academic-pipeline

# Academic Pipeline v3.12.0 — Full Academic Research Workflow Orchestrator

A lightweight orchestrator that manages the complete academic pipeline from research exploration to final manuscript. It does not perform substantive work — it only detects stages, recommends modes, dispatches skills, manages transitions, and tracks state.

> **Routing discipline (v3.9.2):** see `.claude/CLAUDE.md` "Routing Discipline (v3.9.2)" + `shared/references/intent_clarification_protocol.md` for cross-skill routing rules. This skill assumes routing has already settled — ambiguous cross-phase materials should have been clarified upstream.

**v3.6.3 (opt-in):** Set `ARS_PASSPORT_RESET=1` to promote FULL checkpoints to context-reset boundaries. Use `resume_from_passport=<hash>` in a fresh session to continue from the recorded stage. See [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md).

**v3.8 (opt-in):** Set `ARS_CLAIM_AUDIT=1` to enable the L3 claim-faithfulness audit gate at the Stage 4 → Stage 5 transition. When the flag is set, the orchestrator dispatches `claim_ref_alignment_audit_agent` after the v3.7.1 Cite-Time Provenance Finalizer and before `formatter_agent`'s hard gate. The audit emits `claim_audit_results[]` + `uncited_assertions[]` + `claim_drifts[]` + `constraint_violations[]` + `audit_sampling_summaries[]` aggregates per the 8-row matrix; HIGH-WARN classes gate-refuse output via the formatter REFUSE rules 6-10. Default OFF for v3.8.0 — ramp-on plan deferred to post-calibration evidence (spec §5 mode flag rationale). See `agents/claim_ref_alignment_audit_agent.md` and the orchestrator §3.6 prose.

**v2.0 Core Improvements**:
1. **Mandatory user confirmation checkpoints** — Each stage completion requires user confirmation before proceeding to the next step
2. **Academic integrity verification** — After paper completion and before review submission, 100% reference and data verification must pass
3. **Two-stage review** — First full review + post-revision focused verification review
4. **Final integrity check** — After revision completion, re-verify all citations and data are 100% correct
5. **Reproducible** — Standardized workflow producing consistent quality assurance each time
6. **Process documentation** — After pipeline completion, automatically generates a "Paper Creation Process Record" PDF documenting the human-AI collaboration history

## Quick Start

**Full workflow (from scratch):**
```
I want to write a research paper on the impact of AI on higher education quality assurance
```
--> academic-pipeline launches, starting from Stage 1 (RESEARCH)

**Mid-entry (existing paper):**
```
I already have a paper, help me review it
```
--> academic-pipeline detects mid-entry, starting from Stage 2.5 (INTEGRITY)

**Revision mode (received reviewer feedback):**
```
I received reviewer comments, help me revise
```
--> academic-pipeline detects, starting from Stage 4 (REVISE)

**Resume from passport (cross-session context reset, opt-in):**
```
resume_from_passport=<hash> [stage=<n>] [mode=<m>]
```
--> Loads the Material Passport (Schema 9), locates the `kind: boundary` entry matching `<hash>`, and confirms it has no later `kind: resume` entry consuming it. If `pending_decision` is set, the decision prompt fires first to capture the user's branch choice for the audit ledger; the prompt is never skipped, even when the user supplies `stage=`. After the prompt (or immediately if no `pending_decision`), the next stage is determined by: (a) `stage=<n>` CLI override if provided, else (b) the matched option's `next_stage`, else (c) the `next` field recorded in the boundary entry. CLI `stage=`/`mode=` overrides win over option routing.
- **Gate (emit)**: `ARS_PASSPORT_RESET=1` must be set in the emitting session. Without the flag, no `kind: boundary` entries are written and there is nothing to resume from.
- **Gate (resume)**: No flag required. Any session can invoke `resume_from_passport=<hash>` against a passport that carries a valid boundary entry matching the hash.
- **Intent**: Invoke in a *fresh* Claude Code session. Resuming within the same session that emitted the boundary provides no token savings and may drop still-live in-session context.
- **Stage**: Any. Resumes at whatever stage the routing rules above determine.
- **Reference**: [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md) — see §"`resume_from_passport` mode contract".

**Execution flow:**
1. Detect the user's current stage and available materials
2. Recommend the optimal mode for each stage
3. Dispatch the corresponding skill for each stage
4. **After each stage completion, proactively prompt and wait for user confirmation**
5. Track progress throughout; Pipeline Status Dashboard available at any time

---

## Trigger Conditions

### Trigger Keywords

**English**: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow

### Non-Trigger Scenarios

| Scenario | Skill to Use |
|----------|-------------|
| Only need to search materials or do a literature review | `deep-research` |
| Only need to write a paper (no research phase needed) | `academic-paper` |
| Only need to review a paper | `academic-paper-reviewer` |
| Only need to check citation format | `academic-paper` (citation-check mode) |
| Only need to convert paper format | `academic-paper` (format-convert mode) |

### Trigger Exclusions

- If the user only needs a single function (just search materials, just check citations), no pipeline is needed — directly trigger the corresponding skill
- If the user is already using a specific mode of a skill, respect that entry point; the pipeline is opt-in
- The pipeline is optional, not mandatory

---

## Pipeline Stages (10 Stages)

| Stage | Name | Skill / Agent Called | Available Modes | Deliverables |
|-------|------|---------------------|----------------|-------------|
| 1 | RESEAR