research-review-scaffold

name: research-review-scaffold description: Create a low-entropy review/ workspace from a user's research intention. Use when a project needs a literature-review folder with nested agent files, root review docs, a reusable note template, and topic-derived theme folders. Do not use it to seed a paper corpus or to curate an existing review in place without first clarifying the review intention.

Research Review Scaffold

Trigger

• Use when the user wants a review/ folder created from a research topic or research intention.
• Use when the user needs a clean literature-review scaffold before collecting sources.
• Use when the user wants topic-derived theme folders and topic-aware review framing, but not a seeded corpus.
• Do not use this skill to create paper notes, source-index rows, or bibliography entries in the initial scaffold.
• Do not use this skill when the research intention is still too vague to derive stable review themes; refine the intention first.

Inputs

• project_dir: project root where the review workspace should be created
• research_intention: concise statement of the review topic or research question; used to derive a purpose-only review mission, not workflow rules or current task state
• review_dir: optional relative path for the review folder, default review
• chat_context: optional conversation context that helps clarify wording and theme derivation; it must not become durable scope unless intentionally converted into the review mission or explicit scaffold text
• theme_count_hint: optional preferred starting theme count; default behavior is approximately 3 themes
• overwrite: when true, allow replacing existing scaffold files; otherwise skip collisions
• dry_run: when true, return the scaffold plan without writing

Workflow

1. Read research_intention and any chat_context, then clarify the review question until the intended literature scope is stable enough to scaffold. Treat chat context as supporting evidence only; do not persist chat-only instructions as durable review scope unless they are intentionally converted into the mission or scaffold docs.
2. Derive a low-entropy starting theme map from the user's intention. Default to about 3 themes when no theme_count_hint is provided, but do not hard-code a maximum.
3. Resolve the target review folder as project_dir/<review_dir>.
4. Create a self-contained review workspace even when no parent agent workspace exists.
5. Scaffold the four base agent files by invoking the agent-files skill (tool agent_files_init) with target_dir = project_dir/<review_dir>, a purpose-only mission derived from the stabilized research_intention, and the same overwrite flag. The derived mission must not include reusable workflow rules, current repository state, source-collection next steps, or transient objectives. This is the mechanism by which the parent relationship to agent-files is realized — do not re-implement the four base templates locally or patch immutable AGENT.md. On completion the target folder holds:
   • AGENT.md
   • AGENT_GOAL.md
   • AGENT_HARNESS.md
   • AGENT_PROGRESS.md
6. Always scaffold the root review docs:
   • README.md
   • methodology.md
   • summary.md
   • source-index.md
   • references.bib
   • reference-audit.md
   • templates/paper-note-template.md
7. Create numbered theme folders using NN-<theme>/ and preserve user-approved wording for the theme names whenever possible.
8. Initialize topic-aware scaffold text only:
   • summary.md contains framing and placeholder synthesis sections, not final conclusions
   • source-index.md contains only the canonical header row
   • references.bib is empty or stubbed
   • no literature notes, source rows, or bibliography entries are created in v1
9. If the topic crosses domains, mark transfer into the target domain as inference in the scaffold text unless the user clearly scopes the review as cross-domain by design.
10. If overwrite is false, rely on the upstream agent-files compatibility checks for the four AGENT files, including immutable AGENT.md. For review-specific root docs, skip existing files cleanly and return them in files_skipped.
11. If dry_run is true, perform steps 1–3 and 7 (derive the theme map) without writing. Return written=false, the planned review_path, the planned theme_folders, and the list of files that would be created in files_created as intent only; leave files_skipped empty; do not invoke agent_files_init.

Outputs

• review_path
• theme_folders
• files_created
• files_skipped
• summary
• written
• warnings
• open_questions

Failure / Escalation

• If the research intention is too ambiguous to derive a stable review question or theme map, stop with written=false and list the blockers in open_questions.
• If the derived themes are obviously unstable or one-off chat artifacts, refine them with the user before writing.
• If the target folder already exists and overwrite=false, do not replace files silently; rely on agent-files compatibility checks for AGENT files, skip compatible collisions, and report all collisions.
• If deriving the review mission would require embedding workflow rules, current state, or source-collection next steps, stop and ask the user for a cleaner purpose statement.
• If the request expands into corpus building, note taking, or bibliography population, state that those are follow-on review tasks rather than part of the initial scaffold.

Tool Contract

• Read tool.json for the authoritative schema.
• The JSON schema enforces input/output shape only. Semantic checks for purpose-only derived mission text and chat-context persistence are workflow requirements enforced before writing files.
• project_dir and research_intention are required.
• review_dir, chat_context, theme_count_hint, overwrite, and dry_run are optional.
• Return the full output envelope even when no write occurs.