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@6ecfa4f
by Edward Cheng-I Wuimbad0202/academic-research-skills50k stars
3,864

Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates deep-research, academic-paper, and academic-paper-reviewer into a seamless 10-stage workflow with mandatory, coverage-bounded integrity checks, two-stage peer review, and auditable quality-assurance artifacts. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow, 연구부터 논문까지, 연구 주제 설정부터 논문 완성까지, 논문 전체 워크플로, flujo de trabajo académico, investigación a artículo, flujo completo de artículo, pipeline de investigación completa, publicación de investigación, flujo de trabajo completo del artículo.

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Use this Skill: https://skilld.dev/gh/imbad0202/academic-research-skills/academic-pipeline

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referenceschangelog.md

≈1.5k tokens on demand. Your agent reads this file only when SKILL.md points to it.

Changelog

Version Date Changes
2.8 2026-04-21 Collaboration Depth Observer (v3.3.0): New collaboration_depth_agent (Agent Team grows from 3 to 4). Reads dialogue logs at every FULL/SLIM checkpoint and at pipeline completion; scores user-AI collaboration on 4 dimensions (Delegation Intensity / Cognitive Vigilance / Cognitive Reallocation / Zone Classification) per shared/collaboration_depth_rubric.md (rubric v1.0, canonical, CC-BY-NC 4.0). Advisory only — never blocks. MANDATORY checkpoints (2.5 / 4.5) do NOT invoke the observer (integrity gates preserved). Cross-model divergence flagged (not silently averaged) when ARS_CROSS_MODEL set. Rubric credits Wang, S., & Zhang, H. (2026). IJETHE 23:11. DOI 10.1186/s41239-026-00585-x. New lint: scripts/check_collaboration_depth_rubric.py. State tracker gains dialogue_log_ref per stage + collaboration_depth_history[] append-only. Reinforcement row added for checkpoint transitions.
2.7 2026-03-27 Style Profile in Material Passport: Pipeline orchestrator now carries optional Style Profile (Schema 10 in shared/handoff_schemas.md) through all stages. Produced by academic-paper intake Step 10 when user provides past writing samples. Consumed by draft_writer (Stage 2) and report_compiler (Stage 1) as soft writing voice guide. Does not affect integrity verification or review stages. Coordinates with deep-research v2.4 and academic-paper v2.5
2.6 2026-03-08 Handoff Data Schema: Enhanced shared/handoff_schemas.md with 9 comprehensive schemas (RQ Brief, Bibliography, Synthesis, Paper Draft, Integrity Report, Review Report, Revision Roadmap, Response to Reviewers, Material Passport) with full field definitions, type constraints, and validation rules; orchestrator validates output against schemas before each transition. Adaptive Checkpoint System: Replaced static checkpoint template with 3-tier system (FULL/SLIM/MANDATORY) based on stage criticality and user engagement; FULL checkpoints include decision dashboard with metrics; SLIM auto-continues for experienced users; MANDATORY cannot be bypassed at integrity/review/finalization boundaries; awareness guard after 4+ auto-continues. Mode Advisor: New references/mode_advisor.md with unified cross-skill decision tree, common misconceptions table, user archetype recommendations, decision flowchart, and anti-patterns guide. Team Collaboration Protocol: New references/team_collaboration_protocol.md with 5 role definitions, per-transition handoff procedures, git branching/tagging strategy, conflict resolution matrix, and communication templates; state tracker extended with assigned_to, approval_gate, team_notes per stage and schema_validation_log. Phase E Claim Verification: New references/claim_verification_protocol.md with E1 claim extraction, E2 source tracing, E3 cross-referencing; verdict taxonomy (VERIFIED / MINOR_DISTORTION / MAJOR_DISTORTION / UNVERIFIABLE / UNVERIFIABLE_ACCESS); severity mapping (MAJOR_DISTORTION -> SERIOUS, UNVERIFIABLE -> SERIOUS, MINOR_DISTORTION -> MINOR, UNVERIFIABLE_ACCESS -> MEDIUM); integrated into integrity_verification_agent Mode 1 (30% spot-check) and Mode 2 (100%); pass/fail criteria updated to include Phase E verdicts. Mid-Entry Material Passport Check: Pipeline orchestrator now validates Material Passport on mid-entry; decision tree checks verification_status, freshness (< 24 hours), and content modification (version_label comparison); offers skip/spot-check/full re-verify options for Stage 2.5 when passport is valid; passport freshness validation rules added to shared/handoff_schemas.md
2.5 2026-03-08 External Review Protocol: structured intake of real journal reviewer feedback (text/PDF/DOCX); 4-step workflow (parse -> strategic coaching -> revise + Response to Reviewers -> completeness check); differentiated behavior from internal simulated review (no default "accept all", risk assessment per comment, user confirmation of parsed items); explicit capability boundaries (AI verification ≠ reviewer satisfaction)
2.4 2026-03-08 Stage 6 PROCESS SUMMARY: post-pipeline paper creation process record; asks user preferred language (zh/en/both); generates structured MD summarizing full human-AI collaboration history with user quotes, key decisions, iteration details, and lessons learned; mandatory final chapter: Collaboration Quality Evaluation (6 dimensions scored 1-100, bar chart visualization, What Worked Well / Missed Opportunities / Recommendations / Human vs AI Value-Add / Claude's Self-Reflection); compiles to PDF via LaTeX + tectonic; outputs paper_creation_process_zh.pdf + paper_creation_process_en.pdf
2.3 2026-03-08 Stage 5 FINALIZE: mandatory formatting style prompt (APA 7.0 / Chicago / IEEE); PDF must compile from LaTeX via tectonic (no HTML-to-PDF); APA 7.0 uses apa7 document class (man mode) with XeCJK for bilingual support; font stack: Times New Roman + Source Han Serif TC VF + Courier New
2.2 2026-03-05 Checkpoint confirmation semantics (6 user commands with precise actions); mode switching rules (safe/dangerous/prohibited matrix); skill failure fallback matrix (per-stage degradation strategies); state ownership protocol (single source of truth with write access control); material version control (versioned artifacts with audit trail); cross-skill reference to shared/handoff_schemas.md
2.1 2026-03 Added plagiarism detection protocol (Phase D); enhanced integrity_verification_agent with originality verification (D1 WebSearch, D2 self-plagiarism); updated both verification modes
2.0 2026-02 Added Stage 2.5/4.5 integrity checks, two-stage review, mandatory checkpoints, Devil's Advocate, reproducibility guarantees, integrity_verification_agent
1.0 2026-02 Initial version: 5+1 stage pipeline

Source: SKILL.md on GitHub

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    The skill is a complex academic research orchestrator that manages a multi-stage workflow from research to final manuscript. It includes robust security patterns, such as explicit 'instruction-data' boundaries, to protect against malicious content in research materials. The skill relies on local script execution and standard academic tools like Pandoc and Tectonic for its functionality.

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Provenance

Signed by skilld at 6ecfa4f. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub 33 minutes ago.

Activeupdated 2 hours ago

Capability

Other metadata
metadata
{
  "version": "3.22.2",
  "last_updated": "2026-09-25",
  "depends_on": "deep-research, academic-paper, academic-paper-reviewer",
  "status": "active",
  "data_access_level": "raw",
  "task_type": "open-ended",
  "related_skills": [
    "deep-research",
    "academic-paper",
    "academic-paper-reviewer"
  ]
}

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