claim-evidence-matrix
Seed `outline/claim_evidence_matrix.md` from outline+notes; claim-matrix-rewriter rewrites it later from evidence packs.
claim-matrix-rewriter
Rewrite `outline/claim_evidence_matrix.md` as a projection/index of evidence packs (NO PROSE), so claims/axes are driven by `outline/evidence_drafts.jsonl` rather than outline placeholders.
claims-extractor
Use when a review workspace has manuscript text and needs a traceable claim ledger.
concept-graph
Use when an approved tutorial spec exists and the run needs a deterministic prerequisite graph before module planning.
dedupe-rank
Use when a broad paper candidate pool needs deterministic deduplication and a stable core set.
deliverable-selfloop
Score an existing reader-facing deliverable and emit a deterministic PASS/FAIL scorecard plus bounded repair plan; use after synthesis, not to rewrite content.
evidence-binder
Bind addressable evidence IDs from `papers/evidence_bank.jsonl` to each subsection (H3), producing `outline/evidence_bindings.jsonl`.
evidence-draft
Create per-subsection evidence packs (NO PROSE): claim candidates, concrete comparisons, evaluation protocol, limitations, plus citation-backed evidence snippets with provenance.
evidence-selfloop
Evidence self-loop for surveys: read evidence bindings + evidence packs, then write an actionable upstream TODO plan (which stage/skill to fix) before writing more prose.
exercise-builder
Use when a tutorial module plan exists but each module still needs a verifiable teaching loop.
extraction-form
Use when `evidence-review` has screened includes and needs a schema-aligned extraction table.
front-matter-writer
Write the survey's front matter files (Abstract, Introduction, Related Work, Discussion, Conclusion) in paper voice, with high citation density and a single evidence-policy paragraph.
global-reviewer
Global consistency review for survey drafts: terminology, cross-section coherence, and scope/citation hygiene.
grad-paragraph
Write one survey-quality paragraph from evidence packs (tension → contrast → evaluation anchor → limitation).
human-checkpoint
Review and record one pending human checkpoint in a research Workspace; use when a HUMAN Unit is blocked on an `Approve C*` decision, and never treat silence or artifact existence as approval.
idea-brief
Lock an ideation run into a single-source-of-truth brainstorm brief (`output/trace/IDEA_BRIEF.md`) and a replayable multi-query plan (`queries.md`).
idea-direction-generator
Generate a compact pool of discussion-worthy research directions from the signal table, writing `output/trace/IDEA_DIRECTION_POOL.md`.
idea-memo-writer
Synthesize the shortlist into a discussion-ready research idea brainstorm memo, writing `output/REPORT.md`, `output/APPENDIX.md`, and `output/REPORT.json`.
idea-screener
Screen the direction pool with a discussion-first scoring pass, writing `output/trace/IDEA_SCREENING_TABLE.md`.
idea-shortlist-curator
Converge the screened direction pool into a small, discussion-ready shortlist, writing `output/trace/IDEA_SHORTLIST.md`.
idea-signal-mapper
Map paper notes + taxonomy into a signal table of tensions, missing pieces, and promising academic axes for brainstorm discussion. Writes `output/trace/IDEA_SIGNAL_TABLE.md`.
keyword-expansion
Expand and refine search keywords (synonyms, acronyms, exclusions) and update `queries.md`.
latex-compile-qa
Compile a LaTeX project and run basic QA (missing refs, bib errors, broken citations), producing `latex/main.pdf` and a build report.
module-source-coverage
Use when a tutorial module plan exists and the run needs an auditable module-to-source grounding file before prose.
source-ingest
Fetch and normalize supported source-tutorial inputs into local, traceable text artifacts.
source-manifest
Build or validate the source manifest for the source-tutorial pipeline from user-provided URLs/files.
source-tutorial-spec
Use when a `source-tutorial` workspace has ingested sources and needs a grounded tutorial contract before structure planning.
source-tutorial-writer
Use when approved tutorial context packs exist and the run needs the final article-first tutorial deliverable.
survey-visuals
Draft non-prose visuals artifacts (timeline, figure specs) for a survey, grounded in evidence and using citation keys from `citations/ref.bib`.
synthesis-writer
Use when `evidence-review` has completed extraction and needs a bounded narrative synthesis.
taxonomy-builder
Build a 2+ level taxonomy (`outline/taxonomy.yml`) from a core paper set and scope constraints, with short descriptions per node.
terminology-normalizer
Normalize terminology across a draft (canonical terms + synonym policy) without changing citations or meaning.
thesis-chapter-reconstructor
围绕毕业论文主线重构章节：把原论文式叙事改成学位论文式叙事，重写章节目标、内容比重、前后承接与论证方式。
thesis-citation-enhance-review
为中文毕业论文补强并核验引用：找出必须有引文支撑的句子，扩展候选文献，检查引用与论断是否匹配，并回写参考文献与正文引用。
thesis-frontmatter-sync
同步中文毕业论文的非正文部分：摘要、附录、封面、成果、致谢、名单等，确保这些部分与正文口径一致，而不是最后临时补写。
thesis-markdown-aligner
在 Markdown 中间层统一毕业论文的主线、术语、符号、指标、图表口径与章节边界，让整篇论文先在中间层收敛成“一篇论文”。
thesis-question-list
维护中文毕业论文的 `codex_md/question_list.md`：把本轮问题、边界、优先级、协作方案和验收口径结构化，作为整条 thesis pipeline 的控制面。
thesis-source-role-mapper
将中文毕业论文已有材料映射到“毕业论文角色”：把论文、模板、Overleaf 源稿、PDF、图表和实验材料按章节角色、研究问题和证据用途重新归位。
thesis-style-polisher
对中文毕业论文做最终润色与去 AI 味：重点处理章首导言、章末小结、贡献描述、总结与展望中的模板腔、宣传腔与 AI 口癖。
thesis-tex-writeback
把已经在 Markdown 中间层收敛的中文毕业论文内容回写到 `chapters/*.tex` 与相关交付层文件，保持结构、图表、公式、交叉引用与章节承接一致。
thesis-visual-layout-planner
规划中文毕业论文的图表、流程图和版面节奏：先决定哪些图表支撑主线，再做草图、拼版预演与图文映射。
thesis-workspace-init
初始化中文毕业论文工作区：检查学校模板与已有材料的放置位置，明确提示当前还缺什么，建立 `codex_md/` / `claude_md/` / `tmp_layout*/` 等中间层目录，并生成材料盘点与初始工作文件。
transition-weaver
Generate lightweight section/subsection transitions (NO NEW FACTS) to prevent “island” subsections; outputs a transition map that merging/writing can weave in.
tutorial-context-pack
Use when module planning and source coverage are done and the run needs writer-ready per-module packs.
tutorial-selfloop
Run a tutorial-specific quality gate and write a PASS/FAIL report for the final tutorial deliverable.
unit-planner
Instantiate or update a workspace `UNITS.csv` from a selected pipeline and units template (deps/checkpoints/acceptance).
unit-executor
Execute exactly one eligible Unit in an existing research Workspace; use for stepwise or manual semantic execution when status, Attempt, Artifact, Manifest, checkpoint, and acceptance evidence must remain synchronized.
workspace-init
Initialize a missing research Workspace from the repository template without overwriting existing Run state; use before Pipeline binding when the target under `workspaces/` has no valid core artifacts.
writer-context-pack
Build per-H3 writer context packs (NO PROSE): merge briefs + evidence packs + anchor facts + allowed citations into a single deterministic JSONL, so drafting is less hollow and less brittle.
writer-selfloop
Writing self-loop for surveys: run the strict section-quality gate, then rewrite only the failing `sections/*.md` files until the report is PASS.
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