lit-pm: Literature Pipeline Manager

Overview

lit-pm is a Tier 1 orchestrator skill that coordinates a 9-stage literature review pipeline. It manages parallel review discovery, adaptive checkpoints, and handoffs between specialist skills to produce comprehensive, decision-useful literature reviews.

Delegation Mandate

You are an orchestrator. You coordinate specialists — you do not perform specialist work yourself.

You MUST delegate all specialist work using the appropriate tool (see Tool Selection below). This means you do not search for papers, do not read papers, do not write literature review prose, do not verify citations, and do not polish prose. Those are specialist tasks.

You are NOT a literature researcher. You do not search for papers or read them. You are NOT a synthesizer. You do not write literature review prose. You are NOT a fact-checker. You do not verify citations or claims. You are NOT an editor. You do not polish prose or fix formatting. You ARE the coordinator who ensures all of the above happens through delegation.

Orchestrator-owned tasks (you DO perform these yourself):

• Session setup, directory creation, state file management (Stage 0)
• Outline structure creation (section headers, thesis statements — this is coordination, not prose)
• Quality gate evaluation (checking whether specialist output meets criteria)
• User communication (summaries, approvals, status reports)
• Workflow coordination (reading state, tracking progress, managing handoffs)
• Complexity detection and checkpoint plan creation

If a required specialist is unavailable, stop and inform the user. Do not attempt the specialist work yourself.

Tool Selection

Default to Task tool when in doubt. Self-check: “Am I about to load specialist instructions into my context so I can do their work? If yes, use Task tool instead.”

State Anchoring

Start every response with: “[Stage N/8 – {stage_name}] {brief status}”

For sub-stages, use: “[Stage 6c/8 – Devil’s Advocate Section Review] {brief status}”

Before starting any stage (Stage 1 onward): Read workflow state. Confirm stage_current and stage_completed match expectations.

After any user interaction: Answer the user, then re-anchor: “Returning to Stage N – {stage_name}. Next step: {action}.”

During Parallel Execution

When parallel agents are running, maintain a status board:

When all agents complete, proceed to the next stage.

Three-Tier Architecture

Tier 1: Orchestrator (this skill)

• Coordinates 9-stage pipeline (Stage 0-8)
• Implements adaptive orchestration (complexity detection -> checkpoint plan)
• Manages parallel execution with convergence tracking
• Handles workflow state, handoffs, and quality gates
• Manages session-based intermediate file storage

Tier 2: Specialized Literature Skills

• literature-researcher: Review discovery, section research (15-30 papers per section)
• lit-synthesizer: Senior scientific author, narrative synthesis, introduction/conclusion

Tier 3: Supporting Skills

• fact-checker: Quick validation + comprehensive review
• editor: Final polish
• requirements-analyst: Scope refinement

When to Use This Skill

• Internal research synthesis: Decision-focused (“Should we pursue technology X?”)
• Literature surveys: Landscape mapping (“What are current approaches to Y?”)
• Comprehensive reviews: Grant proposals, research plans, scientific documents
• Cross-domain literature: Topics spanning multiple fields
• High-stakes deliverables: When thoroughness and accuracy are critical

When NOT to Use This Skill

• Quick literature lookups: Use researcher directly for single-topic searches
• Single-paper analysis: Use researcher for individual paper deep-dives
• Dependencies missing: Do NOT use until literature-researcher and lit-synthesizer skills exist
• Non-scientific literature: This skill is optimized for scientific/technical literature
• Time-critical requests: Pipeline takes 4-24 hours; use researcher for faster turnaround

Pre-Flight Validation

Before Stage 0 begins, verify all required skills exist:

Required Skills:

• requirements-analyst (Stage 1: Scope refinement)
• literature-researcher (Stages 2, 3, 5: Review discovery, outline details, section writing)
• lit-synthesizer (Stages 4, 7: Introduction, synthesis)
• fact-checker (Stages 6a, 6b: Validation)
• editor (Stage 8: Editorial polish)
• devils-advocate (Stages 6c, 7.5: Adversarial review)

On missing skill: ABORT immediately with clear error: “ERROR: Required skill ‘{skill}’ not found. lit-pm requires all dependencies. See references/stage-specifications.md for skill details.”

The 9-Stage Pipeline

Stage 0: Archival Guidelines Review

Owner: lit-pm (automatic) Checkpoint: Never (always runs automatically) Duration: 2-5 minutes Session Setup: Creates /tmp/lit-pm-session-{YYYYMMDD-HHMMSS}-{PID}/

Initialize workflow session and extract archival guidelines, preferring .archive-metadata.yaml over CLAUDE.md.

Process:

1. Create session directory: /tmp/lit-pm-session-$(date +%Y%m%d-%H%M%S)-$$/
2. Store session path in workflow state for downstream agents

Primary Source: .archive-metadata.yaml

1. Follow the archival compliance check pattern: a. Read the reference document: ~/.claude/skills/archive-workflow/references/archival-compliance-check.md b. If file not found, use graceful degradation (log warning, proceed without archival check) c. Apply the 5-step pattern to all file creation operations
2. Read .archive-metadata.yaml from the repo root
3. Extract naming conventions, directory structure, and project type
4. Include the archival_context block in all downstream stage handoffs

Fallback: CLAUDE.md (Deprecated)

If .archive-metadata.yaml is not found:

1. WARN: “Archival guidelines read from CLAUDE.md (fallback). Run archive-workflow to generate .archive-metadata.yaml for structured guidelines.”
2. Check if .archive-metadata.yaml previously existed:
   • Look for docs/organization/final-organization-report.md
   • If found: WARN “Archival metadata was previously present but is now missing. Re-run archive-workflow.”
3. Read CLAUDE.md and extract guidelines using existing prose extraction logic:
   • Repository organization (directory structure)
   • Naming conventions (review-, analysis-, reference-, etc.)
   • Git rules (commit after edits, no version-numbered files)
   • Document structure requirements
   • PDF acquisition paths
4. Produce archival-guidelines-summary.md as before

Output

Write archival-guidelines-summary.md to the session directory with:

• Source: “.archive-metadata.yaml” or “CLAUDE.md (fallback)”
• Project type, naming conventions, directory structure
• Enforcement mode (from YAML, or “advisory” default)

session_setup:
  session_dir: "/tmp/lit-pm-session-{timestamp}-{pid}/"
  archival_summary_path: "{session_dir}/archival-guidelines-summary.md"
  guidelines_found: boolean
  guidelines_source: string  # ".archive-metadata.yaml" or "CLAUDE.md" or "defaults"
  enforcement_mode: string   # "advisory" | "soft-mandatory" | "hard-mandatory"

Downstream Handoff

Include archival_context block in all specialist dispatches (per the standard archival context block defined in archival-compliance-check.md):

archival_context:
  guidelines_present: true/false
  source: ".archive-metadata.yaml"  # or "CLAUDE.md" or "defaults"
  naming_convention: "kebab-case"
  output_directory: "docs/literature/{topic}/"
  enforcement_mode: "advisory"
  user_override: null

Quality Gate: Session directory created, archival summary written.

Failure Handling:

• .archive-metadata.yaml malformed: Treat as missing, fall back to CLAUDE.md
• CLAUDE.md not found: Use sensible defaults, log warning
• Session directory creation fails: ABORT (cannot proceed without session isolation)

Session Cleanup:

• On successful completion (Stage 8 complete): Delete session directory
• On failure/abort: Retain session directory for debugging (log path to user)

Stage Transition: Stage 0 complete -> PROCEED to Stage 1: Scope Refinement

Stage 1: Scope Refinement

If resuming: Read workflow state to confirm Stage 0 is complete.

Owner: requirements-analyst Checkpoint: ALWAYS (required) Duration: 15-30 minutes Receives: Session directory path from Stage 0

Clarify research question, define success criteria, set boundaries. Complexity detection determines checkpoint plan. User approves scope + checkpoint plan.

Quality Gate: Specific research question, measurable criteria, clear boundaries.

Stage Transition: Stage 1 complete (scope approved) -> PROCEED to Stage 2: Parallel Review Discovery

Stage 2: Parallel Review Discovery

Before starting Stage 2: Read workflow state. Confirm Stages 0-1 are complete.

Launch 2-3 literature-researcher agents using Task tool (see Parallel Execution section below). Checkpoint: Only if HIGH-STAKES complexity Duration: 45-90 minutes (parallel)

Launch parallel agents with diverse search strategies. Analyze convergence (reviews found by multiple agents = high signal). Collect 6-9 reviews total.

Quality Gate: 6-9 reviews, >=2 show convergence, coverage of major themes.

Stage Transition: Stage 2 complete (all agents returned) -> PROCEED to Stage 3: Layered Outline Synthesis

Stage 3: Layered Outline Synthesis

Before starting Stage 3: Read workflow state. Confirm Stages 0-2 are complete.

You create the outline structure (orchestrator task). Delegate section detail proposals to literature-researcher via Task tool. Checkpoint: MEDIUM/COMPLEX/HIGH-STAKES Duration: 30-60 minutes

Create 3-5 section outline with specific theses. Each section gets detailed subsection proposals and assigned reviews.

Quality Gate: 3-5 balanced sections, specific theses, user approval (if checkpoint).

Stage Transition: Stage 3 complete -> PROCEED to Stage 4: Introduction Writing

Stage 4: Introduction Writing

Before starting Stage 4: Read workflow state. Confirm Stages 0-3 are complete. Owner: lit-synthesizer + editor (quick polish) Checkpoint: Never (automatic) Duration: 30-45 minutes

lit-synthesizer writes introduction framing research question and previewing structure. Editor applies quick polish.

Quality Gate: Clear framing, structure preview matches outline.

Stage Transition: Stage 4 complete -> PROCEED to Stage 5: Parallel Section Research & Writing

Stage 5: Parallel Section Research & Writing

Before starting Stage 5: Read workflow state. Confirm Stages 0-4 are complete. Owner: literature-researcher agents (parallel) Checkpoint: Never (gated by Stage 6a) Duration: 3-5 hours per section (parallel)

Section writers conduct targeted research: 15-30 papers per section with recency survey (last 6-12 months). Writers have moderate autonomy to add subsections.

Quality Gate: 15-30 papers cited, recency survey present, thesis addressed.

Stage Transition: Stage 5 sections sent to Stage 6a as they complete. Do NOT wait for all sections.

Stage 6a: Per-Section Quick Validation (BLOCKING)

Owner: fact-checker Checkpoint: Blocking per section Duration: 5-10 minutes per section

Quick checks: paper count, recency survey presence, no placeholders, thesis addressed. Section cannot proceed until PASS.

Quality Gate: All automated checks pass, max 3 revision cycles.

Stage Transition: Section passes 6a -> eligible for Stage 6b. When ALL sections pass 6a AND 6b -> PROCEED to Stage 6c.

Stage 6b: Comprehensive Fact-Check (NON-BLOCKING)

Owner: fact-checker Checkpoint: Never (automatic) Duration: 45-90 minutes

Deep checks: cross-section consistency, citation accuracy (spot-check), quantitative verification. Produces revision list (P0/P1/P2).

Quality Gate: Revision list generated for Stage 8.

(6b is non-blocking. Stage 6c triggers when all sections pass 6a and 6b.)

Stage 6c: Devil’s Advocate Section Review (ALWAYS-ON)

Owner: devils-advocate Checkpoint: ACTIVE (always runs, not user approval) Duration: 30 min/section Trigger: All sections pass Stage 6a/6b

Adversarial review of each section: challenges argument quality, tests assumptions, identifies logical gaps. Max 2 exchanges per section. Pass with uncertainty note on timeout.

Quality Gate: All strategic challenges addressed OR 2 exchanges complete with uncertainty documented.

Scope Separation (vs Fact-Checker):

• devils-advocate CAN challenge: Argument strength, assumption validity, logical coherence, thesis appropriateness, methodology context for claims
• devils-advocate CANNOT challenge: Citation accuracy, whether papers exist, whether values match sources (fact-checker domain)

Stage Transition: Stage 6c complete (all sections reviewed) -> PROCEED to Stage 7: Active Synthesis & Augmentation

Stage 7: Active Synthesis & Augmentation

Before starting Stage 7: Read workflow state. Confirm Stages 0-6c are complete.

Owner: lit-synthesizer (senior author role) Checkpoint: HIGH-STAKES only Duration: 2-4 hours

Senior author reads all sections, identifies cross-cutting themes, restructures for narrative flow, writes conclusion. Authority to add subsections and rewrite transitions. Flags additions >20%.

Quality Gate: Logical flow, themes identified, gaps filled, conclusion synthesizes findings.

Stage Transition: Stage 7 complete -> CHECK: Did synthesis add >=20% content OR is complexity HIGH-STAKES? If YES -> PROCEED to Stage 7.5. If NO -> SKIP to Stage 8: Editorial Polish.

Stage 7.5: Devil’s Advocate Synthesis Review (CONDITIONAL)

Owner: devils-advocate Checkpoint: CONDITIONAL (>=20% additions OR HIGH-STAKES) Duration: 60 min Trigger: (addition_percentage >= 20%) OR (complexity == HIGH-STAKES)

Strategic-level adversarial review of synthesized document: thesis coherence across sections, cross-cutting theme validity, argument flow. Max 2 exchanges.

Quality Gate: Document passes strategic review OR 2 exchanges complete with uncertainty documented.

Stage Transition: Stage 7.5 complete -> PROCEED to Stage 8: Editorial Polish

Stage 8: Editorial Polish

Before starting Stage 8: Read workflow state. Confirm all prior stages are complete. Owner: editor Checkpoint: Never (automatic) Duration: 30-60 minutes

Incorporate P0/P1 revisions from Stage 6b, polish for clarity, ensure voice consistency, final formatting.

Quality Gate: Revisions incorporated, consistent voice, formatted, final read complete.

Post-Pipeline: Git Strategy Advisory (Optional)

After Stage 8 completes and the final document is ready, you MAY invoke git-strategy-advisor via Task tool in post-work mode to get recommendations for how to handle the produced files in version control:

Invocation (via Task tool):

Use git-strategy-advisor to determine git strategy for completed work.

mode: post-work

The advisor analyzes the files produced by the pipeline (review document, notes, synthesis, fact-check report) and recommends branch strategy, push timing, and PR creation based on the actual scope of output.

Response handling: Read the advisor’s summary field. Include in the completion summary for user action.

Confidence handling: If the advisor returns confidence “none” or “low”, silently skip the git strategy section in the completion summary.

Note: git-strategy-advisor analyzes changes within the current git repository only. If this pipeline’s output files are written outside the repository (e.g., to /tmp/ or a user-specified output directory), the advisor will not detect them. In that case, omit the git strategy section from the completion summary.

This is advisory only. If git-strategy-advisor is not available or returns an error, skip this step. lit-pm does not have built-in git logic; the advisor’s recommendation can be passed to the user in the completion summary.

Adaptive Orchestration

See references/adaptive-orchestration.md for full complexity detection logic.

Complexity Detection Dimensions

1. Scope: Paper count (<10 Simple, 10-30 Medium, 30+ Complex), topic breadth, literature maturity
2. Stakes: Keywords (“quick survey” = Low, “grant proposal” = High)
3. User Hints: Explicit flags (–review-outline, –full-auto), time constraints

Checkpoint Plan Table

Checkpoint Types:

• CHECKPOINT: User approval required before proceeding
• Auto: Runs automatically, no user interaction
• ACTIVE: Always runs as quality gate (not user approval)
• Conditional*: Triggers if synthesis adds >=20% content

User Override Options

After proposing checkpoint plan, user can:

• Accept: Proceed with proposed plan
• Reduce: Skip specific checkpoints
• Add: Add checkpoints at additional stages
• Full-auto: --full-auto skips all optional checkpoints

Timeout Configuration

Per-Agent Timeouts:

• literature-researcher: 30 min per search strategy
• lit-synthesizer: 60 min per task
• fact-checker: 10 min (quick), 60 min (comprehensive)
• editor: 30 min

Global Workflow Timeout: 48 hours

Resource Limits

resource_limits:
  max_concurrent_agents: 4       # Hard ceiling
  max_parallel_researchers: 3    # Stage 2: Leave slot for orchestrator
  max_parallel_sections: 3       # Stage 5: Leave slot for fact-checker
  queue_behavior: FIFO           # When limits reached
  queue_timeout: 30 min          # Escalate if not processed

Parallel Execution

Stage 2: Review Discovery (Fan-Out/Fan-In)

Launch 2-3 literature-researcher agents using Task tool:

Agent 1 via Task tool: Description: “Literature researcher: Broad keyword search for {topic}” Prompt: Search using broad keywords. Find 3-5 review papers. Write results to {session_dir}/reviews/agent-1-broad.yaml.

Agent 2 via Task tool: Description: “Literature researcher: Specific technical term search for {topic}” Prompt: Search using specific technical terms. Find 3-5 review papers. Write results to {session_dir}/reviews/agent-2-specific.yaml.

Agent 3 via Task tool: Description: “Literature researcher: Application-focused search for {topic}” Prompt: Search with application focus. Find 3-5 review papers. Write results to {session_dir}/reviews/agent-3-application.yaml.

All three run simultaneously. When all complete, analyze convergence:

• Found by 3/3 agents: high priority (must-read)
• Found by 2/3 agents: medium priority
• Found by 1 agent: coverage breadth

Stage 5: Section Writing (Parallel with Queue)

Launch section writers in parallel using Task tool (max 3 concurrent):

For each section in the approved outline: Launch literature-researcher via Task tool. Description: “Literature researcher: Write section ‘{section_title}'” Prompt: Include section thesis, assigned reviews, subsection structure. Conduct targeted research (15-30 papers). Write output to {session_dir}/sections/{section_id}.md.

As each section completes: Send immediately to Stage 6a for quick validation. If a section times out: Proceed without it, flag the gap for user review.

Handoffs

See references/handoff-schema.md for YAML schema.

Base Handoff Format

handoff:
  version: "1.1"
  stage: integer           # 0-8
  status: enum             # pending | in_progress | complete | failed
  producer: string         # skill that produced handoff
  consumer: string         # skill that receives handoff
  workflow_id: string      # unique identifier
  timestamp: ISO8601       # when created
  session:                 # Added in v1.1
    session_dir: string    # Path to /tmp/lit-pm-session-{...}/
    archival_guidelines_path: string  # Path to archival-guidelines-summary.md

Each stage has additional stage-specific fields documented in the schema.

Session Context Propagation

All downstream agents receive the session context via handoff:

Agents that use archival guidelines:

• literature-researcher: Uses naming conventions for paper notes, PDF storage paths
• lit-synthesizer: Uses document structure requirements, citation format
• editor: Uses writing style, formatting rules
• fact-checker: Uses citation format for validation

Handoff includes:

session_context:
  archival_guidelines_path: "{session_dir}/archival-guidelines-summary.md"
  output_directory: string   # Where final document should be written
  pdf_storage_path: string   # Where to store downloaded PDFs
  naming_convention: object  # File prefix rules

Quality Gates Overview

See references/quality-gates.md for detailed per-stage gates.

Gate Types

Automated Gates (programmatic validation):

• Paper count threshold (>=15 per section)
• Recency survey presence
• Placeholder detection (no “TODO”, “[CITE]”)
• Word count range

Human Judgment Gates (agent assessment):

• Thesis specificity
• Narrative flow
• Cross-cutting theme identification

Quality Floor (Cannot Override)

Even with --full-auto, these checks cannot be skipped:

• Stage 2: minimum 4 reviews, minimum 1 convergence
• Stage 3: minimum 2 sections, max 50% imbalance
• Stage 6c: DA must execute, thesis must be identified for each section

Error Handling Overview

See references/error-handling.md for full compensation matrix.

Key Mechanisms

1. Saga-Style Compensation: Per-stage forward and compensation actions
2. Circuit Breakers: Open after repeated failures, proceed with partial results
3. Atomic State Writes: .tmp -> validate -> rename -> .bak protocol
4. Interrupt Handling: Graceful Ctrl+C with partial state preservation

Workflow State for Resumption

workflow_state:
  workflow_id: "lit-review-{topic}-{date}"
  stage_current: integer          # 0-8
  stage_completed: [list]
  checkpoints_remaining: [list]
  session:                        # Added for session management
    session_dir: string           # /tmp/lit-pm-session-{...}/
    archival_guidelines_path: string
    cleanup_on_complete: boolean  # Default true
  artifacts:
    scope: "/path/to/scope.yaml"
    reviews: "/path/to/reviews.yaml"
    outline: "/path/to/outline.yaml"
    sections_complete: [list]
    sections_in_progress: [list]

Resume with: lit-pm --resume workflow-id

Session Handling on Resume:

• If session directory exists: Reuse existing session
• If session directory missing: Re-run Stage 0 to recreate (non-destructive)

References

• references/stage-specifications.md: Detailed 8-stage process specifications
• references/handoff-schema.md: YAML schema for stage-to-stage communication
• references/error-handling.md: Compensation logic, circuit breakers, recovery
• references/adaptive-orchestration.md: Complexity detection and checkpoint logic
• references/quality-gates.md: Per-stage quality validation criteria

Examples

• examples/hepatocyte-review-example.md: Complete walkthrough of hepatocyte oxygenation review

Invocation

# Standard invocation
lit-pm "Comprehensive review of [topic] for [purpose]"

# With explicit checkpoint control
lit-pm --review-outline "Survey of current approaches to [topic]"
lit-pm --full-auto "Quick survey of [topic]"

# Resume interrupted workflow
lit-pm --resume workflow-id

Dependencies

This skill requires:

• technical-pm Phase 3 parallel execution capabilities
• literature-researcher skill (enhanced from researcher)
• lit-synthesizer skill (new, senior scientific author)
• fact-checker skill (existing)
• editor skill (existing)
• requirements-analyst skill (existing)