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.
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.
12-agent academic paper writing pipeline. 10 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure). 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, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見.
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 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
ARS academic-paper `format-convert` mode — convert to LaTeX / DOCX / PDF / Markdown