Rate-limit-resilient pipeline with checkpoint/resume for long multi-phase sessions. Saves progress to .claude/pipeline-state.json after each phase. Use when starting a complex multi-phase task that risks hitting rate limits, when resuming an interrupted session, or when orchestrating work spanning commits, GitHub issues, and large file changes.

Reference high

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Checkpoint Resume

Rate-limit-resilient pipeline orchestrator. Saves progress to .claude/pipeline-state.json after every phase so long sessions survive interruptions.

Quick Reference

Category	Rule	Impact	Key Pattern
Phase Ordering	`$\{CLAUDE_SKILL_DIR\}/rules/ordering-priority.md`	CRITICAL	GitHub issues/commits first, file-heavy phases last
State Writes	`$\{CLAUDE_SKILL_DIR\}/rules/state-write-timing.md`	CRITICAL	Write after every phase, never batch
Mini-Commits	`$\{CLAUDE_SKILL_DIR\}/rules/checkpoint-mini-commit.md`	HIGH	Every 3 phases, checkpoint commit format

Total: 3 rules across 3 categories

On Invocation

If .claude/pipeline-state.json exists: run scripts/show-status.sh to display progress, then ask to resume, pick a different phase, or restart. Load Read("$\{CLAUDE_SKILL_DIR\}/references/resume-decision-tree.md") for the full decision tree.

If no state file exists: ask the user to describe the task, build an execution plan, write initial state via scripts/init-pipeline.sh <branch>, begin Phase 1.

Execution Plan Structure

{
  "phases": [
    { "id": "create-issues", "name": "Create GitHub Issues", "dependencies": [], "status": "pending" },
    { "id": "commit-scaffold", "name": "Commit Scaffold", "dependencies": [], "status": "pending" },
    { "id": "write-source", "name": "Write Source Files", "dependencies": ["commit-scaffold"], "status": "pending" }
  ]
}

Phases with empty dependencies may run in parallel via Task sub-agents (when they don't share file writes).

After Each Phase

Update .claude/pipeline-state.json — see Read("$\{CLAUDE_SKILL_DIR\}/rules/state-write-timing.md")
Every 3 phases: create a mini-commit — see Read("$\{CLAUDE_SKILL_DIR\}/rules/checkpoint-mini-commit.md")

References

Load on demand with Read("$\{CLAUDE_SKILL_DIR\}/references/<file>"):

File	Content
`references/pipeline-state-schema.md`	Full field-by-field schema with examples
`references/pipeline-state.schema.json`	Machine-readable JSON Schema for validation
`references/resume-decision-tree.md`	Logic for resuming, picking phases, or restarting

Scripts

scripts/init-pipeline.sh <branch> — print skeleton state JSON to stdout
scripts/show-status.sh [path] — print human-readable pipeline status (requires jq)

Key Decisions

Decision	Recommendation
Phase granularity	One meaningful deliverable per phase (a commit, a set of issues, a feature)
Parallelism	Task sub-agents only for phases with empty `dependencies` that don't share file writes
Rate limit recovery	State is already saved — re-invoke `/checkpoint-resume` to continue

Rules (3)

Create periodic mini-commits so rate-limit hits do not lose uncommitted pipeline work — HIGH

Checkpoint Mini-Commit

Every 3 completed phases, create a mini-commit that captures work in progress. This provides a git recovery point even if later phases fail.

When to commit:

Phase 1 done → state write only
Phase 2 done → state write only
Phase 3 done → state write + mini-commit  ← checkpoint
Phase 4 done → state write only
Phase 5 done → state write only
Phase 6 done → state write + mini-commit  ← checkpoint

Mini-commit format:

git add -A
git commit -m "checkpoint: phases N-M complete

Completed:
- Phase N: <name>
- Phase N+1: <name>
- Phase N+2: <name>

Remaining: <count> phases

Co-Authored-By: Claude <noreply@anthropic.com>"

Incorrect — one giant commit at the end:

# Do 12 phases of work...
git add -A
git commit -m "feat: complete all pipeline work"
# If phases 10-12 fail, no checkpoint exists

Correct — checkpoint every 3 phases:

# After phase 3
git commit -m "checkpoint: phases 1-3 complete\n\nCo-Authored-By: Claude <noreply@anthropic.com>"
# After phase 6
git commit -m "checkpoint: phases 4-6 complete\n\nCo-Authored-By: Claude <noreply@anthropic.com>"

Key rules:

Count is based on completed phases in the current pipeline run, not total commits
Stage everything (git add -A) — the checkpoint captures full work-in-progress state
Never skip a checkpoint because "almost done" — rate limits don't warn first
Include Co-Authored-By attribution in every checkpoint commit

Order pipeline phases to process high-value work first before rate limits hit — CRITICAL

Phase Ordering Priority

When a rate limit hits, work done in the current session is lost. Order phases so the hardest-to-reconstruct work finishes first.

Priority order (highest → lowest value if lost):

GitHub issue creation (lost = no tracking, no auto-close links)
Git commits with code changes (lost = untracked work)
File creation / large edits (recoverable from context)
Documentation / reference updates (lowest risk to lose last)

Incorrect — file-heavy phases scheduled before issue creation:

{
  "phases": [
    { "id": "write-files", "name": "Write all source files" },
    { "id": "create-issues", "name": "Create GitHub issues" },
    { "id": "commit", "name": "Commit changes" }
  ]
}

Correct — issues and commits scheduled first:

{
  "phases": [
    { "id": "create-issues", "name": "Create GitHub issues" },
    { "id": "commit-scaffold", "name": "Commit initial scaffold" },
    { "id": "write-files", "name": "Write all source files" },
    { "id": "commit-final", "name": "Commit completed work" }
  ]
}

Key rules:

Always schedule gh issue create calls in the first phase
Commits with Closes #N references come second — they link issues
Independent phases with no shared dependencies run in parallel via Task sub-agents
Never defer issue creation to "after the code is done"

Write state after each phase so rate-limit interruptions preserve all prior progress — CRITICAL

State Write Timing

Write .claude/pipeline-state.json immediately after every phase completes. Never accumulate updates.

Incorrect — batching state writes to the end:

// Run all phases, then save state once
for (const phase of phases) {
  await runPhase(phase);
}
await writeState({ completed_phases: phases }); // Lost if interrupted!

Correct — write state after every phase:

for (const phase of phases) {
  await runPhase(phase);
  // Write immediately — before starting next phase
  await writeState({
    completed_phases: [...prev.completed_phases, { ...phase, timestamp: new Date().toISOString() }],
    current_phase: nextPhase,
    remaining_phases: phasesAfterNext,
    updated_at: new Date().toISOString()
  });
}

State write checklist (after each phase):

Move completed phase into completed_phases with timestamp
Add commit_sha if the phase produced a git commit
Set current_phase to the next pending phase
Remove completed phase from remaining_phases
Update updated_at
Update context_summary.file_paths with any new files created

Key rules:

Write state BEFORE starting the next phase, not after
Never batch multiple phase completions into one write
If a phase produces a commit, capture the SHA: git rev-parse --short HEAD
The state file is the source of truth for resume — it must be current

References (2)

Pipeline State Schema

The pipeline state file (.claude/pipeline-state.json) is the source of truth for checkpoint/resume. It is validated against .claude/schemas/pipeline-state.schema.json.

Top-Level Shape

{
  "completed_phases": [...],
  "current_phase": {...},
  "remaining_phases": [...],
  "context_summary": {...},
  "created_at": "2026-02-19T10:00:00Z",
  "updated_at": "2026-02-19T10:45:00Z"
}

completed_phases

Array of phases that finished successfully. Append-only — never remove entries.

{
  "id": "create-issues",
  "name": "Create GitHub Issues",
  "timestamp": "2026-02-19T10:05:00Z",
  "commit_sha": "a1b2c3d"   // optional — only if phase produced a commit
}

current_phase

The phase actively being executed. progress_description is a free-text note describing partial work done so far within this phase — helps resume after interruption.

{
  "id": "write-source",
  "name": "Write Source Files",
  "progress_description": "Completed auth module, starting billing module"
}

Set current_phase to null when all phases are done.

remaining_phases

Ordered list of phases not yet started. Remove a phase from here when it moves to current_phase.

{
  "id": "final-commit",
  "name": "Final Commit",
  "dependencies": ["write-source", "write-tests"]
}

dependencies: IDs of phases that must complete before this one. Empty array = can run immediately or in parallel.

context_summary

Compact context snapshot for restoring session state after interruption.

{
  "branch": "feat/issue-42-new-feature",
  "key_decisions": [
    "Used postgres not mongo for user storage",
    "Chose REST over GraphQL for external API"
  ],
  "file_paths": [
    "/Users/dev/project/src/auth/login.ts",
    "/Users/dev/project/src/billing/invoice.ts"
  ]
}

Update file_paths each time a phase creates or significantly modifies files.

Full Example

{
  "completed_phases": [
    {
      "id": "create-issues",
      "name": "Create GitHub Issues",
      "timestamp": "2026-02-19T10:05:00Z"
    },
    {
      "id": "scaffold-commit",
      "name": "Commit Initial Scaffold",
      "timestamp": "2026-02-19T10:20:00Z",
      "commit_sha": "a1b2c3d"
    }
  ],
  "current_phase": {
    "id": "write-source",
    "name": "Write Source Files",
    "progress_description": "auth module done, starting billing"
  },
  "remaining_phases": [
    {
      "id": "write-tests",
      "name": "Write Tests",
      "dependencies": ["write-source"]
    },
    {
      "id": "final-commit",
      "name": "Final Commit",
      "dependencies": ["write-source", "write-tests"]
    }
  ],
  "context_summary": {
    "branch": "feat/issue-42-dashboard",
    "key_decisions": ["REST over GraphQL", "Postgres for storage"],
    "file_paths": ["/project/src/auth/login.ts"]
  },
  "created_at": "2026-02-19T10:00:00Z",
  "updated_at": "2026-02-19T10:22:00Z"
}

Resume Decision Tree

Use this decision tree when /checkpoint-resume is invoked to determine the correct action.

On Invocation

Does .claude/pipeline-state.json exist?
│
├── NO → Ask user to describe the multi-phase task
│         → Build execution plan
│         → Write initial state file
│         → Begin Phase 1
│
└── YES → Read the state file
          → Show resume summary (see format below)
          → Ask: "Resume from [current_phase.name]? (y/n/restart)"
          │
          ├── y → Continue from current_phase
          │        (respect progress_description for partial phases)
          │
          ├── n → Ask: "Abandon pipeline or pick a different phase?"
          │        ├── abandon → Delete state file, start fresh
          │        └── pick    → List remaining_phases, let user choose
          │
          └── restart → Confirm with user → Delete state file → restart

Resume Summary Format

Show this before asking the user to confirm:

Pipeline: <task description from context_summary or phases>
Branch: <context_summary.branch>

Completed (N phases):
  ✓ Phase 1: Create GitHub Issues  (10:05)
  ✓ Phase 2: Commit Scaffold       (10:20, sha: a1b2c3d)

In progress:
  → Phase 3: Write Source Files
    Progress: auth module done, starting billing

Remaining (M phases):
  · Phase 4: Write Tests
  · Phase 5: Final Commit

Resume from "Write Source Files"? (y/n/restart)

When State File is Corrupted

If .claude/pipeline-state.json fails JSON parse or schema validation:

Warn the user: "State file is malformed"
Show raw content so user can assess what was completed
Ask: "Attempt manual recovery or start fresh?"
Do NOT silently overwrite — the file may contain the only record of completed work

Parallel Phase Execution

Phases with empty dependencies arrays can run concurrently via Task sub-agents:

Phase A (dependencies: [])  ─┐
Phase B (dependencies: [])  ─┤─ Run in parallel via Task
Phase C (dependencies: [A]) ─┘─ Wait for A, then run

Only parallelize when:

Both phases have empty or satisfied dependencies
Phases do NOT write to the same files
Phases do NOT both run git commit (would cause conflicts)

Checkpoint Resume

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