mars-research-foundations

name	mars-research-foundations
description	Build the project-level research foundations baseline before protocol design by producing domain context, methodology/theory synthesis, source catalog updates, reference-ledger updates, and library-grade inventory coverage.
argument-hint	<project-key> [--refresh-sources] [--refresh-library] [--context-label <label>]
agent	mars-research-scientist
allowed-tools	Read, Write, Bash, Glob, Grep, Fetch, AskQuestions

Create the project-level research foundations that must exist before experiment protocol design or execution begins.

This skill produces two project-scoped baseline artifacts:

• foundations/DOMAIN-CONTEXT.md
• foundations/METHODOLOGY-AND-THEORY.md

and ensures they are backed by:

• sources/SOURCE-CATALOG.md
• sources/REFERENCE-LEDGER.md
• inventory/INVENTORY-INDEX.md plus library-grade inventory entries

This skill exists because experiment-scoped methodology and context bundles are too late to establish the basic research posture of a project.

Project baseline inputs: - `PROJECT-OVERVIEW.md` - `claims/CLAIMS.md` - `claims/HYPOTHESES.md` - `definitions/DEFINITIONS.md` - `definitions/DEFINITIONS-INDEX.md` - `experiments/EXPERIMENT-CANDIDATES.md` - `experiments/EXPERIMENTS.md`

Project knowledge-stack artifacts:

• sources/SOURCE-CATALOG.md
• sources/REFERENCE-LEDGER.md
• inventory/INVENTORY-INDEX.md
• inventory/*.md

Template sources:

• implementation/mars/templates/domain-context-template.md
• implementation/mars/templates/methodology-theory-baseline-template.md

This skill should use source discovery and inventory extraction patterns when authorities are missing or under-extracted.

1. Read current project scope and experiment intent. - Resolve the research setting, decision surface, and experiment family. - Identify which authorities belong in the `domain context` versus the `methodology and theory` baseline.

2. Build or refresh the authority base.

   • Ensure required authorities are present in sources/SOURCE-CATALOG.md.
   • Ensure protocol-level authorities are promoted into sources/REFERENCE-LEDGER.md with clear usage scopes.
   • If missing, use source-discovery workflow before continuing.

3. Build or refresh the reference library.

   • Ensure inventory/INVENTORY-INDEX.md covers the active authorities.
   • Expand inventory artifacts so they are library-grade: enough extracted content to support later protocol design without re-discovery.
   • Library-grade means preserving reusable constructs, cautions, experiment relevance, and adaptation notes, not only short snippets.

4. Write foundations/DOMAIN-CONTEXT.md.

   • Explain the project setting, regimes, prior-art context, and failure modes.
   • Make the external-validity frame explicit.

5. Write foundations/METHODOLOGY-AND-THEORY.md.

   • Explain the methodology posture, theory baseline, authority map, and implications for experiment design.
   • Record any unresolved authority split or scope ambiguity explicitly.

6. Enforce the foundations gate.

   • Protocol design should remain blocked if either foundations artifact is missing.
   • Protocol design should remain blocked if primary authorities are not source-cataloged, ledgered, and library-inventoried.

7. Return a compact foundations summary and the next recommended command.

- The two foundations artifacts should be consultable by a later protocol author without needing to re-read the source discovery conversation. - Inventory should behave like a reusable reference library, not a citation cache. - Domain-context and methodology/theory synthesis must be separate; do not collapse them into one unfocused document. - Authority ambiguities must be explicit. Return:

## Research Foundations Summary

- Project: <project-key>
- Domain context: ready | needs-work
- Methodology/theory baseline: ready | needs-work
- Source catalog status: ready | needs-work
- Reference library status: ready | needs-work
- Protocol-design readiness: PASS | BLOCK

### Artifacts

- <path>
- <path>

### Next Command

1. <exact command>

- This skill establishes project-level research baselines. - It does not replace experiment-scoped `methodology.md`, `protocol.md`, or `context.md`. - When the foundations baseline is incomplete, protocol design should not proceed.