Rules reference

Nine files under .claude/rules/. Every agent and skill is bound by them.

evidence-standard.md

Every fact carries a verbatim source quote, a source ID, and an implication. Missing any of the three means the fact is dropped. No paraphrasing. No inferred numbers. No implications without consequences.

scoring-axes.md

Three independent axes: Scale, Cost, Quality. No composite score. Per-axis confidence required. Cost decomposes into procurement chain links (specimen_source, provider, assay_execution, etc.). Quality has four sub-axes (pre-analytical, confounders, platform validation, provenance depth).

model-allocation.md

Opus orchestrates, never processes. Sonnet runs the heavy phases (extract, resolve, merge, score). No Opus-on-Opus delegation. Python scripts run without an LLM.

example-rotation.md

Domain framing rotates across three domains: A (neuro fluid biomarker), B (oncology tissue genomics), C (microbiome stool sequencing). Prevents the system from defaulting to plasma metabolomics framing.

transparency-principles.md

Provenance over bypass. The system scores provenance depth, not channel type. Both sides (buyers and suppliers) use the same wiki. Hidden chains are flagged, never silenced. Negative results count.

entity-schema.md

The YAML frontmatter contract enforced by the pre-write hook. Required fields for every entity. Type-specific fields for data_opportunity, institution, and bundle. Closed enums. Format rules. See Entity Schema for the full specification.

wiki-conventions.md

Slug rules per entity type. Article shape (frontmatter, title, summary, dimensions, open questions, links). Index files are auto-generated and hand-edits are overwritten. See Wiki Conventions for the full specification.

autonomy.md

Do the best thing, then report what you did. Do not ask questions you can answer yourself. If the wiki is thin, trigger ingest. Persist every decision to disk. Surface thin results plainly.

_commandments.md

Eleven-line banner injected into every Sonnet subagent dispatch. The short form of all rules. Pre-loaded at token 0 so rules survive context compaction. Saves ~3K tokens per spawn versus reading full rule files.

How rules are enforced

Hooks enforce entity-schema.md at write time. Bad frontmatter blocks the write.
The commandments banner injects the 11 core rules into every subagent context.
Lint catches drift after the fact: missing quotes, low provenance depth, broken links.
The lockfile detects accidental edits to rule files.