mars-research-knowledge-stack-normalization

name	mars-research-knowledge-stack-normalization
description	Normalize a brownfield research project to the MARS knowledge-stack contract using dependency-ordered waves across definitions, references, context bundles, inventory, and experiment artifacts.
argument-hint	<project-key> [--audit|--execute] [--wave <W1..W8>] [--dry-run]
agent	mars-research-planner
allowed-tools	Read, Write, Bash, Glob, Grep, AskQuestions

Convert fragmented brownfield research artifacts into a consistent MARS execution stack.

This skill is for projects with scattered definitions/references/context assets that block reliable protocol execution and evidence adjudication.

Target project contracts: - `research/projects//PROJECT.yaml` - `research/projects//definitions/*` - `research/projects//protocols/*` - `research/projects//sources/*` - `research/projects//inventory/*` - `research/projects//experiments/*` - `research/projects//registry/*` - `research/projects//results/*`

MARS references:

• implementation/mars/definitions/RESEARCH-KNOWLEDGE-STACK-CONTRACT.md
• implementation/mars/definitions/EXPERIMENT-BUNDLE-CONTRACT.md
• implementation/mars/definitions/MARS-PIPELINE.md

W1. Candidate extraction - enumerate definition, reference, context, and resource candidate artifacts

W2. Taxonomy and ID policy

• finalize definition-ID and reference-status vocabularies

W3. Definitions/protocol coupling

• align definition index and protocol checklist anchor requirements

W4. Source authority normalization

• normalize ledger statuses, authority sources, and waivers

W5. Inventory linkage normalization

• ensure source-to-inventory linkage and index coverage

W6. Experiment source backfill

• ensure every scheduled experiment has source-selection artifact with pins

W7. Context bundle backfill

• ensure every scheduled experiment has context bundle minimum contract

W8. Compliance sweep and closure

• run structure checks, publish residual risks, and capture follow-up backlog

1. Run `--audit` first to classify current artifact completeness by wave. 2. Ask decision-gate questions when policy choices have multiple viable options. 3. Execute waves in order unless a specific `--wave` is requested. 4. Stop on blockers and publish exact remediation obligations with file targets. 5. After wave execution: - refresh experiment navigation artifacts (`./tools/update_project_experiments_index.sh `), - run structural validation (`./tools/check_research_structure.sh`). 6. Publish execution summary and residual risk list. - No wave can be marked complete without artifact evidence. - Reference authority normalization must preserve waiver auditability. - Context bundles must include source-role matrix, terminology map, metric map, conflict log, and open risks. - Backfill actions must be deterministic and reproducible. Return:

## Knowledge Stack Normalization Summary
- Project: <project-key>
- Mode: audit | execute
- Waves completed: <list>
- Waves blocked: <list>
- Critical blockers: <n>

### Artifacts Updated
- <path>

### Residual Risks
1. <risk>

### Next Actions
1. <action>
2. <action>