ars-mark-read
The ars-mark-read command records that a user has personally read one or more sources in an academic research project by logging citation keys to a session-scoped YAML file adjacent to the active Material Passport. Use this command after reviewing a source to allow the finalizer to promote low-confidence reference markers to confirmed status, while keeping the literature corpus itself immutable.
mkdir -p ~/.claude/commands && curl -fsSL https://raw.githubusercontent.com/Imbad0202/academic-research-skills/HEAD/commands/ars-mark-read.md -o ~/.claude/commands/ars-mark-read.mdars-mark-read.md
Acknowledge that the user has personally read the source(s) backing the named citation key(s), so the next finalizer pass can promote `<!--ref:slug LOW-WARN-->` to `<!--ref:slug ok-->` for each acknowledged slug. Per v3.6.8 spec §3.6, the signal is stored in a session-scoped peer file `<passport-stem>_human_read_log.yaml` next to the active Material Passport; `literature_corpus[]` is adapter-owned and is NEVER mutated to carry `human_read_source`. The dispatching agent substitutes `<path>` below with the active Material Passport path from session context before executing (the quoting is preserved so paths containing spaces remain a single argument). The CLI handles validation (citation_key must exist in `literature_corpus[]`; on miss emit `[ARS-MARK-READ ERROR: citation_key '<slug>' not in literature_corpus[]]` and refuse to write), 4 fail-fast environment checks (no active passport / passport not found / parent unreadable / read-log unwritable), and append-only write per §3.6 firm rule 3. Implementation: ```bash python3 scripts/ars_mark_read.py $ARGUMENTS --passport-path "<path>" ``` Mode reference: `docs/design/2026-04-30-ars-v3.6.8-trust-provenance-and-drift-transparency-spec.md` §3.6 + Step 7.
12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆.
Multi-perspective academic paper review with dynamic reviewer personas. Simulates 5 independent reviewers (EIC + 3 peer reviewers + Devil's Advocate) with field-specific expertise. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy.
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 integrity verification, two-stage peer review, and reproducible quality gates. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow.
ARS deep-research `three-way-scan` mode — WHY / HOW / WHAT paper comparison
ARS academic-paper `abstract-only` mode — bilingual abstract + keywords
ARS /ars-cache-invalidate — drop cached verification entries for a citation key
ARS academic-paper `citation-check` mode — citation error report
ARS academic-paper `disclosure` mode — venue-specific AI-usage statement