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.
_template_reference_first
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agent-survey-corpus
Download a small corpus of open-access arXiv survey/review PDFs about agentic systems and extract text for style learning.
anchor-sheet
Extract per-subsection “anchor facts” (NO PROSE) from evidence packs so the writer is forced to include concrete numbers/benchmarks/limitations instead of generic summaries.
draft-polisher
Audit-style editing pass for `output/DRAFT.md`: remove template boilerplate, improve coherence, and enforce citation anchoring.
evaluation-anchor-checker
Audit and rewrite evaluation/numeric claims to ensure they carry minimal protocol context (task + metric + constraint) and avoid underspecified model naming.
evidence-auditor
Use when `paper-review` needs a claim-by-claim evidence gap report grounded in an extracted claim ledger.
latex-scaffold
Scaffold a LaTeX project (`latex/main.tex`, optional bibliography wiring, structure) from an existing Markdown draft.
limitation-weaver
Rewrite limitation passages so the paper keeps limitations without falling into count-based slot phrases (e.g., \\\"Two limitations…\\\") across many H3s.
literature-engineer
Multi-route literature expansion + metadata normalization for evidence-first surveys.
manuscript-ingest
Use when `paper-review` needs a canonical manuscript text artifact before claim extraction.
module-planner
Use when a tutorial concept DAG exists and the run needs an ordered teaching plan with objectives and outputs.
novelty-matrix
Use when `paper-review` needs overlap/delta positioning against provided related work.
opener-variator
Rewrite subsection openers so they stop reading like a generated table-of-contents: remove \\\"overview/narration\\\" stems and reduce repeated opener cadences across H3s.
outline-budgeter
Merge/simplify an over-fragmented outline to hit a paper-like section budget (NO PROSE): target final ToC ~6–8 H2, fewer thicker H3.
outline-builder
Convert a taxonomy (`outline/taxonomy.yml`) into a bullet-only outline (`outline/outline.yml`) with sections/subsections.
outline-refiner
Planner-pass coverage + redundancy report for an outline+mapping, producing `outline/coverage_report.md` and `outline/outline_state.jsonl`.
paper-notes
Write structured notes for each paper in the core set into `papers/paper_notes.jsonl` (summary/method/results/limitations).
paragraph-curator
Deterministically compact final H3 bodies to the active delivery profile's paragraph budget without deleting prose or changing citation-block order.
pdf-text-extractor
Download PDFs (when available) and extract plain text to support full-text evidence, writing `papers/fulltext_index.jsonl` and `papers/fulltext/*.txt`.
pipeline-auditor
Audit/regression checks for the evidence-first survey pipeline: citation health, per-section coverage, placeholder leakage, and template repetition.
pipeline-router
Route an unbound research Goal to one Workflow or materialize its initial C0 kickoff block; use during initial binding, not for later checkpoint summaries or approval.
post-merge-voice-gate
Post-merge paper-voice gate: inspect the reader-facing draft for planner-talk and axis-label artifacts, then route fixes to the actual source.
prose-writer
Write `output/DRAFT.md` (or `output/SNAPSHOT.md`) from an approved outline and evidence packs, using only verified citation keys from `citations/ref.bib`.
protocol-writer
Use when `evidence-review` needs an operational protocol before screening and extraction.
redundancy-pruner
Remove repeated boilerplate across sections (methodology disclaimers, generic transitions, repeated summaries) while preserving citations and meaning.
research-pipeline-runner
Run a research Workflow end to end when the user requests a survey, brief, review, tutorial, or idea exploration; route an unbound goal, execute one eligible Unit at a time, and stop at checkpoints or diagnosed failures.
rubric-writer
Use when `paper-review` has claims plus evidence gaps and needs the final referee-style report.
schema-normalizer
Normalize cross-skill JSONL interfaces (ids + titles + citation key formats) so downstream skills do not rely on best-effort joins.
screening-manager
Use when an approved `evidence-review` protocol needs to be applied to a candidate pool.
section-bindings
Bind papers to chapter-level sections first, writing `outline/section_bindings.jsonl` and `outline/section_binding_report.md`.
section-briefs
Build chapter-level briefs (`outline/section_briefs.jsonl`) from chapter skeleton plus section bindings before stable H3 decomposition.
section-logic-polisher
Logic coherence pass for per-H3 section files: enforce a clear paragraph-1 thesis and surface paragraph-island risks (connector stats are diagnostic, not a quota) before merging.
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