paperclipai/paperclip · error · Error

Worktree seed manifest does not exist at ${markers.manifest}

Error message

Worktree seed manifest does not exist at ${markers.manifest}.

What it means

updateWorktreeSeedManifest() records each phase transition (started/succeeded/failed) into the existing manifest; it refuses to invent one. readWorktreeSeedManifest returned null, meaning no manifest file exists at the resolved marker path — either it was never created (markWorktreeSeedPending must run first) or it disappeared mid-seed (concurrent cleanup), or the wrong configPath resolved to different marker paths.

Source

Thrown at cli/src/commands/worktree.ts:2000

  // New manifests are authoritative. Legacy files are removed so no caller can
  // mistake a stale binary marker for current verified seed state.
  rmSync(markers.complete, { force: true });
  rmSync(markers.pending, { force: true });
}

function updateWorktreeSeedManifest(input: {
  configPath: string;
  phase: WorktreeSeedPhase;
  status: "started" | "succeeded" | "failed";
  state?: WorktreeSeedManifest["state"];
  message?: string;
  snapshotAt?: string | null;
  migrationRevision?: string | null;
  now?: Date;
}): WorktreeSeedManifest {
  const markers = resolveWorktreeSeedMarkerPaths(input.configPath);
  const current = readWorktreeSeedManifest(input.configPath);
  if (!current) throw new Error(`Worktree seed manifest does not exist at ${markers.manifest}.`);
  const at = (input.now ?? new Date()).toISOString();
  const nextState = input.state ?? current.state;
  const diagnostic = {
    phase: input.phase,
    status: input.status,
    at,
    ...(input.message
      ? { message: input.message.slice(0, WORKTREE_SEED_DIAGNOSTIC_MESSAGE_LIMIT) }
      : {}),
  };
  const next: WorktreeSeedManifest = {
    ...current,
    phase: input.phase,
    state: nextState,
    snapshotAt: input.snapshotAt === undefined ? current.snapshotAt : input.snapshotAt,
    migrationRevision:
      input.migrationRevision === undefined ? current.migrationRevision : input.migrationRevision,
    startedAt: current.startedAt ?? (input.status === "started" ? at : null),

View on GitHub (pinned to a7e689b3c3)

Solutions

1. Run the full ensureWorktreeSeeded flow (it creates the pending manifest before updating) instead of calling update directly
2. Make sure no cleanup/deletion runs against the worktree markers while a seed is in progress
3. Verify the configPath passed to the seed matches the worktree's actual config location

import { existsSync } from 'node:fs';
import { resolveWorktreeSeedMarkerPaths, markWorktreeSeedPending } from './worktree-lib';

if (!existsSync(resolveWorktreeSeedMarkerPaths(configPath).manifest)) {
  markWorktreeSeedPending({ configPath, sourceConfigPath, targetInstanceId, seedMode: 'minimal' });
}
updateWorktreeSeedManifest({ configPath, phase, status });

When it happens

Trigger: Calling updateWorktreeSeedManifest before markWorktreeSeedPending ever created the manifest; another process deleting the marker files while a seed runs; passing a configPath whose resolved marker directory differs from the one the manifest was written under.

Common situations: A cleanup command racing an in-flight seed on the same worktree; invoking seed helpers out of order in custom automation; moving/renaming the worktree config so marker paths change.

Related errors

• Invalid worktree seed manifest at ${manifestPath}: ${error i
• Invalid worktree seed manifest at ${manifestPath}.
• Worktree seed manifest target instance does not match the re
• Worktree seed source diagnostics changed while waiting for t
• Failed to create a pending worktree seed manifest.

AI-assisted analysis of paperclipai/paperclip@a7e689b3c3 (2026-08-21). Data as JSON: /api/errors/4884e4265b112e61. Report an issue: GitHub.