research-execute

Research Execute Skill

Description

Executes the research code in src/ to generate result artifacts in results/. This is Phase 3.5 of the research pipeline, sitting between Implementation (Phase 3) and Testing & Visualization (Phase 4).

Reads execution commands deterministically from the YAML frontmatter of plan/research_plan.md — no keyword heuristics, no entry-point guessing. The full run command is defined once during planning and executed here.

Usage

/research-execute [path/to/output/dir]

Arguments

• $ARGUMENTS — Optional path to the research output directory. If not provided, uses the most recent outputs/*/ directory.

Instructions

Claude-Only Mode

When --claude-only is active, there are no Gemini/Codex calls in this skill. All steps are performed by Claude directly.

Step 0: Locate Research Plan & Check Prerequisites

1. Find the active research output directory (from $ARGUMENTS or most recent outputs/*/).
2. Read plan/research_plan.md and parse the YAML frontmatter:

   ---
   languages: ["rust", "python"]
   ecosystem: ["cargo", "uv"]
   execution_cmd: "bash run_all.sh"
   dry_run_cmd: "bash run_all.sh --dry-run"
   expected_outputs:
     - "results/metrics.csv"
     - "results/checkpoint.pt"
   estimated_runtime: "~30 minutes"
   ---
   

3. Prefer execution_manifest.json: Check if execution_manifest.json exists in the output directory root. If it does, read execution fields from this file instead of the YAML frontmatter:

   {
     "schema_version": "1.0.0",
     "languages": ["rust", "python"],
     "ecosystem": ["cargo", "uv"],
     "execution_cmd": "bash run_all.sh",
     "dry_run_cmd": "bash run_all.sh --dry-run",
     "expected_outputs": [
       {"path": "results/metrics.csv", "required": true},
       {"path": "results/checkpoint.pt", "required": false}
     ],
     "estimated_runtime": "~30 minutes"
   }
   

   If execution_manifest.json exists, it takes precedence over YAML frontmatter fields. If it does not exist, fall back to the YAML frontmatter (backward compatibility).
4. If the frontmatter is missing or has no execution_cmd: announce the problem to the user and ask them to provide the execution command manually. Do not guess. Suggest adding the frontmatter to research_plan.md following the schema above.
5. Verify src/ exists and contains at least one file.