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:
- Core principles (
core/principles.md) — bilingual reader by default, translate for meaning, never degrade to a summary, copyright caution. - Source-format fragment — how to extract text, figures, and tables for this input.
- Reading workflow (
core/workflow.md) — the six-step source-map-first process. - 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.
