Execution Workspaces And Runtime Services

This guide documents the intended runtime model for projects, execution workspaces, and issue runs in Paperclip.

Paperclip now presents this as a workspace-command model:

• Services are long-running commands that stay supervised.
• Jobs are one-shot commands that run once and exit.
• Raw runtime JSON is still available for advanced config, but it is no longer the primary mental model.

Project runtime configuration

You can define how to run a project on the project workspace itself.

• Project workspace runtime config describes the services and jobs available for that project checkout.
• This is the default runtime configuration that child execution workspaces may inherit.
• Defining the config does not start anything by itself.

Runtime control: manual and heartbeat-driven

Workspace commands can be controlled manually from the UI, and heartbeat runs also start services automatically.

• Project workspace services are started and stopped from the project workspace UI, and project jobs can be run on demand there.
• Execution workspace services are started and stopped from the execution workspace UI, and execution-workspace jobs can be run on demand there.
• Heartbeat runs also auto-start the workspace's runtime services at the beginning of an issue run. ensureRuntimeServicesForRun (server/src/services/workspace-runtime.ts, called from server/src/services/heartbeat.ts) starts each service whose desired state resolves to running — which is the default when no explicit per-service desired state is set. A running service that matches an existing reuse key is reused rather than restarted.
• You can opt a service out of that auto-start by setting its desired state to stopped/manual in the runtime config; those services stay UI-controlled.
• Paperclip does not automatically restart workspace services on server boot — services only come back up when the next run (or a manual start) brings them up.

Execution workspace inheritance

Execution workspaces isolate code and runtime state from the project primary workspace.

• An isolated execution workspace has its own checkout path, branch, and local runtime instance.
• The runtime configuration may inherit from the linked project workspace by default.
• The execution workspace may override that runtime configuration with its own workspace-specific settings.
• The inherited configuration answers "which commands exist and how to run them", but any running service process is still specific to that execution workspace.

Issues and execution workspaces

Issues are attached to execution workspace behavior, not to automatic runtime management.

• An issue may create a new execution workspace when you choose an isolated workspace mode.
• An issue may reuse an existing execution workspace when you choose reuse.
• Multiple issues may intentionally share one execution workspace so they can work against the same branch and running runtime services.
• Running an issue auto-starts the workspace's running-desired runtime services for the duration of the run (see "Runtime control" above); it does not stop them when the run ends unless they are ephemeral and no other run holds a lease.

Execution workspace lifecycle

Execution workspaces are durable until a human closes them.

• The UI can archive an execution workspace.
• Closing an execution workspace stops its runtime services and cleans up its workspace artifacts when allowed.
• Shared workspaces that point at the project primary checkout are treated more conservatively during cleanup than disposable isolated workspaces.

Resolved workspace logic during heartbeat runs

Heartbeat resolves a workspace for the run (code location and session continuity) and also brings up that workspace's runtime services.

1. Heartbeat resolves a base workspace for the run.
2. Paperclip realizes the effective execution workspace, including creating or reusing a worktree when needed.
3. Paperclip persists execution-workspace metadata such as paths, refs, and provisioning settings.
4. Heartbeat passes the resolved code workspace to the agent run.
5. Heartbeat calls ensureRuntimeServicesForRun to start the workspace's running-desired runtime services, running the lazy runtime provision command first if one is configured and has not yet run (see "Lazy runtime provisioning" below).

Lazy runtime provisioning

Some workspaces need heavy one-time setup — seeding a database, warming caches — before their runtime services can start. That work can be deferred to the first runtime-service start instead of running eagerly during workspace preparation.

• Configure a runtime provision command on the project's workspace strategy (Project properties → execution workspace), or override it per execution workspace on the workspace's Configuration tab.
• When set, workspace preparation stays lean and the command runs exactly once, immediately before the first runtime-service start for that workspace. Leaving it empty keeps the legacy eager path (all setup during workspace provisioning).
• The command's outcome is recorded as a workspace_runtime_provision operation on the execution workspace and surfaced on the workspace detail page:
  • Deferred — configured but not yet run (no runtime service has started yet).
  • Provisioned at <time> — the command completed successfully.
  • Provisioning failed — the command failed; the workspace detail links to the runtime logs for the failing operation.
• While the command runs, the runtime service shows a Provisioning… state before it transitions to starting/running.

Private repositories and repo-only project workspaces

A project workspace can be repo-only: a Repo URL with no local path. The server then materializes a managed checkout on demand (git clone into a managed directory) and, for isolated git_worktree runs, refreshes the base ref (git fetch) before preparing each worktree. Both operations run on the server, outside any agent process — so agent-scoped credential env bindings do not apply to them.

For private GitHub repositories, store a token as a company secret named one of GITHUB_TOKEN, GH_TOKEN, or PAPERCLIP_GITHUB_TOKEN (checked in that order; Settings → Secrets). The server resolves it per run and authenticates managed clones and base-ref fetches with it. Details and caveats:

• Scope: only https://github.com/... repo URLs are authenticated this way. SSH URLs, GitHub Enterprise hosts, and other providers keep ambient behavior (system git config/credential helpers on the server host). URLs that embed their own credentials are never overridden.
• Fallback: with no matching company secret, the server falls back to a GITHUB_TOKEN or GH_TOKEN variable in the server process environment (useful for self-hosted single-tenant deployments), then to unauthenticated access — public repos keep working with no setup.
• The token never appears in command lines, URLs, or on disk; it is passed to git through an ephemeral credential helper. Each resolution is recorded as a secret access event.
• This is separate from the agent push credential: agents pushing branches/PRs still need GH_TOKEN/GITHUB_TOKEN bound at agent or project scope (see deploy/secrets) so the token reaches the agent process env. The same company secret can back both uses via a binding.

Cross-run persistence (no-remote-git contract)

Code state moves between runs through the local execution-workspace cwd alone — not through a git remote.

• Each run's prepare step bundles the local worktree to the run's remote dir over ssh, with no git remote configured.
• The adapter's restore step at the end of the run writes any new remote commits back into the local worktree directly.
• Adapters must never git push from runtime code, and must never assume a remote exists.
• A failed restore is a run-level error and records workspace_finalize=failed on the execution workspace, which gates dependent issue wakes until the next successful finalize.

The invariant is enforced by the "no-remote-git contract" case in packages/adapter-utils/src/ssh-fixture.test.ts, which asserts a remote-only commit reaches the local worktree with no remote configured at any point.

Current implementation guarantees

With the current implementation:

• Project workspace command config is the fallback for execution workspace UI controls.
• Execution workspace runtime overrides are stored on the execution workspace.
• Heartbeat runs auto-start the workspace's running-desired runtime services (via ensureRuntimeServicesForRun); services set to stopped/manual stay UI-controlled.
• A configured runtime provision command runs once, lazily, before the first runtime-service start.
• Server startup does not auto-restart workspace services.