Academic Pipeline — 10-Stage End-to-End (Hermes Edition)

📄 License: CC BY-NC 4.0 · Copyright (c) 2026 Cheng-I Wu
🔗 Original: Imbad0202/academic-research-skills
🔄 Adaptation: Orchestration pipeline implemented via delegate_task instead of Claude Code's internal agent system. All agent definitions, references, and quality standards preserved unchanged from original. This adaptation is distributed under the same CC BY-NC 4.0 license.

Orchestrates the full academic workflow from research idea to publication-ready output.

10 Stages

| Stage | Skill Used | Key Output | |-------|-----------|------------| | 1. Planning | intake + mode selection | Project Plan with stage gating | | 2. Research | deep-research (full/quick) | RQ Brief + Methodology + Bibliography + Synthesis | | 3. Paper Draft | academic-paper (full) | Complete paper draft | | 4. Peer Review | academic-paper-reviewer (full) | 5-panel review + Editorial Decision | | 5. Revision | academic-paper (revision) | Revised draft + tracked changes | | 6. Polish | academic-paper (revision) | Final polished manuscript | | 7. Ethics Check | academic-paper-reviewer (quick) | Ethics clearance | | 8. AI Disclosure | academic-paper (disclosure) | Venue-specific AI statement | | 9. Format | academic-paper (format-convert) | LaTeX/DOCX/PDF + cover letter | | 10. Deliver | file output | Publication package |

Hermes Execution

The orchestrator (main Hermes agent):

Stage 1: Clarify user intent → select modes → create Project Plan
Stage 2-6: Sequential delegate_task calls, each loading the relevant skill
Stage 7-9: Lightweight parallel or sequential based on dependencies
Stage 10: Write final package to disk

Key Checkpoints

Stage 1→2: User approves Project Plan
Stage 2→3: Research report accepted by user
Stage 4→5: Review decision received
Stage 6→7: Polished draft ready

Resume Support

Pipeline state stored in ~/.hermes/sessions/. User can resume with:

Continue the academic pipeline from Stage 4

Usage Patterns

Full pipeline:

Take "AI impact on HE quality assurance" through the full pipeline to publication-ready manuscript

Partial pipeline:

Start from Stage 3 with my existing deep-research output

Resume:

Resume pipeline from Stage 5 with reviewer comments: [comments]

Integration with Hindsight Memory

Pipeline state and key outputs are retained to Hindsight for long-term tracking:

hindsight memory retain --content "[stage_output]" --tags "pipeline,stage-N"

Critical Rules

⚠️ Each stage MUST complete before the next begins
⚠️ User confirmation at all IRON RULE checkpoints
⚠️ Ground truth isolation: review stage must NOT see author identity

Security & Privacy

Orchestration disclosure: This pipeline orchestrates multiple skills (research → writing → review) via delegate_task. All content passes through the AI provider's workflow. Use only with topics you are comfortable processing through AI.

Tool access: This pipeline delegates to sub-skills which independently control their own tool access. No stage is granted terminal, web, or system tools beyond what each sub-skill permits.

Agent files: All agents/ directories across sub-skills contain academic prompt templates, NOT system prompt overrides.