });
+  }
+});

scripts/dev-home.sh

@@ -4,62 +4,10 @@ default_dev_paseo_root() {
   git rev-parse --show-toplevel 2>/dev/null || pwd
 }
 
-copy_json_tree() {
-  local source_dir="$1"
-  local target_dir="$2"
-
-  if [ ! -d "$source_dir" ]; then
-    return
-  fi
-
-  mkdir -p "$target_dir"
-  if command -v rsync >/dev/null 2>&1; then
-    rsync -a --include='*/' --include='*.json' --exclude='*' "$source_dir/" "$target_dir/"
-    return
-  fi
-
-  while IFS= read -r -d '' source_file; do
-    local relative_path="${source_file#"$source_dir"/}"
-    local target_file="$target_dir/$relative_path"
-    mkdir -p "$(dirname "$target_file")"
-    cp "$source_file" "$target_file"
-  done < <(find "$source_dir" -type f -name '*.json' -print0)
-}
-
-has_files() {
-  [ -d "$1" ] && [ -n "$(find "$1" -mindepth 1 -maxdepth 1 -print -quit 2>/dev/null)" ]
-}
-
 seed_worktree_paseo_home() {
-  local source_home="${PASEO_DEV_SEED_HOME:-$HOME/.paseo}"
-  local target_home="$1"
-
-  if [ ! -d "$source_home" ]; then
-    echo "  Seed:    skipped (${source_home} missing)"
-    return
-  fi
-
-  if [ "$source_home" = "$target_home" ]; then
-    echo "  Seed:    skipped (source is target)"
-    return
-  fi
-
-  if [ "${PASEO_DEV_RESET_HOME:-0}" = "1" ]; then
-    rm -rf "$target_home"
-  elif has_files "$target_home"; then
-    echo "  Seed:    skipped (${target_home} already has data)"
-    return
-  fi
-
-  mkdir -p "$target_home"
-  echo "  Seed:    copying metadata from ${source_home}"
-  copy_json_tree "$source_home/agents" "$target_home/agents"
-  copy_json_tree "$source_home/projects" "$target_home/projects"
-  if [ -f "$source_home/config.json" ]; then
-    cp "$source_home/config.json" "$target_home/config.json"
-  fi
-
-  echo "  Seed:    copied metadata from ${source_home}"
+  local script_dir
+  script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+  node "$script_dir/seed-dev-home.mjs" "${PASEO_DEV_SEED_HOME:-$HOME/.paseo}" "$1"
 }
 
 configure_dev_daemon_config() {

scripts/seed-dev-home.mjs

@@ -0,0 +1,84 @@
+import {
+  cpSync,
+  realpathSync,
+  existsSync,
+  mkdirSync,
+  readdirSync,
+  rmSync,
+  statSync,
+  readFileSync,
+  writeFileSync,
+} from "node:fs";
+import { join } from "node:path";
+import { pathToFileURL } from "node:url";
+
+export function seedPaseoHome(source, target) {
+  if (!existsSync(source)) {
+    console.log(`  Seed:    skipped (${source} missing)`);
+    return;
+  }
+
+  if (source === target) {
+    console.log("  Seed:    skipped (source is target)");
+    return;
+  }
+
+  if (process.env.PASEO_DEV_RESET_HOME !== "1" && hasEntries(target)) {
+    console.log(`  Seed:    skipped (${target} already has data)`);
+    return;
+  }
+
+  const configPath = join(source, "config.json");
+  const config = existsSync(configPath)
+    ? JSON.parse(readFileSync(configPath, "utf8").replace(/^\uFEFF/, ""))
+    : { version: 1 };
+
+  if (process.env.PASEO_DEV_RESET_HOME === "1") {
+    rmSync(target, { recursive: true, force: true });
+  }
+
+  mkdirSync(target, { recursive: true });
+  console.log(`  Seed:    copying metadata from ${source}`);
+  copyJsonTree(join(source, "agents"), join(target, "agents"));
+  copyJsonTree(join(source, "projects"), join(target, "projects"));
+
+  // A snapshot does not own the source daemon's pending work. Recovery normalizes
+  // copied running records on startup without sending a prompt when disabled.
+  config.agents = { ...config.agents, resumeOnStartup: false };
+  writeFileSync(join(target, "config.json"), JSON.stringify(config, null, 2));
+
+  console.log(`  Seed:    copied metadata from ${source}`);
+}
+
+// Durable JSON metadata only. Runtime files (pid files, sockets, logs) must not be copied.
+function copyJsonTree(source, target) {
+  if (!existsSync(source)) {
+    return;
+  }
+
+  cpSync(source, target, {
+    recursive: true,
+    dereference: true,
+    filter: (path) => isDirectory(path) || path.endsWith(".json"),
+  });
+}
+
+function hasEntries(path) {
+  try {
+    return readdirSync(path).length > 0;
+  } catch {
+    return false;
+  }
+}
+
+function isDirectory(path) {
+  try {
+    return statSync(path).isDirectory();
+  } catch {
+    return false;
+  }
+}
+
+if (process.argv[1] && import.meta.url === pathToFileURL(realpathSync(process.argv[1])).href) {
+  seedPaseoHome(process.argv[2], process.argv[3]);
+}

scripts/seed-worktree-dev-state.mjs

@@ -1,5 +1,5 @@
 #!/usr/bin/env node
-import { cpSync, existsSync, mkdirSync, readdirSync, rmSync, statSync } from "node:fs";
+import { cpSync, existsSync, mkdirSync } from "node:fs";
 import { dirname, join } from "node:path";
 
 // Worktree setup runs through a stable script shell: bash on macOS/Linux, but PowerShell
@@ -7,6 +7,8 @@ import { dirname, join } from "node:path";
 // `./scripts/*.sh`) cannot express this step portably, so the seeding lives in Node — the
 // one interpreter every Paseo checkout already depends on.
 
+import { seedPaseoHome } from "./seed-dev-home.mjs";
+
 const sourceRoot = process.env.PASEO_SOURCE_CHECKOUT_PATH;
 const targetRoot = process.env.PASEO_WORKTREE_PATH || process.cwd();
 
@@ -14,55 +16,12 @@ if (!sourceRoot || sourceRoot === targetRoot) {
   process.exit(0);
 }
 
-seedPaseoHome();
+seedPaseoHome(
+  process.env.PASEO_DEV_SEED_HOME || join(sourceRoot, ".dev/paseo-home"),
+  join(targetRoot, ".dev/paseo-home"),
+);
 copyServerEnv();
 
-function seedPaseoHome() {
-  const source = process.env.PASEO_DEV_SEED_HOME || join(sourceRoot, ".dev/paseo-home");
-  const target = join(targetRoot, ".dev/paseo-home");
-
-  if (!existsSync(source)) {
-    console.log(`  Seed:    skipped (${source} missing)`);
-    return;
-  }
-
-  if (source === target) {
-    console.log("  Seed:    skipped (source is target)");
-    return;
-  }
-
-  if (process.env.PASEO_DEV_RESET_HOME === "1") {
-    rmSync(target, { recursive: true, force: true });
-  } else if (hasEntries(target)) {
-    console.log(`  Seed:    skipped (${target} already has data)`);
-    return;
-  }
-
-  mkdirSync(target, { recursive: true });
-  console.log(`  Seed:    copying metadata from ${source}`);
-  copyJsonTree(join(source, "agents"), join(target, "agents"));
-  copyJsonTree(join(source, "projects"), join(target, "projects"));
-
-  const config = join(source, "config.json");
-  if (existsSync(config)) {
-    cpSync(config, join(target, "config.json"));
-  }
-
-  console.log(`  Seed:    copied metadata from ${source}`);
-}
-
-// Durable JSON metadata only. Runtime files (pid files, sockets, logs) must not be copied.
-function copyJsonTree(source, target) {
-  if (!existsSync(source)) {
-    return;
-  }
-
-  cpSync(source, target, {
-    recursive: true,
-    filter: (path) => isDirectory(path) || path.endsWith(".json"),
-  });
-}
-
 function copyServerEnv() {
   const source = join(sourceRoot, "packages/server/.env");
   const target = join(targetRoot, "packages/server/.env");
@@ -77,19 +36,3 @@ function copyServerEnv() {
   cpSync(source, target);
   console.log(`  Env:     copied ${source}`);
 }
-
-function hasEntries(path) {
-  try {
-    return readdirSync(path).length > 0;
-  } catch {
-    return false;
-  }
-}
-
-function isDirectory(path) {
-  try {
-    return statSync(path).isDirectory();
-  } catch {
-    return false;
-  }
-}