Full-Paper Markdown Reader — Router

Routing protocol

First distinguish creating a reader from answering a question or translating an excerpt. For a source-linked question, read references/grounding-rules.md and inspect only the relevant source material; reuse existing source-map IDs when available. Do not regenerate the reader or require a full source map before answering. For an explicit excerpt request, apply extraction, translation, and grounding rules to that excerpt. The full-artifact workflow below applies when the user requests a reader or full-paper translation.

For a new task, load the core and matching resources below. Reuse already loaded guidance on follow-ups; load more only when the task needs it.

1. Load the manifest and the core layer

Read manifest.yaml. It declares the source_format axis, the allowed values, and the file paths each value maps to.

Also read every file listed under always_load. These hold the core principles, the reading workflow, and the output contract that apply to every reading job, plus the shared Terminology Ledger used to build the recurring-term table.

2. Detect the source format

Decide the source_format value using the manifest's detect: hint and the user's input:

• pdf-text — selectable-text PDF. Default.
• scanned-pdf — image-only or OCR-required PDF.
• html — publisher or preprint HTML page.
• doi-arxiv — a bare DOI or arXiv link that must be resolved first.
• pasted-text — pasted prose or notes with no retrievable original layout.

State the detected value in one short line to the user before processing, so they can correct you cheaply. A source may map to more than one value (for example a DOI that resolves to a PDF); load the resolution fragment first, then the fragment for the resolved artifact.

3. Load the matching fragment(s)

Read the file mapped for the detected source_format. Do not read every fragment in static/. Load only what step 2 selected.

4. Build the reader using the loaded material

Apply the loaded fragments in this priority order:

1. Core principles (core/principles.md) — bilingual reader by default, translate for meaning, never degrade to a summary, copyright caution.
2. Source-format fragment — how to extract text, figures, and tables for this input.
3. Reading workflow (core/workflow.md) — the six-step source-map-first process.
4. Output contract (core/output-contract.md) — required files and the pre-response verification checklist.

Build the Terminology Ledger as you translate (../nature-shared/core/terminology-ledger.md); it becomes the paper.md recurring-term table and the source_map.json glossary.

If constraints prevent full processing, still create a draft reader and label missing pages, figures, or low-confidence crops in translation_notes.md. Do not switch to summary mode.

5. Reach for references only when needed

The files under references/ are deep references, not defaults. Open them on demand per the references.on_demand table in the manifest:

• detailed figure/table cropping and placement → references/figure-extraction.md.
• exact field schema for paper.md / source_map.json → references/output-spec.md.
• equations, mathematical expressions, chemical formulae, or image-only formulae → references/equation-handling.md.
• answering follow-up questions with source citations → references/grounding-rules.md.