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Output Manifest Protocol

Maintain a MANIFEST.md in the project root only when a run produces more than 15 artifacts. Below that threshold, do not create one: a manifest for a handful of files is itself a duplicate index that has to be kept in sync with the files it lists — the very duplication this protocol family exists to prevent (see output-composition.md). When the threshold is met, append one entry per output file as below.

Threshold rationale: the original "log every output to MANIFEST" rule is what drove the MANIFEST.md clutter in small idea-discovery runs. A manifest earns its keep only when there are enough artifacts that an index genuinely helps.

Format

If MANIFEST.md does not exist, create it with this header:

# Research Output Manifest

> Auto-maintained by ARIS skills. Tracks all generated artifacts across the research lifecycle.

| Timestamp | Skill | File | Stage | Description |
|-----------|-------|------|-------|-------------|

Then append one row per output file written:

| 2025-06-15 14:30 | /idea-creator | idea-stage/IDEA_REPORT_20250615_143022.md | idea-discovery | 12 ideas generated from "LLM reasoning" direction |
| 2025-06-15 14:30 | /idea-creator | idea-stage/IDEA_REPORT.md | idea-discovery | latest copy |

Stage Values

Stage Skills
idea-discovery /idea-creator, /idea-discovery, /novelty-check, /research-review
implementation /research-refine, /research-refine-pipeline, /experiment-plan, /experiment-bridge, /run-experiment
review /auto-review-loop
paper /paper-writing, /paper-write, /paper-compile

Pre-flight Check

Before writing output, if the skill depends on a prerequisite file from a previous stage:

  1. Check if the prerequisite file exists at its expected stage-scoped path (e.g., idea-stage/IDEA_REPORT.md, review-stage/AUTO_REVIEW.md)
  2. If not found at the stage-scoped path, check the legacy root-level path (e.g., ./IDEA_REPORT.md, ./AUTO_REVIEW.md) — see Path Fallback Rule
  3. If not found at either path, warn: "⚠️ Expected {file} (from {skill}) but not found. Run {skill} first?"
  4. Do not block — the user may have the file elsewhere or want to proceed anyway