Long-Running Agent Setup

Turn a spec into a working long-running agent — phases, tasks, verification, and the operating prompt — in one shot.

This skill converts planning documents and specs into the file structure a long-running Claude agent uses to execute multi-session work: a claude-task.json task tracker, a claude-prompt.md operating manual, and a preserved SPEC.md. Before generating files it asks how autonomous the agent should be, so the prompt and task structure match.

Triggers

• "set up a long-running agent for..."
• "convert this spec into phases"
• "I have a spec, build out the agent task structure"
• "make a claude-task.json for this plan"
• "break this plan into phases with verification"
• "spin up an autonomous build of..."

Source of Truth

Before doing anything, fetch and read this blog post for the core patterns:

https://www.anthropic.com/engineering/effective-harnesses-for-long-running-agents

The blog defines the effective patterns for long-running coding agents. Apply them directly. Key takeaways: phase-based work with verification checkpoints, granular task enumeration, JSON task tracking, git checkpointing per task, never weaken/remove tests to make a phase pass.

Core Workflow

1. Gather Inputs

Request from the user:

• Spec / planning doc — the document to convert (required). Will be preserved as SPEC.md.
• Project name — short identifier; used in headings and the JSON project field.
• Output location — where to create files (default: a new directory at the user's choice).

If the user has the spec inline in chat or pointed at a file path, read it. If multiple files together form the spec (e.g., a SPEC.md + a data_model.md + a workflows.md), read all of them.

2. Read the Blog

Fetch the Anthropic blog post above. The patterns to apply:

• Phase-based work with verification checkpoints — verification is required before advance, in either operating mode
• Explicit feature/task enumeration — granular, single-task focus
• Task file as progress tracker — JSON, not markdown (the model is less likely to corrupt it)
• Git checkpointing after each task — task-XXX: brief description
• Strong constraints — never delete or weaken tests/verification

3. Decompose into Phases and Tasks

Break the spec into:

Phases (3–10 typically):

• Logical groupings of related work
• Each phase has a verification block with description + steps
• Verification steps should be machine-checkable where possible (commands + thresholds, not "looks good")

Tasks (per phase):

• Granular, implementable units (4–10 steps each is typical)
• Each task has a description, a steps array, and passes: false initially
• Tasks reference their parent phase

Example structure:

Phase 1: Project Foundation (3 tasks)
  - setup-001: Initialize project structure
  - setup-002: Create environment config
  - types-001: Define core interfaces
  Verification: "npx tsc --noEmit returns exit 0; no errors"

Phase 2: Storage & Skills (5 tasks)
  - storage-001: Create storage interface
  - skill-001..004: Create skill files
  Verification: "Confirm skills load via test harness; storage round-trip test passes"

4. Ask the User: Autonomy Mode

Before generating files, ask the user how autonomous the agent should be using AskUserQuestion. This decision shapes both claude-prompt.md and claude-task.json.

Use this exact question structure:

question: "How autonomous should this long-running agent be?"
header: "Autonomy"
multiSelect: false
options:
  - label: "Orchestrator mode"
    description: "Claude self-verifies at phase boundaries and continues to the next phase automatically. Stops only on auth/credentials, scope decisions not in the spec, destructive/visible-to-others actions, or persistent blockers. Best when you don't want to babysit and the spec is detailed."
  - label: "Phase-checkpoint mode"
    description: "Claude stops at every phase boundary, prints the verification steps, and waits for you to confirm before continuing. Best for high-risk projects, when verification needs human judgment, or when you want frequent visibility into what's been built."

The answer determines:

• Which claude-prompt.md template to use (Step 6)
• Whether to add orchestrator-specific fields to claude-task.json (Step 5)

If the user picks Other and writes a freeform answer, interpret it: words like "autonomous / orchestrator / no babysit / keep going" → orchestrator. Words like "checkpoint / stop / verify / supervise / approval" → checkpoint. Genuinely ambiguous → re-ask with a sharper question.

Save the chosen mode as MODE (orchestrator or checkpoint) for use in the next steps.

5. Generate claude-task.json

Create the task file using templates/task-template.json as the base structure:

• phases array with verification steps
• tasks array with passes: false initially
• Tasks reference their parent phase via phase field

If MODE = orchestrator, also include:

• Top-level mode: "orchestrator" field
• Top-level orchestrator_notes summarizing the operating model
• Per-phase auto_advance: true | false — true when the phase's verification is fully programmatic (commands + thresholds with no human judgment); false for phases that need human review (e.g., a final hardening phase with a "comprehensive docs" check)
• Per-task dispatch_hint field — one of self, sub_agent_general, sub_agent_explore, or out_of_scope. Heuristics:
  • sub_agent_general for: PDF/document extraction, per-vendor / per-shop / per-region / per-customer parallel work, DB exploration involving 5+ queries, code-review/critic passes, anything taking 15+ tool calls
  • sub_agent_explore for: cross-repo search, "where is X used" hunts
  • self for: small DDL/config edits, single-file scripts, orchestration decisions, anything < 5 tool calls
• Per-task dispatch_reason — one short line explaining the choice

If MODE = checkpoint, no extra fields are needed beyond the base template.

Output: {project-root}/claude-task.json

6. Generate claude-prompt.md

Use the template that matches MODE:

• MODE = orchestrator → templates/claude-prompt-template-orchestrator.md
• MODE = checkpoint → templates/claude-prompt-template.md

Key sections to customize in either template:

• Project overview and goal
• Key files list (SPEC.md, claude-task.json, any reference docs)
• Phases table showing all phases with status
• File structure target
• Any technical decisions specific to the project that the spec already settled

Output: {project-root}/claude-prompt.md

7. Keep the SPEC

The original spec should remain as SPEC.md for the agent to reference when it needs detailed requirements during execution.

If the input was a single file: copy it to SPEC.md. If the input was multiple files: either bundle them into one SPEC.md with a clear table of contents, OR keep them separate and have the generated claude-prompt.md list them under "Key Files."

Output Structure

{project-root}/
├── claude-prompt.md      # Agent operating manual (orchestrator OR checkpoint variant)
├── claude-task.json      # Phases and tasks (extra fields if orchestrator mode)
└── SPEC.md               # Original planning doc (preserved for reference)

Starting the Agent

Instruct the user to point a fresh agent session at the prompt:

@claude-prompt.md

The agent will read claude-task.json, find the current phase, and:

• Orchestrator mode: work through tasks, self-verify at each phase boundary, continue to the next phase automatically. Stop only on documented escalation cases.
• Checkpoint mode: complete all tasks in the current phase, then stop and print verification steps for the user to run.

Patterns That Apply in Both Modes

1. Verification is required before advance — never auto-declare completion without running checks
2. Complete ALL tasks in phase before phase verification — no stopping mid-phase
3. Git commit after each task — task-XXX: description
4. Never skip phases — sequential progression
5. Task file is the source of truth — agent reads and updates it
6. Never weaken/remove tests or verification to make a phase "pass" — fix the root cause instead

The two modes differ only in who runs the verification at phase boundaries:

• Orchestrator mode: the agent runs them programmatically and continues
• Checkpoint mode: the agent prints them and waits for the human

Reference Materials

• templates/claude-prompt-template.md — Phase-checkpoint mode template (default for high-risk or visibility-sensitive projects)
• templates/claude-prompt-template-orchestrator.md — Orchestrator-mode template (autonomous; stops only on escalation)
• templates/task-template.json — Base claude-task.json structure (mode-specific fields are described in Step 5)