auto-paper-intake

name	auto-paper-intake
description	Internal Harness instruction source for auto-paper-intake. Route through visible Harness aliases or hook contracts instead of invoking directly.

Auto Paper Intake

Purpose

Create the run configuration and source inventory. Do not write manuscript prose or make claim decisions in intake.

Inputs

Collect or infer:

• paper_id
• target_venue
• target_name
• draft_path
• tex_roots
• bib_paths
• figure_paths
• figure_requirement_status
• materials_dir
• reference_paths
• experiment_evidence_index when docs/30_evidence/Experiment_Evidence_Index.{json,md} exists
• artifact_dir
• objective
• scope
• output_language
• compile_command
• human_gate_policy
• forbidden_directions

If a field cannot be inferred from files or user brief, write unknown and add a USER_GATE question to intake_report.md.

For blog, review, survey, or tutorial targets, set citation policy explicitly. Use citation_target_count: unknown or a positive target unless the operator explicitly asks for an uncited opinion memo.

Discovery

If the artifact directory is empty or missing, initialize the run scaffold first:

• .agents/skills/auto-paper/scripts/init_artifacts.py --paper-id <paper_id> --artifact-dir <artifact_dir> --workflow <workflow>

Templates are placeholders. Replace unknown values during intake and keep future-phase templates as scaffolds until their owning phase runs.

Use rg --files to find .tex, .bib, figures, notes, PDFs, Markdown files, CSV/JSON result files, and local reports. Index experiment evidence only through docs/30_evidence/Experiment_Evidence_Index.*; do not include iteration_log.json in source_index.md as a normal data source. If it is read for planning, mark it as a weak signal and cross-check with run artifacts or iteration reports. Prefer deterministic scripts when available:

• .agents/skills/auto-paper/scripts/init_artifacts.py
• .agents/skills/auto-paper/scripts/reference_inventory.py
• .agents/skills/auto-paper/scripts/tex_inventory.py
• .agents/skills/auto-paper/scripts/figure_requirement_scan.py
• .agents/skills/auto-paper/scripts/latex_guard.py

For PDF and Markdown materials, run or emulate figure_requirement_scan.py to search for figure/table cues. Record all matches in figure_requirement_scan.md with source locations. If the scan finds candidate figures or tables, set the next owner to $auto-paper-figure or layout and do not leave the need only in the raw PDF text.

If compile_command is present, run a non-mutating baseline compile or static guard. If absent, record compile_command: unknown.

Outputs

Write under auto_paper_output/<paper_id>/:

• config.yaml
• source_index.md
• tex_inventory.json
• intake_report.md
• experiment_source_map.md when an experiment evidence index is present
• figure_requirement_scan.md when PDFs, Markdown notes, or source materials were scanned for figure/table needs

Do not write .auto_paper/ or .auto_iterate/ manually.

Gate Ledger

Report a Gate ledger entry with commands run, artifacts written, any USER_GATE or NOT_RUN reason, and the next owner before handoff.