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## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents do that work in isolated git worktrees, and a managed
worktree runs its own Paperclip instance with a cloned database
> - That clone needs a seed source, and the source must come from
server-owned registration, never from state the workspace itself can
rewrite
> - The seed-source resolver requires the registered base project
workspace to hold its own `.paperclip/config.json`
> - A managed project workspace is a plain `git clone`, and no code
writes that file into it
> - Every isolated worktree provision, deferred seed, and workspace
repair therefore fails on a managed checkout
> - This pull request lets a named source supply the config when the
base checkout has none
> - The benefit is that managed worktrees provision again, and the seed
source stays server-owned
## Linked Issues or Issue Description
No public GitHub issue exists for this problem. It is described below.
**What happened?**
Agent runs that need an isolated worktree fail during provisioning. The
provision command exits with this error (paths redacted):
```
Execution workspace provision command "bash ./scripts/provision-worktree.sh" failed:
Registered base project workspace has no canonical Paperclip config:
<instance-home>/instances/default/projects/<company-id>/<project-id>/<repo>/.paperclip/config.json
```
`resolveRegisteredWorktreeSeedSource` sets `registeredConfigPath` to
`<baseCwd>/.paperclip/config.json` whenever the caller names a
registered base workspace. It then requires that file to exist.
`scripts/provision-worktree.sh` applies the same rule.
A managed project workspace never has that file.
`materializeManagedProjectWorkspace` creates it with `git clone` and a
rename, so the checkout holds repository content only. The control plane
keeps its config at `<home>/instances/<id>/config.json` instead.
The failure reaches three paths: worktree provisioning, deferred seeding
through `worktree ensure-seeded`, and workspace repair.
The behavior changed in #11671. That pull request replaced a fallback
chain with a single hard requirement. Fixture code in
`scripts/__tests__/provision-worktree-self-heal.test.mjs` writes a
config into the fake base workspace, so tests kept passing.
**Expected behavior**
A managed worktree provisions and seeds from the registered source. The
seed manifest still never selects that source.
**Steps to reproduce**
1. Register the Paperclip repository as a project with a `repoUrl`, so
the server materializes a managed checkout.
2. Assign an issue to an agent whose workspace strategy is
`git_worktree`.
3. Watch the workspace operation log for the provision command.
4. The command exits non-zero with the error above.
**Paperclip version or commit**
Reproduced on `master` at 01ddc26a3.
**Deployment mode**
`local_trusted`, single instance.
**Database mode**
Embedded PostgreSQL.
**Operating system**
Linux, Node.js 22.
**Related pull requests**
- Refs #11671 — introduced the requirement this pull request relaxes.
- Refs #11733 — open work on seed-source preflight. It reads the same
base-workspace config path and skips when the file is absent. It does
not change source selection.
- Refs #11735 — open work on provisioning reliability. It edits the same
four files and will need a rebase after either lands.
## What Changed
- `resolveRegisteredWorktreeSeedSource` sets the registered config path
only when `<baseCwd>/.paperclip/config.json` exists. This makes the
existing `registeredConfigPath ?? explicitSource` branch reachable for a
plain checkout.
- A base workspace that does hold its own config stays authoritative. A
mismatched explicit source is still rejected.
- The resolver throws a named error when the base workspace has no
config and no source is named.
- `readInstanceId` accepts an instance-root config at
`<home>/instances/<id>/config.json`. That layout names its instance by
directory and has no adjacent `.env`. Validation reuses
`resolvePaperclipInstanceId`.
- `scripts/provision-worktree.sh` and
`scripts/provision-worktree-runtime.sh` name the control plane's
instance config as the source when the base workspace has none. The
canonical-path and symlink checks stay.
- The workspace repair route supplies the same fallback, and only when
the base workspace has no config of its own.
- `doc/DEVELOPING.md` records the two source layouts.
## Verification
- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`
— 10 tests pass. The fixture no longer writes a config into the base
workspace, so it models a real managed checkout. One test now creates
that config mid-test, which covers both layouts.
- `npx vitest run src/worktree-seed-source.test.ts` in `packages/shared`
— 4 tests pass. Two are new: one resolves an instance-root source, and
one still fails closed when no source exists.
- `npx vitest run src/__tests__/workspace-runtime.test.ts
src/__tests__/execution-workspaces-routes.test.ts
src/__tests__/execution-workspace-runtime-control-conflict.test.ts
src/__tests__/workspace-operations-reconciliation.test.ts
src/__tests__/worktree-seed-server-spawn.test.ts` in `server` — all
pass. Run them one file at a time. They share one test database, and
concurrent runs fail teardown.
- `npx vitest run src/__tests__/worktree.test.ts` in `cli` — 63 tests
pass.
- `pnpm --filter @paperclipai/shared typecheck` — clean.
- Manual check on a live instance: the resolver now returns the instance
config as the source for a managed checkout, with the source instance
`default` and a distinct target instance.
## Risks
Low to moderate.
- The relaxed rule applies only when the base workspace holds no config.
A base workspace that holds one keeps full authority, so the trust model
from #11671 is unchanged. The seed manifest still never selects the
source.
- The instance-id fallback reads a directory name. It applies only to
the `<home>/instances/<id>/config.json` layout, and
`resolvePaperclipInstanceId` rejects an unsafe segment.
- #11735 edits the same four files. Whichever pull request lands second
needs a rebase.
- `pnpm --filter @paperclipai/server typecheck` currently fails on this
checkout with duplicate `drizzle-orm` type instantiations. The failure
is present with and without this change, and the error count is
identical. It comes from an unrelated lockfile state, not from this pull
request.
## Model Used
Claude Opus 5 (`claude-opus-5`), by Anthropic, running in Claude Code.
Extended thinking was on. The model used file, search, and shell tools
to diagnose the failure on a live instance and to run the test suites.
## 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
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge
🤖 Generated with [Claude Code](https://claude.com/claude-code)
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
188 lines
8.1 KiB
TypeScript
188 lines
8.1 KiB
TypeScript
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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import { afterEach, describe, expect, it } from "vitest";
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import { resolveCanonicalWorktreeSeedSource } from "./worktree-seed-source.js";
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const cleanup: string[] = [];
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function makeInstance(prefix: string, instanceId: string) {
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const cwd = fs.mkdtempSync(path.join(os.tmpdir(), prefix));
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cleanup.push(cwd);
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const configDir = path.join(cwd, ".paperclip");
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const configPath = path.join(configDir, "config.json");
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fs.mkdirSync(configDir, { recursive: true });
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fs.writeFileSync(configPath, "{}\n");
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fs.writeFileSync(path.join(configDir, ".env"), `PAPERCLIP_INSTANCE_ID=${instanceId}\n`);
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return { cwd, configPath, instanceId };
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}
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/**
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* A control plane's own instance root: `<home>/instances/<id>/config.json`, which
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* names its instance by directory and has no adjacent .env.
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*/
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function makeInstanceRoot(instanceId: string) {
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const home = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-seed-home-"));
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cleanup.push(home);
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const configDir = path.join(home, "instances", instanceId);
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fs.mkdirSync(configDir, { recursive: true });
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const configPath = path.join(configDir, "config.json");
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fs.writeFileSync(configPath, "{}\n");
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return { configPath, instanceId };
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}
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/** A managed project checkout: a plain clone with no `.paperclip` of its own. */
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function makePlainCheckout() {
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const cwd = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-seed-checkout-"));
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cleanup.push(cwd);
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return cwd;
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}
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afterEach(() => {
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for (const dir of cleanup.splice(0)) fs.rmSync(dir, { recursive: true, force: true });
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});
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describe("resolveCanonicalWorktreeSeedSource", () => {
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it("returns only the registered base workspace config", () => {
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const source = makeInstance("paperclip-seed-source-", "source-instance");
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const target = makeInstance("paperclip-seed-target-", "target-instance");
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expect(resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: source.cwd,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toMatchObject({
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baseWorkspaceCwd: source.cwd,
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configPath: source.configPath,
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targetConfigPath: target.configPath,
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});
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});
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it("takes the named source when the base workspace carries no config of its own", () => {
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const baseCwd = makePlainCheckout();
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const source = makeInstanceRoot("default");
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const target = makeInstance("paperclip-seed-target-", "target-instance");
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expect(resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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explicitSourceConfigPath: source.configPath,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toMatchObject({
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baseWorkspaceCwd: baseCwd,
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configPath: source.configPath,
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instanceId: "default",
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});
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});
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it("rejects a dangling config symlink instead of falling back to the named source", () => {
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const baseCwd = makePlainCheckout();
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fs.mkdirSync(path.join(baseCwd, ".paperclip"), { recursive: true });
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fs.symlinkSync(path.join(baseCwd, "absent.json"), path.join(baseCwd, ".paperclip", "config.json"));
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const source = makeInstanceRoot("default");
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const target = makeInstance("paperclip-seed-dangling-target-", "target-instance");
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expect(() => resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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explicitSourceConfigPath: source.configPath,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/Registered source Paperclip config does not exist/);
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});
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it("fails closed when the declared config cannot be inspected", () => {
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const baseCwd = makePlainCheckout();
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// `.paperclip` as a regular file makes lstat report ENOTDIR, not ENOENT.
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fs.writeFileSync(path.join(baseCwd, ".paperclip"), "not a directory\n");
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const source = makeInstanceRoot("default");
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const target = makeInstance("paperclip-seed-unreadable-target-", "target-instance");
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expect(() => resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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explicitSourceConfigPath: source.configPath,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/cannot be inspected \(ENOTDIR\)/);
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});
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it("rejects a dangling .paperclip symlink instead of falling back to the named source", () => {
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const baseCwd = makePlainCheckout();
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// Resolving `.paperclip` fails before the probe reaches config.json, so the config
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// entry reports ENOENT even though this workspace is malformed rather than plain.
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fs.symlinkSync(path.join(baseCwd, "absent-dir"), path.join(baseCwd, ".paperclip"));
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const source = makeInstanceRoot("default");
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const target = makeInstance("paperclip-seed-dangling-parent-target-", "target-instance");
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expect(() => resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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explicitSourceConfigPath: source.configPath,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/cannot be inspected \(ENOENT on its \.paperclip symlink target\)/);
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});
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it("takes the named source when .paperclip is a symlink to a directory with no config", () => {
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const baseCwd = makePlainCheckout();
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const linked = path.join(baseCwd, "linked-config-dir");
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fs.mkdirSync(linked, { recursive: true });
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fs.symlinkSync(linked, path.join(baseCwd, ".paperclip"));
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const source = makeInstanceRoot("default");
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const target = makeInstance("paperclip-seed-linked-empty-target-", "target-instance");
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const resolved = resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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explicitSourceConfigPath: source.configPath,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: source.configPath, instanceId: source.instanceId },
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manifestTargetInstanceId: target.instanceId,
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});
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expect(resolved.configPath).toBe(source.configPath);
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expect(resolved.instanceId).toBe("default");
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});
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it("fails closed when the base workspace carries no config and none is named", () => {
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const baseCwd = makePlainCheckout();
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const target = makeInstance("paperclip-seed-unnamed-target-", "target-instance");
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expect(() => resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: baseCwd,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: { configPath: target.configPath, instanceId: target.instanceId },
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/no Paperclip config of its own/);
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});
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it("fails closed without registration and when source equals target", () => {
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const target = makeInstance("paperclip-seed-same-target-", "target-instance");
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const diagnostic = { configPath: target.configPath, instanceId: target.instanceId };
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expect(() => resolveCanonicalWorktreeSeedSource({
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: diagnostic,
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/not registered/);
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expect(() => resolveCanonicalWorktreeSeedSource({
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registeredBaseWorkspaceCwd: target.cwd,
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targetConfigPath: target.configPath,
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expectedTargetInstanceId: target.instanceId,
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manifestSource: diagnostic,
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manifestTargetInstanceId: target.instanceId,
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})).toThrow(/same canonical file/);
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});
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});
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