fix(scripts): self-heal isolated workspace provisioning when the base CLI is broken (#10574)
## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Agents run tasks in isolated execution workspaces that are provisioned as git worktrees by `scripts/provision-worktree.sh` > - The script runs the base workspace's CLI (`cli/src/index.ts` via the base `tsx` install) to seed each new worktree, and it only checked that those files exist > - pnpm links each package's `node_modules` into a hash-versioned virtual store; a lockfile change followed by a partial or filtered install prunes old hashed dirs without relinking every package, leaving dangling symlinks > - A CLI with dangling symlinks fails ESM resolution (`ERR_MODULE_NOT_FOUND`) at boot, so provisioning aborts with `setup_failed` — deterministically, on every retry, with no self-heal path > - This pull request makes provisioning health-check the CLI by actually booting it, repair the base install when the check fails, and degrade to the no-CLI fallback config instead of failing the run > - The benefit is that a class of permanent `setup_failed` loops becomes self-healing, and workspace provisioning survives a broken base CLI ## Linked Issues or Issue Description No public GitHub issue exists; the underlying bug is described here per `bug_report.yml`. Related PR: #10578 self-heals the sibling workspace-validation failure loop uncovered by the same incident diagnosis. **What happened?** Isolated-workspace runs failed at provision time with `setup_failed`. Every retry failed identically. One observed incident burned 4 runs across two adapters before the task was stranded. **Expected behavior** Provisioning either succeeds or degrades gracefully; a broken base CLI install repairs itself instead of permanently blocking all new worktrees. **Steps to reproduce** In the base workspace, cause a lockfile-affecting dependency bump plus a partial/filtered `pnpm install` so a package symlink (e.g. `cli/node_modules/drizzle-orm`) dangles into a pruned virtual-store dir. Start any isolated-workspace run. Provision fails with `ERR_MODULE_NOT_FOUND` and the run ends `setup_failed`; retries never recover. **Paperclip version or commit** master as of the branch point of this PR. **Deployment mode** Local trusted deployment with git-worktree isolated workspaces. ## What Changed - `base_cli_healthy` now boots the base CLI (`--help`) instead of only testing file existence, which exercises the top-level import graph. - New `repair_base_workspace_install`: when the health check fails, run a non-interactive `pnpm install --prod=false --force --frozen-lockfile` in the base workspace. `--force` guarantees relinking when pnpm's up-to-date heuristics would skip dangling symlinks; `--frozen-lockfile` keeps the repair from mutating the shared lockfile. - The repair install is serialized with `flock` on a lock file inside the resolved git dir (`git rev-parse --absolute-git-dir`), so locking also covers base workspaces that are linked worktrees, where `.git` is a file. - If every CLI candidate is unusable (including a base CLI the repair could not fix), provisioning falls back to the existing no-CLI fallback config writer (loudly, on stderr) instead of failing the run. A CLI that runs and fails `worktree init` still fails provisioning with its real exit code — that deliberate fail-closed policy is unchanged and covered by an existing server regression test. - Fixed a latent bug: `run_isolated_worktree_init` returned 0 unconditionally after the init subshell, so callers treated a failed init as success. Exit codes now propagate. ## Verification - Reproduced the incident state (dangling `cli/node_modules/drizzle-orm` symlink); the base CLI failed with the exact `ERR_MODULE_NOT_FOUND` seen in the incident run logs. - Ran the patched script against a fresh scratch worktree: health check failed → locked repair install ran (~26 s warm) → symlink relinked → `worktree init` completed → exit 0 with `.paperclip/config.json` and `.env` written. - Happy path (healthy base CLI): provisioning behavior unchanged, exit 0. - Verified `git rev-parse --absolute-git-dir` resolves a real directory for both a normal checkout and a linked worktree. - New hermetic tests: `node --test ./scripts/__tests__/provision-worktree-self-heal.test.mjs` (4 tests: healthy CLI used, broken CLI degrades, locked repair end-to-end with a fake pnpm, init failure propagates). Not yet wired into a CI workflow. - `server`: the existing `realizeExecutionWorkspace` fail-closed regression test ("fails instead of writing an unseeded fallback config when worktree init errors after CLI detection succeeds") passes against the new script. - `bash -n scripts/provision-worktree.sh` is clean. ## Risks - Low risk overall: the script only adds recovery paths; the happy path is unchanged. - The repair install runs in the shared base workspace. It is bounded by `--frozen-lockfile` (no lockfile mutation) and serialized by `flock`, but it can add ~30 s to the first provision after a base install breaks. - If the repair cannot fix the CLI and no other CLI candidate exists, runs now continue with an unseeded fallback config instead of failing; that is intentional, and the fallback path already existed. Genuine `worktree init` failures from a working CLI still fail the run. ## Model Used Claude Fable 5 (Anthropic, model ID `claude-fable-5`), extended thinking, agentic tool use (Claude Code harness). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: Paperclip <noreply@paperclip.ing>
This commit is contained in:
Dotta
GitHub
parent
3176e1f4b9
commit
79eff0aea1
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@ -0,0 +1,204 @@
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import assert from "node:assert/strict";
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import { spawnSync } from "node:child_process";
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import test from "node:test";
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import fs from "node:fs";
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import os from "node:os";
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import path from "node:path";
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const script = new URL("../provision-worktree.sh", import.meta.url).pathname;
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// Keep the PATH minimal so the fallback ladder is deterministic: node must be
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// reachable, but a globally installed `paperclipai` must not shadow the paths
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// under test.
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const testPath = [path.dirname(process.execPath), "/usr/bin", "/bin"].join(":");
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const cleanupDirs = [];
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function makeTempDir(prefix) {
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const dir = fs.mkdtempSync(path.join(os.tmpdir(), prefix));
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cleanupDirs.push(dir);
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return dir;
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}
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test.after(() => {
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for (const dir of cleanupDirs) {
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fs.rmSync(dir, { recursive: true, force: true });
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}
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});
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/**
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* Writes a fake base workspace whose "tsx runner" is a plain node script, so
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* the provision script's health check and init call can be steered per test.
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*
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* helpExit: exit code for `... index.ts --help` (the health check boot).
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* initExit: exit code for `... index.ts worktree init ...`; on 0 the fake CLI
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* writes a marker config so tests can tell CLI init from fallback.
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*/
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function makeBaseWorkspace({ helpExit, initExit }) {
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const baseCwd = makeTempDir("paperclip-provision-base-");
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const runnerPath = path.join(baseCwd, "cli", "node_modules", "tsx", "dist", "cli.mjs");
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const entryPath = path.join(baseCwd, "cli", "src", "index.ts");
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fs.mkdirSync(path.dirname(runnerPath), { recursive: true });
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fs.mkdirSync(path.dirname(entryPath), { recursive: true });
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fs.writeFileSync(entryPath, "// fake CLI entry\n");
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fs.writeFileSync(
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runnerPath,
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`
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import fs from "node:fs";
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const cliArgs = process.argv.slice(3);
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if (cliArgs.includes("--help")) {
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if (${helpExit} !== 0) console.error("ERR_MODULE_NOT_FOUND: drizzle-orm");
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process.exit(${helpExit});
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}
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if (cliArgs[0] === "worktree" && cliArgs[1] === "init") {
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if (${initExit} !== 0) {
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console.error("fake worktree init failure");
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process.exit(${initExit});
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}
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fs.mkdirSync(".paperclip", { recursive: true });
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fs.writeFileSync(".paperclip/config.json", JSON.stringify({ $meta: { source: "fake-cli" } }));
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fs.writeFileSync(".paperclip/.env", "PAPERCLIP_IN_WORKTREE=true\\n");
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process.exit(0);
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}
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process.exit(0);
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`,
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);
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return baseCwd;
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}
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function runProvision(baseCwd, { pathPrefix } = {}) {
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const worktreeCwd = makeTempDir("paperclip-provision-worktree-");
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const worktreesHome = makeTempDir("paperclip-provision-home-");
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const result = spawnSync("bash", [script], {
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cwd: worktreeCwd,
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encoding: "utf8",
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env: {
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PATH: pathPrefix ? `${pathPrefix}:${testPath}` : testPath,
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HOME: os.homedir(),
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PAPERCLIP_WORKSPACE_BASE_CWD: baseCwd,
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PAPERCLIP_WORKSPACE_CWD: worktreeCwd,
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PAPERCLIP_WORKSPACE_BRANCH: "feature/provision-test",
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PAPERCLIP_WORKTREES_DIR: worktreesHome,
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PAPERCLIP_HOME: path.join(worktreesHome, "no-such-instance-home"),
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},
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});
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return { result, worktreeCwd, worktreesHome };
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}
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function readWorktreeConfig(worktreeCwd) {
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const configPath = path.join(worktreeCwd, ".paperclip", "config.json");
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assert.ok(fs.existsSync(configPath), `expected ${configPath} to exist`);
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return JSON.parse(fs.readFileSync(configPath, "utf8"));
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}
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test("uses the base CLI when its import graph boots", () => {
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const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
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const { result, worktreeCwd } = runProvision(baseCwd);
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assert.equal(result.status, 0, result.stderr);
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const config = readWorktreeConfig(worktreeCwd);
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assert.equal(config.$meta.source, "fake-cli");
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});
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test("falls back to an isolated config when the base CLI cannot boot", () => {
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// Simulates the dangling pnpm symlink incident: the runner and entry files
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// exist, but booting the CLI fails ESM resolution. The base has no
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// package.json/pnpm-lock.yaml, so the repair install is not possible and the
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// script must degrade to the no-CLI fallback config instead of failing.
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const baseCwd = makeBaseWorkspace({ helpExit: 1, initExit: 0 });
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const { result, worktreeCwd, worktreesHome } = runProvision(baseCwd);
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assert.equal(result.status, 0, result.stderr);
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assert.match(result.stderr, /writing isolated fallback config/);
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const config = readWorktreeConfig(worktreeCwd);
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assert.equal(config.$meta.source, "configure");
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const dataDir = config.database.embeddedPostgresDataDir;
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assert.ok(
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!path.relative(worktreesHome, dataDir).startsWith(".."),
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`expected ${dataDir} to live under ${worktreesHome}`,
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);
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const env = fs.readFileSync(path.join(worktreeCwd, ".paperclip", ".env"), "utf8");
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assert.match(env, /PAPERCLIP_IN_WORKTREE=true/);
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});
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test("repairs an unhealthy base install under the lock and then uses the CLI", (t) => {
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const hasTools = ["flock", "git"].every(
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(tool) => spawnSync("bash", ["-lc", `command -v ${tool}`], { env: { PATH: testPath } }).status === 0,
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);
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if (!hasTools) {
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t.skip("flock or git not available on this host");
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return;
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}
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// The CLI's health is controlled by a flag file, and a fake `pnpm install`
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// creates that flag — modeling a forced reinstall that relinks the store.
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const baseCwd = makeTempDir("paperclip-provision-repair-base-");
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const healthFlag = path.join(baseCwd, "cli-healthy.flag");
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const runnerPath = path.join(baseCwd, "cli", "node_modules", "tsx", "dist", "cli.mjs");
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const entryPath = path.join(baseCwd, "cli", "src", "index.ts");
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fs.mkdirSync(path.dirname(runnerPath), { recursive: true });
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fs.mkdirSync(path.dirname(entryPath), { recursive: true });
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fs.writeFileSync(entryPath, "// fake CLI entry\n");
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fs.writeFileSync(
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runnerPath,
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`
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import fs from "node:fs";
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const cliArgs = process.argv.slice(3);
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if (cliArgs.includes("--help")) {
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process.exit(fs.existsSync(${JSON.stringify(healthFlag)}) ? 0 : 1);
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}
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if (cliArgs[0] === "worktree" && cliArgs[1] === "init") {
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fs.mkdirSync(".paperclip", { recursive: true });
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fs.writeFileSync(".paperclip/config.json", JSON.stringify({ $meta: { source: "fake-cli" } }));
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fs.writeFileSync(".paperclip/.env", "PAPERCLIP_IN_WORKTREE=true\\n");
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process.exit(0);
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}
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process.exit(0);
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`,
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);
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fs.writeFileSync(path.join(baseCwd, "package.json"), "{}\n");
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fs.writeFileSync(path.join(baseCwd, "pnpm-lock.yaml"), "lockfileVersion: '9.0'\n");
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spawnSync("git", ["init", "-q", baseCwd], { env: { PATH: testPath } });
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const fakeBin = makeTempDir("paperclip-provision-fakebin-");
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const installLog = path.join(baseCwd, "pnpm-invocations.log");
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fs.writeFileSync(
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path.join(fakeBin, "pnpm"),
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`#!/usr/bin/env bash
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if [[ "$1" == "install" ]]; then
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echo "$@" >> ${JSON.stringify(installLog)}
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touch ${JSON.stringify(healthFlag)}
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exit 0
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fi
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exit 1
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`,
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{ mode: 0o755 },
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);
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const { result, worktreeCwd } = runProvision(baseCwd, { pathPrefix: fakeBin });
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assert.equal(result.status, 0, result.stderr);
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const config = readWorktreeConfig(worktreeCwd);
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assert.equal(config.$meta.source, "fake-cli");
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const installs = fs.readFileSync(installLog, "utf8").trim().split("\n");
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assert.equal(installs.length, 1, `expected exactly one repair install, got: ${installs.join(" | ")}`);
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assert.match(installs[0], /--force/);
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assert.match(installs[0], /--frozen-lockfile/);
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assert.ok(
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fs.existsSync(path.join(baseCwd, ".git", "paperclip-provision-repair.lock")),
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"expected the repair lock file inside the resolved git dir",
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);
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});
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test("a failed CLI init fails provisioning instead of being masked as success", () => {
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// Regression test for the masked `return 0` after the init subshell: a CLI
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// that passes the health check but fails `worktree init` signals a real
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// problem, so the script must propagate the failure rather than report
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// success or write an unseeded fallback config over it.
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const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 3 });
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const { result, worktreeCwd } = runProvision(baseCwd);
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assert.equal(result.status, 3, result.stderr);
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assert.match(result.stderr, /fake worktree init failure/);
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assert.ok(!fs.existsSync(path.join(worktreeCwd, ".paperclip", "config.json")));
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});
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@ -31,32 +31,89 @@ source_env_path="$(dirname "$source_config_path")/.env"
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mkdir -p "$paperclip_dir"
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run_isolated_worktree_init() {
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local base_cli_runner="$base_cwd/cli/node_modules/tsx/dist/cli.mjs"
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local base_cli_entry="$base_cwd/cli/src/index.ts"
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base_cli_runner_path="$base_cwd/cli/node_modules/tsx/dist/cli.mjs"
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base_cli_entry_path="$base_cwd/cli/src/index.ts"
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if [[ -f "$base_cli_runner" && -f "$base_cli_entry" ]]; then
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base_cli_files_present() {
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[[ -f "$base_cli_runner_path" && -f "$base_cli_entry_path" ]]
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}
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# File existence is not enough: pnpm links package node_modules into the
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# versioned virtual store, so a lockfile change plus a partial/filtered install
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# in the base workspace leaves dangling symlinks that fail ESM resolution at
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# runtime. Actually boot the CLI to prove its import graph resolves.
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base_cli_healthy() {
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base_cli_files_present || return 1
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(cd "$base_cwd" && node "$base_cli_runner_path" "$base_cli_entry_path" --help >/dev/null 2>&1)
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}
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repair_base_workspace_install() {
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command -v pnpm >/dev/null 2>&1 || return 1
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[[ -f "$base_cwd/package.json" && -f "$base_cwd/pnpm-lock.yaml" ]] || return 1
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echo "Base workspace CLI at $base_cli_entry_path failed its health check (typically dangling pnpm symlinks after a partial install); repairing with pnpm install in $base_cwd." >&2
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# --force guarantees relinking even when pnpm's up-to-date heuristics would
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# otherwise skip the dangling symlinks; --frozen-lockfile keeps the repair
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# from mutating the shared base workspace's lockfile.
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local repair_cmd=(pnpm install --prod=false --force --frozen-lockfile --config.confirmModulesPurge=false)
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# Resolve the real git dir so locking also covers base workspaces that are
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# linked worktrees, where "$base_cwd/.git" is a file rather than a directory.
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local repair_lock_dir=""
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if command -v git >/dev/null 2>&1; then
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repair_lock_dir="$(git -C "$base_cwd" rev-parse --absolute-git-dir 2>/dev/null || true)"
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fi
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if [[ ! -d "$repair_lock_dir" && -d "$base_cwd/.git" ]]; then
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repair_lock_dir="$base_cwd/.git"
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fi
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if command -v flock >/dev/null 2>&1 && [[ -d "$repair_lock_dir" ]]; then
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# The post-repair verification must run under the same lock: a concurrent
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# provision's forced install could be mid-relink during an unlocked check
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# and fail a repair that actually succeeded. Holding the lock also means a
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# process that queued behind a peer's repair can skip its own reinstall.
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(
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cd "$worktree_cwd"
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node "$base_cli_runner" "$base_cli_entry" worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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cd "$base_cwd" || exit 1
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exec 9>"$repair_lock_dir/paperclip-provision-repair.lock"
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flock 9
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if base_cli_healthy; then
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echo "Base workspace CLI became healthy while waiting for the repair lock; skipping reinstall." >&2
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exit 0
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fi
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env -u NODE_ENV CI=true "${repair_cmd[@]}" >&2 || exit 1
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base_cli_healthy
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)
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return 0
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else
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(cd "$base_cwd" && env -u NODE_ENV CI=true "${repair_cmd[@]}" >&2 && base_cli_healthy)
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fi
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}
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ensure_base_cli_healthy() {
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base_cli_files_present || return 1
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base_cli_healthy && return 0
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repair_base_workspace_install
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}
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run_isolated_worktree_init() {
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if ensure_base_cli_healthy; then
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(
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cd "$worktree_cwd" &&
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node "$base_cli_runner_path" "$base_cli_entry_path" worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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)
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return
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fi
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if command -v pnpm >/dev/null 2>&1 && pnpm paperclipai --help >/dev/null 2>&1; then
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(
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cd "$worktree_cwd"
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pnpm paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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cd "$worktree_cwd" &&
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pnpm paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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)
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return 0
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return
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fi
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if command -v paperclipai >/dev/null 2>&1; then
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(
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cd "$worktree_cwd"
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paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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cd "$worktree_cwd" &&
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paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
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)
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return 0
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return
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fi
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return 127
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@ -67,9 +124,7 @@ paperclipai_command_available() {
|
|||
return 0
|
||||
fi
|
||||
|
||||
local base_cli_tsx_path="$base_cwd/cli/node_modules/tsx/dist/cli.mjs"
|
||||
local base_cli_entry_path="$base_cwd/cli/src/index.ts"
|
||||
if command -v node >/dev/null 2>&1 && [[ -f "$base_cli_tsx_path" ]] && [[ -f "$base_cli_entry_path" ]]; then
|
||||
if command -v node >/dev/null 2>&1 && base_cli_files_present; then
|
||||
return 0
|
||||
fi
|
||||
|
||||
|
|
@ -429,9 +484,24 @@ else
|
|||
echo "Existing isolated Paperclip worktree config is stale for this host; regenerating." >&2
|
||||
fi
|
||||
if paperclipai_command_available; then
|
||||
run_isolated_worktree_init
|
||||
if run_isolated_worktree_init; then
|
||||
:
|
||||
else
|
||||
init_exit_code=$?
|
||||
if [[ "$init_exit_code" -eq 127 ]]; then
|
||||
# Every CLI candidate was unusable (e.g. an unhealthy base install that
|
||||
# the repair could not fix); degrade instead of stranding the run.
|
||||
echo "No usable paperclipai CLI found; writing isolated fallback config without DB seeding." >&2
|
||||
write_fallback_worktree_config
|
||||
else
|
||||
# A CLI that ran and failed signals a real problem; do not paper over
|
||||
# it with an unseeded fallback config.
|
||||
echo "paperclipai worktree init failed (exit $init_exit_code); failing provisioning instead of writing an unseeded fallback config." >&2
|
||||
exit "$init_exit_code"
|
||||
fi
|
||||
fi
|
||||
else
|
||||
echo "paperclipai CLI not available in this workspace; writing isolated fallback config without DB seeding." >&2
|
||||
echo "paperclipai worktree init unavailable; writing isolated fallback config without DB seeding." >&2
|
||||
write_fallback_worktree_config
|
||||
fi
|
||||
fi
|
||||
|
|
|
|||
Loading…
Reference in New Issue