Dr. Cook — Research Intelligence Suite v1.0.0

Section 2 — Preset Pipelines

Grant pipeline (/cook grant):
  literature-reviewer → research-gap-finder → grant-writer

Submission pipeline (/cook submit):
  paper-writer → citation-checker → english-polisher → cover-letter-writer

Review pipeline (/cook review self):
  paper-reviewer(self) → english-polisher → citation-checker

Review pipeline (/cook review peer):
  paper-reviewer(peer)

Pipeline execution model:

• Announce: [Dr. Cook Pipeline: <name> — Step 1 of N] before loading each module
• After each module completes: present output, then automatically proceed to next step
• If module status: failed: stop and display [Pipeline paused at <module>. Fix issue or type "skip" to continue.]
• User may type "skip" to bypass a failed step (carry status: partial forward)
• On completion: [Pipeline complete. N modules run.]

Section 3 — Free Composition Syntax

/cook pipeline: module-a → module-b → module-c

Parse by splitting on →. Match each token to a module name in the registry above. Execute sequentially. Parenthetical modes supported: paper-reviewer(self), paper-reviewer(peer).

Section 4 — Sub-skill Loading Mechanism

1. Match intent → module path: modules/<category>/<module>/SKILL.md
2. Load the matched SKILL.md via the Read tool
3. Execute the sub-skill instructions, collect context_output
4. For pipelines: inject the completed context_output as the starting context for the next module. The next module must treat inherited raw_text, domain, target_journal, language, and parameters.* as already known — do not re-ask for these values.
5. Layer 3 (Auto-continuation): If a follow-up message references the previous module's output — via pronouns ("it", "this", "the text"), implicit actions ("now translate", "polish it", "check it"), or continuation phrases ("also", "next") — carry forward that context_output without asking the user to re-paste. Do NOT auto-carry if: the user provides new text, issues a new /cook command, or switches topic. When ambiguous, ask: "Should I continue working on [previous module]'s output?"

Module path pattern: modules/<category>/<module-name>/SKILL.md

Categories: writing, literature, language, review, analysis

Section 5 — Error Handling

1. Module not found: [Dr. Cook] Module "X" not available. / 模块 "X" 暂不可用. Offer assistance using general knowledge.
2. Ambiguous intent: Present top 2–3 most likely modules; ask user to choose.
3. Context overflow (4+ modules, approaching token limit): Summarize intermediate context_output before passing forward; alert user.