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https://github.com/paperclipai/paperclip.git
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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>
175 lines
6.5 KiB
Bash
Executable File
175 lines
6.5 KiB
Bash
Executable File
#!/usr/bin/env bash
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set -euo pipefail
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base_cwd="${PAPERCLIP_WORKSPACE_BASE_CWD:?PAPERCLIP_WORKSPACE_BASE_CWD is required}"
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worktree_cwd="${PAPERCLIP_WORKSPACE_CWD:?PAPERCLIP_WORKSPACE_CWD is required}"
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paperclip_home="${PAPERCLIP_HOME:-$HOME/.paperclip}"
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paperclip_instance_id="${PAPERCLIP_INSTANCE_ID:-default}"
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paperclip_dir="$worktree_cwd/.paperclip"
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worktree_config_path="$paperclip_dir/config.json"
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seed_manifest_path="$paperclip_dir/seed-manifest.json"
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if [[ ! -d "$base_cwd" ]]; then
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echo "Base workspace does not exist: $base_cwd" >&2
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exit 1
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fi
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if [[ ! -d "$worktree_cwd" ]]; then
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echo "Derived worktree does not exist: $worktree_cwd" >&2
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exit 1
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fi
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if [[ -e "$seed_manifest_path" ]]; then
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seed_manifest_state="$(SEED_MANIFEST_PATH="$seed_manifest_path" node <<'EOF'
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const fs = require("node:fs");
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try {
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const value = JSON.parse(fs.readFileSync(process.env.SEED_MANIFEST_PATH, "utf8"));
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const complete = value?.version === 2
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&& value?.state === "verified"
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&& value?.phase === "complete"
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&& typeof value?.source?.instanceId === "string" && value.source.instanceId.length > 0
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&& typeof value?.source?.configPath === "string" && value.source.configPath.length > 0
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&& (value?.seedMode === "minimal" || value?.seedMode === "full")
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&& typeof value?.snapshotAt === "string" && value.snapshotAt.length > 0
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&& typeof value?.migrationRevision === "string" && value.migrationRevision.length > 0
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&& typeof value?.targetInstanceId === "string" && value.targetInstanceId.length > 0
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&& typeof value?.attemptId === "string" && value.attemptId.length > 0
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&& typeof value?.startedAt === "string"
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&& typeof value?.finishedAt === "string"
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&& Array.isArray(value?.diagnostics)
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&& value.diagnostics.some((entry) => entry?.phase === "complete" && entry?.status === "succeeded" && typeof entry?.at === "string");
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process.stdout.write(complete ? "verified" : "incomplete");
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} catch {
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process.stdout.write("invalid");
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}
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EOF
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)"
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if [[ "$seed_manifest_state" == "verified" ]]; then
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echo "Worktree database has a verified seed manifest; skipping runtime provisioning." >&2
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exit 0
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fi
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fi
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if [[ ! -f "$worktree_config_path" ]]; then
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initial_provision_script="$base_cwd/scripts/provision-worktree.sh"
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if [[ ! -f "$initial_provision_script" ]]; then
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echo "Worktree config does not exist and the built-in provision script is unavailable: $worktree_config_path" >&2
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exit 1
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fi
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echo "Worktree config is missing; running the built-in worktree provisioner before database seeding." >&2
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(
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cd "$worktree_cwd" &&
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bash "$initial_provision_script"
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)
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fi
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if [[ ! -f "$worktree_config_path" ]]; then
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echo "Worktree config still does not exist after built-in provisioning: $worktree_config_path" >&2
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exit 1
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fi
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# The CLI derives the source from PAPERCLIP_WORKSPACE_BASE_CWD, which the control
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# plane injects from the registered project-workspace row. A base workspace that is
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# a plain checkout carries no instance config of its own, so name the control plane's
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# own registered instance config explicitly. The seed manifest stays diagnostic
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# evidence only and must never choose the clone source.
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if [[ -L "$base_cwd/.paperclip" && ! -d "$base_cwd/.paperclip" ]]; then
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echo "Registered base project workspace .paperclip is a broken symlink: $base_cwd/.paperclip" >&2
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exit 1
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fi
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source_config_args=()
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if [[ ! -e "$base_cwd/.paperclip/config.json" && ! -L "$base_cwd/.paperclip/config.json" ]]; then
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source_config_path="${PAPERCLIP_CONFIG:-$paperclip_home/instances/$paperclip_instance_id/config.json}"
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# A human may invoke this after sourcing `worktree env`, which points
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# PAPERCLIP_CONFIG at the target. Naming the target as its own source is never
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# right, so leave the source to the CLI in that case.
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if [[ "$source_config_path" != "$worktree_config_path" ]]; then
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source_config_args=(--from-config "$source_config_path")
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fi
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fi
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base_cli_runner_path="$base_cwd/cli/node_modules/tsx/dist/cli.mjs"
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base_cli_entry_path="$base_cwd/cli/src/index.ts"
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base_cli_files_present() {
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[[ -f "$base_cli_runner_path" && -f "$base_cli_entry_path" ]]
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}
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base_cli_healthy() {
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base_cli_files_present || return 1
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(cd "$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 $base_cwd." >&2
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local repair_cmd=(pnpm install --prod=false --force --frozen-lockfile --config.confirmModulesPurge=false)
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local repair_lock_dir=""
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if command -v git >/dev/null 2>&1; then
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repair_lock_dir="$(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 "$repair_lock_dir" ]]; then
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(
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cd "$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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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_ensure_seeded() {
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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" "$base_cli_entry_path" worktree ensure-seeded --config "$worktree_config_path" "${source_config_args[@]}"
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)
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return
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fi
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if command -v pnpm >/dev/null 2>&1 && pnpm paperclipai --help >/dev/null 2>&1; then
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(
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cd "$worktree_cwd" &&
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pnpm paperclipai worktree ensure-seeded --config "$worktree_config_path" "${source_config_args[@]}"
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)
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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 "$worktree_cwd" &&
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paperclipai worktree ensure-seeded --config "$worktree_config_path" "${source_config_args[@]}"
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)
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return
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fi
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return 127
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}
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if run_ensure_seeded; then
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exit 0
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else
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exit_code=$?
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if [[ "$exit_code" -eq 127 ]]; then
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echo "No usable paperclipai CLI found; cannot seed the worktree database." >&2
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fi
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exit "$exit_code"
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fi
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