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Command Reference

Folio exposes nine commands: one full-pipeline entry point and eight stage-specific sub-commands. Every sub-command can run standalone on an existing workspace.

/folio

Run the full pipeline or resume from a checkpoint.

/folio [idea] [materials_path]
Argument Required Description
idea No One-line research idea (prompted if omitted)
materials_path No Path to raw materials folder (prompted if omitted)
  • If no workspace exists, runs the full pipeline from Stage 0.
  • If a workspace path is provided and logs/checkpoints.md exists, offers to resume from the last completed stage.

/folio:init

Initialize a workspace and collect intent.

/folio:init [idea] [materials_path]
Argument Required Description
idea No Research idea
materials_path No Path to raw materials

Entry condition: No existing workspace required.

Produces: workspace/ directory with canonical layout, intent.json, raw materials copied into inputs/raw_materials/.

Scripts run: init_workspace.py

/folio:prep

Normalize, classify, and route materials.

/folio:prep [workspace_path]
Argument Required Description
workspace_path Yes Path to an initialized workspace

Entry condition: Stage 0 (init) complete. intent.json must exist.

Produces: Classified inputs (idea.md, experimental_log.md, venue_profile.md, manifests), route.json with mode recommendation.

Scripts run: classify_materials.py, route_mode.py, validate_inputs.py

Gates: Gate A (input completeness) -- validate_inputs.py must exit 0.

Checkpoints: Human Checkpoint 1 (prep approval) and routing checkpoint (mode confirmation).

/folio:plan

Mode-specific planning.

/folio:plan [workspace_path]
Argument Required Description
workspace_path Yes Path to a prepped workspace

Entry condition: Stage 1 (prep) complete. Mode confirmed in route.json.

Produces: outline.json, claim_ledger.json, figure_plan.json, literature_plan.json. White paper and hybrid modes also produce perspectives.json, question_tree.json, argument_graph.md.

Gates: Gate B (plan coherence) -- outline must cover all claims in the ledger.

Checkpoints: Human Checkpoint 2 (planning approval before drafting).

/folio:support

Build evidence, literature, and figures.

/folio:support [workspace_path]
Argument Required Description
workspace_path Yes Path to a planned workspace

Entry condition: Stage 2 (plan) complete.

Produces: citations/citation_pool.json, citations/refs.bib, generated figures in figures/generated/, figures/captions.json, tables/generated/.

Gates: Gate C (support completeness) -- every claim in the ledger must have at least one supporting artifact or an explicit gap marker.

/folio:draft

Compose the manuscript.

/folio:draft [workspace_path]
Argument Required Description
workspace_path Yes Path to a supported workspace

Entry condition: Stage 3 (support) complete.

Produces: drafts/paper.tex (research paper / hybrid) or drafts/paper.md (white paper / hybrid), section files in drafts/sections/.

Gates: Gate D (draft completeness) -- all outline sections present, no unresolved <!-- GAP --> markers in required sections.

/folio:review

IP scan, critical review, and repair.

/folio:review [workspace_path]
Argument Required Description
workspace_path Yes Path to a drafted workspace

Entry condition: Stage 4 (draft) complete.

Produces: reviews/review_round_N.md, reviews/scorecard.json, reviews/ip_safety_report.md. Regressions are repaired automatically; the draft is updated in place.

Scripts run: scan_redlines.py

Gates: IP Gate -- scan_redlines.py must exit 0 (no unacknowledged violations). Review Gate -- scorecard overall must not regress between rounds.

Checkpoints: Human Checkpoint 3 (final approval before export).

/folio:export

Finalize and package the manuscript.

/folio:export [workspace_path]
Argument Required Description
workspace_path Yes Path to a reviewed workspace

Entry condition: Stage 5 (review) complete. Checkpoint 3 approved.

Produces: final/ bundle (paper source, refs.bib, figures, optional compiled PDF). White paper and hybrid modes also produce exports/executive_summary.md and exports/bd_talking_points.md.

Scripts run: package_exports.py, compile_package.sh (if LaTeX toolchain available)

/folio:status

Show pipeline state for a workspace.

/folio:status [workspace_path]
Argument Required Description
workspace_path Yes Path to any workspace

Entry condition: Workspace directory must exist.

Produces: No artifacts. Prints a table of completed stages, pending checkpoints, active mode, and any blocking gate failures. Reads from logs/checkpoints.md and logs/run_log.md.

Resume behavior

When invoked on a workspace that already has progress:

  1. /folio reads logs/checkpoints.md and offers to resume from the next incomplete stage.
  2. Any stage command (e.g., /folio:draft) checks that its entry conditions are met. If prior stages are incomplete, it reports what is missing rather than silently failing.
  3. Re-running a completed stage overwrites its artifacts. The previous versions are logged in logs/run_log.md.

Examples

# Full pipeline from scratch
/folio "Benchmarking LLM routing strategies" ~/research/llm-routing/

# Initialize only, then come back later
/folio:init "Benchmarking LLM routing strategies" ~/research/llm-routing/

# Check where a workspace stands
/folio:status workspace/

# Jump straight to review on a drafted workspace
/folio:review workspace/

# Re-export after manual edits to the draft
/folio:export workspace/