or<TBD>for cells (DO NOT fabricate numbers). Every non-label data cell MUST be a placeholder; table headers and row labels may be concrete, but metric values, percentages, counts, scores, latency, costs, and confidence intervals must remain---or<TBD> until real experiments are supplied. Use booktabs (\toprule, \midrule, \bottomrule``) for clean spacing.

      Header row comes from TABLE_PLAN columns; row labels come from
      rows_shape (expand the shape into concrete row names like
      "Baseline-A", "Baseline-B", "Ours", "Ours w/o module X", …).
      Caption is caption_hint verbatim. Label MUST be
      ``\label{tab:<id>}``.

      Experiment design:
      {{ outputs.experiment_design | truncate(8000) }}

      Reply with ONLY the concatenated LaTeX table environments,
      one per TABLE_PLAN entry, between sentinel comments:

      % BEGIN_TABLE_PLACEHOLDERS
      \begin{table}[t]
        \centering
        \begin{tabular}{lccc}
          \toprule
          Method & Acc & F1 & Latency \\
          \midrule
          Baseline-A & --- & --- & --- \\
          Baseline-B & --- & --- & --- \\
          Ours       & --- & --- & --- \\
          \bottomrule
        \end{tabular}
        \caption{<caption_hint>}
        \label{tab:tab1}
      \end{table}
      ... (repeat per TABLE_PLAN entry)
      % END_TABLE_PLACEHOLDERS
- id: analysis_outline
  label: "分析大纲"
  label_en: "Analysis outline"
  kind: llm_chat
  depends_on: [experiment_design, figure_placeholders, table_placeholders]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract"
  with:
    system: "You design analysis-chapter outlines that bind every figure/table to a claim and an analysis dimension."
    task: |
      Produce the Analysis chapter outline. Each subsection must
      ``\ref{fig:...}`` or ``\ref{tab:...}`` AT LEAST ONE artefact
      you actually have (do not reference figures/tables that don't
      exist in the placeholders below). Cover every ANALYSIS_DIMENSION
      from experiment_design.

      Experiment design:
      {{ outputs.experiment_design | truncate(8000) }}

      Figure placeholders (label IDs you may \ref):
      {{ outputs.figure_placeholders | truncate(3000) }}

      Table placeholders (label IDs you may \ref):
      {{ outputs.table_placeholders | truncate(3000) }}

      PAPER_MODE depth control:
      - FULL_MANUSCRIPT: 1 subsection per analysis dimension; each
        with potential_findings (3 bullets) + threats_to_validity
        (1–2 bullets).
      - COMPACT_SKELETON: 1 subsection per dimension; potential_findings
        (1 bullet); skip threats_to_validity.

      Reply in this exact shape between sentinels:

      % BEGIN_ANALYSIS_OUTLINE
      \subsection{Performance}
      \label{sec:analysis-performance}
      References: \ref{fig:fig1}, \ref{tab:tab1}.
      Potential findings:
      \begin{itemize}
        \item ...
      \end{itemize}
      Threats to validity:
      \begin{itemize}
        \item ...
      \end{itemize}

      \subsection{Ablation}
      ... (repeat per ANALYSIS_DIMENSION)
      % END_ANALYSIS_OUTLINE
- id: outline
  label: "大纲"
  label_en: "Outline"
  kind: llm_chat
  depends_on: [source_pack, experiment_design]
  when: "'PAPER_MODE: COMPILE_ONLY' not in outputs.paper_contract"
  with:
    system: "You design long-form LaTeX paper outlines with citation plans."
    task: |
      Create a paper outline matching TARGET_PAGES from paper_preferences
      research-paper outline with enough section depth for a substantial
      manuscript. Every section must name planned cite keys from the
      bibliography. Tie the Method section to experiment_design's
      variables/datasets/baselines and the Results section to the
      figure/table plan (by id).

      Paper preferences:
      {{ outputs.paper_preferences | truncate(2000) }}

      Source pack:
      {{ outputs.source_pack | truncate(6000) }}

      Experiment design:
      {{ outputs.experiment_design | truncate(6000) }}

      Cite keys hint:
      {{ outputs.refbib | truncate(8000) }}
- id: citation_plan
  label: "引用计划"
  label_en: "Citation plan"
  kind: llm_chat
  depends_on: [outline, source_pack, refbib]
  when: "'PAPER_MODE: COMPILE_ONLY' not in outputs.paper_contract"
  with:
    system: "You plan citation placement for clean BibTeX/LaTeX manuscripts. You ONLY use cite keys that exist in the provided bibliography — never invent keys."
    task: |
      Build a citation plan that follows CITATION_TARGET and
      CITATION_STRATEGY from paper_preferences. If the user did not give
      an explicit citation count, derive a target from target length,
      source availability, audience, and venue style instead of using a
      fixed number. Use only keys that appear in the BibTeX below (every
      key must be present verbatim — verify by string match before you
      write it). Attach citations to claims, not paragraphs in bulk.

      Topic and mode:
      TOPIC: {{ outputs.paper_contract | truncate(1200) }}, MODE: {{ outputs.paper_contract | truncate(400) }}, PAGES: {{ outputs.paper_contract | truncate(400) }}

      Outline:
      {{ outputs.outline | truncate(6000) }}

      Source pack:
      {{ outputs.source_pack | truncate(8000) }}

      Bibliography (authoritative — cite keys MUST come from here):
      {{ outputs.refbib | truncate(8000) }}

      Paper preferences (authoritative for length/citation targets):
      {{ outputs.paper_preferences | truncate(2000) }}
# ─── Plan→Write→Unify (FULL_MANUSCRIPT mode only) ──────────────────
# The explicit full path writes section-by-section, unifies the manuscript,
# runs quality gates, compiles a PDF, and delivers the artifact.
- id: writing_plan
  label: "写作计划"
  label_en: "Writing plan"
  kind: llm_chat
  depends_on: [paper_preferences, outline, citation_plan, experiment_design, figure_placeholders, table_placeholders, analysis_outline, refbib]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    system: "You build a writing blueprint for a long-form academic manuscript. The blueprint is consumed verbatim by per-section authors; precision matters more than prose."
    task: |
      Synthesize the upstream planning outputs into a single
      authoritative WRITING_PLAN that every section author must
      obey. Lock terminology, notation, claim mapping, and
      per-section length budget BEFORE any prose is written.

      Paper facts:
      TOPIC: {{ outputs.paper_contract | truncate(1200) }}
      MODE: {{ outputs.paper_contract | truncate(400) }}
      LANGUAGE: {{ outputs.paper_contract | truncate(400) }}
      TARGET_PAGES: {{ outputs.paper_contract | truncate(400) }}
      AUDIENCE: {{ outputs.paper_contract | truncate(400) }}

      Preferences:
      {{ outputs.paper_preferences | truncate(2000) }}

      Outline:
      {{ outputs.outline | truncate(6000) }}

      Experiment design:
      {{ outputs.experiment_design | truncate(6000) }}

      Citation plan:
      {{ outputs.citation_plan | truncate(6000) }}

      Bibliography (cite keys MUST come from here):
      {{ outputs.refbib | truncate(4000) }}

      Figure placeholders (IDs only):
      {{ outputs.figure_placeholders | truncate(1500) }}

      Table placeholders (IDs only):
      {{ outputs.table_placeholders | truncate(1500) }}

      Length/citation budget rules:
      - Treat paper_preferences.LENGTH_STRATEGY and TARGET_LENGTH as
        authoritative; do not use a fixed default page or word budget when
        the user requested a different length.
      - This writing plan is the length-control point. Solve length by
        allocating enough section scope, subclaims, evidence, analysis,
        and limitations now; do not assume a downstream checker will fix
        an undersized manuscript later.
      - Convert the requested compiled-page target into an approximate
        total word budget using the paper language, figure/table count,
        and venue style. For normal academic article formatting, set the
        minimum total target_words to at least TARGET_PAGES × 820 English
        words (or the equivalent dense prose units for non-English text).
        Do not reduce below TARGET_PAGES × 760 for figures/tables; instead
        add analysis, limitations, related-work synthesis, and method detail.
      - Allocate words across sections according to the requested paper
        type and contribution shape. A method-heavy paper should give
        more budget to Method; an empirical paper should give more to
        Experiments/Results; a survey should give more to Related Work.
      - The sum of PER_SECTION_BLUEPRINT.*.target_words must meet or
        exceed the minimum total target_words implied by TARGET_PAGES. If
        the target is 12 pages, the blueprint should normally allocate at
        least 9,840 total words across abstract/introduction/related_work/
        method/experiments/discussion/conclusion.
      - In every PER_SECTION_BLUEPRINT entry, target_words is a
        lower-bound writing budget. It is not a ceiling. Give each
        section enough planned subclaims, paragraphs, evidence, analysis,
        and transitions that a section author can satisfy at least 90% of
        target_words without padding.
      - Do not return an undersized section from any non-abstract section author.
      - Treat paper_preferences.CITATION_TARGET and CITATION_STRATEGY as
        authoritative. If they are AUTO, derive a citation budget
        proportional to target length and available verified references;
        never invent citations to hit a count.
      - Return explicit per-section target_words and cite_keys budgets
        that downstream section authors must obey.

      Return EXACTLY this structure (no preamble, no markdown headings):

      TITLE:
      <final paper title, ≤16 words>

      ABSTRACT_DRAFT:
      <120-220 word draft abstract — section authors may polish but
      may not change the thesis, scope, terminology, or
      PLACEHOLDER_RESULT_TOKEN. Do not invent empirical numbers.>

      NARRATIVE_ARC:
      - thesis: <one sentence>
      - story_beats:
          1. <intro beat>
          2. <related-work positioning>
          3. <method core idea>
          4. <experimental verification>
          5. <discussion+conclusion takeaway>

      KEY_CLAIMS:
      - C1: <one sentence, must be defensible by an experiment>
      - C2: ...
      - ...
      - Cn: ... (5-8 total)

      NOTATION_LOCK:
      - symbol: $\theta$  meaning: model parameters
      - symbol: $\mathcal{D}$  meaning: dataset
      - (list every symbol that will appear in math)

      TERMINOLOGY_LOCK:
      - "ours" (proposed method)  forbidden_aliases: ["our method", "the proposed", "本文方法", "the method"]
      - "DPR" (baseline)  forbidden_aliases: ["dpr", "Dpr"]
      - ... (every named entity that appears more than once)

      PER_SECTION_BLUEPRINT:
        abstract:
          target_words: <int>
          key_claims: [C1, C2, ...]
          cite_keys: []           # abstract never cites
          figures: []
          must_mention: [TITLE, PLACEHOLDER_RESULT_TOKEN]
        introduction:
          target_words: <int>
          key_claims: [C1, C2]
          cite_keys: [ref_x, ref_y, ...]   # from citation_plan
          figures: []
          structure: [motivation, problem, contributions]
          contributions_count: <int>
        related_work:
          target_words: <int>
          key_claims: []
          cite_keys: [ref_x, ...]
          figures: []
          structure: [survey by axis]
        method:
          target_words: <int>
          key_claims: [C3, C4]
          cite_keys: [...]
          figures: [fig1, ...]
          tables: []
          structure: [overview → component A → component B → algorithm box]
          notation_introduced: [θ, f_φ, ...]
        experiments:
          target_words: <int>
          key_claims: [C5, C6]
          cite_keys: [...]
          figures: [fig2, ...]
          tables: [tab1, ...]
          structure: [setup → main results → ablations]
          must_include_baselines: [...]
        discussion:
          target_words: <int>
          key_claims: [C7]
          cite_keys: [...]
          figures: []
          structure: [insights → limitations → threats_to_validity]
        conclusion:
          target_words: <int>
          key_claims: [C1-Cn 重申]
          cite_keys: []
          figures: []
          must_call_back_to_abstract: yes

      CROSS_SECTION_DEPENDENCIES:
      - method.NOTATION_LOCK symbols MUST be reused verbatim in experiments + discussion
      - intro.contributions_count MUST equal method.structure step count
      - abstract.PLACEHOLDER_RESULT_TOKEN == experiments.PLACEHOLDER_RESULT_TOKEN
      - experiments, discussion, and conclusion MUST use the same
        qualitative result placeholder until real experiment outputs
        are supplied; do not state exact numeric improvements.

      WRITING_VOICE:
      - tense: <e.g. "we present / we observe", active>
      - perspective: <e.g. third-person except contributions list>
      - formality: academic; no contractions, no marketing language
      - language: {{ outputs.paper_contract | truncate(400) }}

      PLACEHOLDER_RESULT_TOKEN:
      <one stable phrase such as "the planned evaluation will test
      the thesis across performance, robustness, and efficiency axes";
      use this same phrase in abstract, experiments, discussion, and
      conclusion. Do not invent empirical numbers.>
- id: section_abstract
  label: "摘要段"
  label_en: "Abstract section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the ABSTRACT section. Follow the writing plan
      and produce a single dense paragraph 4-6 sentences covering
      problem → approach → key result → significance.

      section: abstract
      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan:
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint:
      {{ outputs.refbib | truncate(2000) }}

      Output rules:
      - Use \begin{abstract} ... \end{abstract}.
      - Do not include \cite{...}.
      - Match TERMINOLOGY_LOCK and NOTATION_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.abstract.target_words
      - For the abstract, follow the 4-6 sentence contract first; do not
        expand it just to satisfy the long-form page target.
      - Only output the LaTeX fragment. No commentary, no fences.
- id: section_introduction
  label: "引言段"
  label_en: "Introduction section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_abstract]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the INTRODUCTION section.

      section: introduction
      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      previous_section_tail (last paragraphs of the abstract):
      {{ outputs.section_abstract | truncate(2000) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan (your assigned cite keys are listed under introduction:):
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint (only these keys exist in the bibliography):
      {{ outputs.refbib | truncate(2000) }}

      Output rules:
      - Start with \section{Introduction}.
      - Structure: motivation → problem → prior-work clusters → gap →
        our contributions (numbered \begin{enumerate}) → paper roadmap.
      - Use only cite keys assigned to introduction in citation_plan,
        and only keys present in cite_keys_hint.
      - Match TERMINOLOGY_LOCK and NOTATION_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.introduction.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned motivation, prior-work contrast,
        contribution detail, and roadmap prose if short. Do not return an
        undersized section.
      - Output ONLY the LaTeX fragment for this section. No fences.
- id: section_related_work
  label: "相关工作"
  label_en: "Related work"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_introduction]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the RELATED WORK section.

      section: related_work

      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      previous_section_tail (last paragraphs of the introduction):
      {{ outputs.section_introduction | truncate(2000) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan (your assigned cite keys are listed under related_work:):
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint (only these keys exist in the bibliography):
      {{ outputs.refbib | truncate(2500) }}

      Output rules:
      - Start with \section{Related Work}.
      - Survey by 2-4 thematic axes (e.g. efficiency / fidelity /
        agentic / dataset construction). Use \subsection for each.
      - Cite from your assigned keys; do not introduce new claims.
      - Do NOT include figures/tables here.
      - Match TERMINOLOGY_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.related_work.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned thematic comparisons, citation synthesis,
        and explicit gap analysis if short. Do not return an undersized
        section.
      - Output ONLY the LaTeX fragment. No fences, no preamble.
- id: section_method
  label: "方法段"
  label_en: "Methods section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_related_work, figure_placeholders]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the METHOD section.

      section: method
      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      previous_section_tail (last paragraphs of related work):
      {{ outputs.section_related_work | truncate(2000) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan:
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint:
      {{ outputs.refbib | truncate(2500) }}

      figure_placeholders (you may reference these via \ref{fig:<id>} when relevant):
      {{ outputs.figure_placeholders | truncate(2000) }}

      Output rules:
      - Start with \section{Method}.
      - Use \subsection{Setup}, \subsection{Algorithm} (or {Approach}),
        \subsection{Instrumentation}, and \subsection{Baselines}.
      - Introduce notation per writing_plan.NOTATION_LOCK
        (every symbol used later in experiments/discussion MUST
        be defined here).
      - You may inline ONE figure environment from figure_placeholders
        that supports method exposition; reference it via \ref{fig:<id>}.
      - Match TERMINOLOGY_LOCK / NOTATION_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.method.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned assumptions, definitions, algorithmic
        detail, instrumentation, and reproducibility notes if short. Do
        not return an undersized section.
      - Output ONLY the LaTeX fragment. No fences.
- id: section_experiments
  label: "实验段"
  label_en: "Experiments section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_method, figure_placeholders, table_placeholders]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the EXPERIMENTS / RESULTS section. Use the
      paper-section-author "results" contract.

      section: results
      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      previous_section_tail (last paragraphs of method):
      {{ outputs.section_method | truncate(2500) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan:
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint:
      {{ outputs.refbib | truncate(2500) }}

      figure_placeholders (inline ALL remaining figures here):
      {{ outputs.figure_placeholders | truncate(4000) }}

      table_placeholders (inline ALL tables here):
      {{ outputs.table_placeholders | truncate(4000) }}

      Output rules:
      - Start with \section{Experiments}.
      - Inline EVERY figure and table from figure_placeholders /
        table_placeholders that has not already been inlined in method.
      - Reference via \ref{fig:<id>} and \ref{tab:<id>}.
      - Structure: \subsection{Setup} → \subsection{Main Results} →
        \subsection{Ablations} → \subsection{Sensitivity}.
      - Use writing_plan.PLACEHOLDER_RESULT_TOKEN for the headline
        evidence claim. Do not state exact numeric improvements,
        percentages, scores, latency reductions, or win rates unless
        they are explicitly present in user-provided experiment data.
      - Use ONLY notation/terminology locked in writing_plan.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.experiments.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned setup, metric rationale, baseline
        comparison, ablation interpretation, sensitivity analysis, and
        failure-case discussion if short. Do not return an undersized
        section.
      - Output ONLY the LaTeX fragment. No fences.
- id: section_discussion
  label: "讨论段"
  label_en: "Discussion section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_experiments, analysis_outline]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the DISCUSSION section.

      section: discussion
      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      previous_section_tail (last paragraphs of experiments):
      {{ outputs.section_experiments | truncate(2500) }}

      outline:
      {{ outputs.outline | truncate(3000) }}

      citation_plan:
      {{ outputs.citation_plan | truncate(3000) }}

      cite_keys_hint:
      {{ outputs.refbib | truncate(2500) }}

      analysis_outline (use this as the structural blueprint):
      {{ outputs.analysis_outline | truncate(4000) }}

      Output rules:
      - Start with \section{Discussion}.
      - Inline the analysis_outline subsections verbatim where they
        fit, but expand each with 1-2 paragraphs of substantive
        commentary referencing concrete experiment results.
      - End the section with explicit \subsection{Limitations} and
        \subsection{Threats to Validity}.
      - Match TERMINOLOGY_LOCK / NOTATION_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.discussion.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned interpretation, boundary conditions,
        limitations, threats to validity, and implications if short. Do
        not return an undersized section.
      - Output ONLY the LaTeX fragment.
- id: section_conclusion
  label: "结论段"
  label_en: "Conclusion section"
  kind: agent
  skill: paper-section-author
  depends_on: [writing_plan, section_discussion, section_abstract]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    task: |
      You are writing the CONCLUSION section. Must close the loop on the abstract.

      section: conclusion

      writing_plan:
      {{ outputs.writing_plan | truncate(8000) }}

      abstract (the conclusion must echo its claims):
      {{ outputs.section_abstract | truncate(1500) }}

      previous_section_tail (discussion ending):
      {{ outputs.section_discussion | truncate(2000) }}

      Output rules:
      - Start with \section{Conclusion}.
      - Cover: 1) restated thesis + headline result, 2) key contributions
        reiterated, 3) scope and limitations, 4) future-work pointer. Use
        as many concise paragraphs as the writing_plan target_words
        requires; do not cap the conclusion at 2-3 paragraphs when the
        requested page target is long.
      - No new claims, no new figures, no \cite{}.
      - Match TERMINOLOGY_LOCK exactly.
      - target_words from writing_plan.PER_SECTION_BLUEPRINT.conclusion.target_words.
      - Length floor: target_words is a lower-bound writing budget. Do
        not return until the section reaches at least 90% of target_words;
        expand with plan-aligned synthesis and implications if short. Do
        not return an undersized section.
      - Output ONLY the LaTeX fragment.
- id: persist_sections
  label: "保存章节"
  label_en: "Save sections"
  kind: tool_call
  tool: exec_command
  tool_allowlist: [exec_command]
  depends_on: [section_abstract, section_introduction, section_related_work, section_method, section_experiments, section_discussion, section_conclusion]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  tool_args:
    # Persist large section bodies to disk and return only a compact
    # manifest. This keeps later LLM steps from repeatedly ingesting the
    # full manuscript and reduces repeated context-compaction pressure.
    command: |
      python3 - <<'PY'
      import os, re
      from pathlib import Path

      def clean(text):
          text = re.sub(r'^```(?:latex|tex)?\s*\n', '', text or '', flags=re.MULTILINE)
          text = re.sub(r'\n```\s*$', '', text)
          return text.strip()

      sections = {
          'abstract':     os.environ.get('SEC_ABSTRACT', ''),
          'introduction': os.environ.get('SEC_INTRO', ''),
          'related_work': os.environ.get('SEC_RELATED', ''),
          'method':       os.environ.get('SEC_METHOD', ''),
          'experiments':  os.environ.get('SEC_EXPERIMENTS', ''),
          'discussion':   os.environ.get('SEC_DISCUSSION', ''),
          'conclusion':   os.environ.get('SEC_CONCLUSION', ''),
      }
      out_dir = Path('paper') / 'sections'
      out_dir.mkdir(parents=True, exist_ok=True)

      print('SECTION_ARTIFACTS:')
      total = 0
      for name, text in sections.items():
          body = clean(text)
          path = out_dir / f'{name}.tex'
          path.write_text(body, encoding='utf-8')
          chars = len(body)
          total += chars
          first_line = next((line.strip() for line in body.splitlines() if line.strip()), '')
          print(f'- {name}: path={path.as_posix()} chars={chars} first_line={first_line[:120]!r}')
      print(f'TOTAL_SECTION_CHARS: {total}')
      print('CONTEXT_POLICY: downstream steps must read section files from disk and pass only paths/summaries to LLM prompts')
      PY
    workdir: "{{ inputs.workspace_dir }}"
    timeout: 30
    env:
      SEC_ABSTRACT:    "{{ outputs.section_abstract }}"
      SEC_INTRO:       "{{ outputs.section_introduction }}"
      SEC_RELATED:     "{{ outputs.section_related_work }}"
      SEC_METHOD:      "{{ outputs.section_method }}"
      SEC_EXPERIMENTS: "{{ outputs.section_experiments }}"
      SEC_DISCUSSION:  "{{ outputs.section_discussion }}"
      SEC_CONCLUSION:  "{{ outputs.section_conclusion }}"
- id: assemble_manuscript_tex
  label: "组装 TEX"
  label_en: "Assemble TEX"
  kind: tool_call
  tool: exec_command
  tool_allowlist: [exec_command]
  depends_on: [writing_plan, persist_sections, refbib]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  tool_args:
    # Concatenate section artifact files into a full LaTeX document and
    # write it to paper/paper.tex. Return a compact manifest instead of
    # echoing the full manuscript back into the meta context.
    command: |
      python3 - <<'PY'
      import os, re, sys
      from pathlib import Path

      section_dir = Path('paper') / 'sections'
      sections = {
          'abstract':     section_dir / 'abstract.tex',
          'introduction': section_dir / 'introduction.tex',
          'related_work': section_dir / 'related_work.tex',
          'method':       section_dir / 'method.tex',
          'experiments':  section_dir / 'experiments.tex',
          'discussion':   section_dir / 'discussion.tex',
          'conclusion':   section_dir / 'conclusion.tex',
      }
      section_text = {
          name: path.read_text(encoding='utf-8') if path.is_file() else ''
          for name, path in sections.items()
      }
      bib = os.environ.get('BIB_TEXT', '').strip()
      # Extract TITLE from the writing_plan envelope. Falls back to the
      # raw topic when the LLM omits a TITLE line so the PDF gets a
      # meaningful title regardless.
      writing_plan = os.environ.get('WRITING_PLAN', '')
      topic_fallback = os.environ.get('TOPIC', 'Untitled Manuscript')
      tm = re.search(r'^\s*TITLE\s*:\s*(.+?)\s*$', writing_plan, re.MULTILINE)
      raw_title = (tm.group(1).strip() if tm else topic_fallback) or topic_fallback
      # LaTeX-escape the title so user-provided text can't break the preamble.
      def latex_escape(s):
          s = s.replace('\\', r'\textbackslash{}')
          for ch in '&%$#_{}':
              s = s.replace(ch, '\\' + ch)
          s = s.replace('~', r'\textasciitilde{}')
          s = s.replace('^', r'\textasciicircum{}')
          return s

      def scrub_placeholder_table_cells(tex):
          """Scrub numeric-looking data cells from placeholder tables."""
          numeric = re.compile(
              r'^\s*(?:\\textbf\{)?[-+]?\d[\d,]*(?:\.\d+)?\s*(?:%|ms|s|x|MB|GB|points?)?(?:\})?\s*$',
              re.I,
          )
          out = []
          in_tabular = False
          after_midrule = False
          for line in tex.splitlines():
              if r'\begin{tabular}' in line:
                  in_tabular = True
                  after_midrule = False
                  out.append(line)
                  continue
              if in_tabular and r'\end{tabular}' in line:
                  in_tabular = False
                  after_midrule = False
                  out.append(line)
                  continue
              if in_tabular and r'\midrule' in line:
                  after_midrule = True
                  out.append(line)
                  continue
              if in_tabular and after_midrule and '&' in line and r'\bottomrule' not in line:
                  suffix = r' \\' if line.rstrip().endswith(r'\\') else ''
                  row = line.rstrip()
                  if suffix:
                      row = row[:-2].rstrip()
                  cells = [cell.strip() for cell in row.split('&')]
                  if len(cells) > 1:
                      cells = [cells[0], *('---' if numeric.match(cell) else cell for cell in cells[1:])]
                      indent = re.match(r'^\s*', line).group(0)
                      line = indent + ' & '.join(cells) + suffix
              out.append(line)
          return '\n'.join(out)
      title_tex = latex_escape(raw_title)
      # Build preamble — load xeCJK if title or any section has CJK
      any_cjk = (re.search(r'[一-鿿]', raw_title) is not None) or any(
          re.search(r'[一-鿿]', v) for v in section_text.values()
      )
      preamble = [
          r"\documentclass{article}",
          r"\usepackage{xeCJK}" if any_cjk else r"% no CJK",
          r"\usepackage{graphicx}",
          r"\usepackage{booktabs}",
          r"\usepackage{amsmath,amssymb}",
          r"\usepackage{hyperref}",
          r"\usepackage{geometry}",
          r"\geometry{margin=2.5cm}",
          r"\title{" + title_tex + r"}",
          r"\author{OpenSquilla meta-paper-write}",
          r"\date{\today}",
          r"\begin{document}",
          r"\maketitle",
      ]
      body_parts = [
          section_text['abstract'],     # \begin{abstract}...\end{abstract}
          section_text['introduction'], # \section{Introduction}...
          section_text['related_work'],
          section_text['method'],
          section_text['experiments'],
          section_text['discussion'],
          section_text['conclusion'],
      ]
      tail = [
          r"\bibliographystyle{plain}",
          r"\bibliography{references}",
          r"\end{document}",
      ]
      tex = '\n'.join(preamble) + '\n\n' + '\n\n'.join(p for p in body_parts if p) + '\n\n' + '\n'.join(tail)
      tex = scrub_placeholder_table_cells(tex)
      paper_dir = Path('paper')
      paper_dir.mkdir(exist_ok=True)
      tex_path = paper_dir / 'paper.tex'
      bib_path = paper_dir / 'references.bib'
      tex_path.write_text(tex, encoding='utf-8')
      bib_path.write_text(bib if bib else '% no verified references', encoding='utf-8')
      print(f'MANUSCRIPT_PATH: {tex_path.resolve()}')
      print(f'REFERENCES_PATH: {bib_path.resolve()}')
      print(f'MANUSCRIPT_CHARS: {len(tex)}')
      print(f'REFERENCES_CHARS: {len(bib)}')
      print('COMPILE_NOTES:')
      print('- assembled section-by-section via paper-section-author')
      print(f'- sections present: {", ".join(k for k, v in section_text.items() if v)}')
      print(f'- total section chars: {sum(len(v) for v in section_text.values())}')
      print('- context policy: full manuscript persisted on disk; downstream prompts should use path/summary only')
      PY
    workdir: "{{ inputs.workspace_dir }}"
    timeout: 30
    env:
      BIB_TEXT:        "{{ outputs.refbib }}"
      WRITING_PLAN:    "{{ outputs.writing_plan }}"
      TOPIC:           "{{ outputs.paper_contract | truncate(400) }}"
- id: consistency_pass
  label: "一致性检查"
  label_en: "Consistency check"
  kind: llm_chat
  depends_on: [writing_plan, assemble_manuscript_tex]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract"
  with:
    system: "You are the consistency auditor for an academic manuscript. You inspect compact manifests and return actionable checks without rewriting the full manuscript."
    task: |
      Review the assembled manuscript manifest against the writing plan.
      Do NOT request or reproduce the full manuscript text in this step.
      The full manuscript is persisted on disk; keep this output compact
      so long paper runs do not trigger repeated context compaction.

      Drift to check:
      1. Terminology: any synonym variant of a TERMINOLOGY_LOCK term
         should be flagged for later repair.
      2. Notation: any math symbol that disagrees with NOTATION_LOCK
         should be flagged.
      3. Numbers: if abstract / experiments / discussion mention the
         same headline metric with different values, flag the drift.
      4. Cite keys: ensure every \cite{...} key exists in the
         REFERENCES_BIB block; citation_map performs the exact parse.
      5. Section ordering: keep abstract → intro → related → method →
         experiments → discussion → conclusion.

      Writing plan (authoritative):
      {{ outputs.writing_plan | truncate(8000) }}

      Assembled manuscript manifest:
      {{ outputs.assemble_manuscript_tex | truncate(2000) }}

      Output EXACTLY:
      MANUSCRIPT_PATH: <copy MANUSCRIPT_PATH from assembled manifest>
      REFERENCES_PATH: <copy REFERENCES_PATH from assembled manifest>
      COMPILE_NOTES:
      - consistency_findings: <one line per possible drift, OR "none">
      CONTEXT_POLICY: artifact-only; full manuscript omitted from prompt/output

- id: final_manuscript_package
  label: "终稿打包"
  label_en: "Final package"
  kind: llm_chat
  depends_on: [paper_contract, outline, citation_plan, refbib, figure_placeholders, table_placeholders, analysis_outline]
  when: "'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  with:
    system: "You write clean LaTeX manuscripts. Output only the requested manuscript package. NEVER invent cite keys — every \\cite{...} you emit MUST exist verbatim in REFERENCES_BIB below."
    task: |
      Draft a full manuscript package. The default output must be clean
      LaTeX-ready paper text, not planning notes. Do not include markdown
      fences, chat commentary, progress notes, or tool logs.

      Paper mode:
      TOPIC: {{ outputs.paper_contract | truncate(1200) }}, MODE: {{ outputs.paper_contract | truncate(400) }}, PAGES: {{ outputs.paper_contract | truncate(400) }}

      Mode behavior:
      - FULL_MANUSCRIPT: produce enough substance for
        TARGET_LENGTH from paper_preferences as compiled pages, using
        the user-requested or derived CITATION_TARGET instead of a fixed
        reference count. Distribute verified citation keys across
        abstract, introduction, related work, method, results, discussion,
        limitations, and conclusion.
      - COMPACT_SKELETON: produce a compact LaTeX-ready manuscript
        skeleton with section goals, planned citations, and expansion
        notes; do not pretend it is a finished paper of the requested
        length. For this
        mode, the final package MUST include an explicit manuscript plan,
        a target-length expansion plan, limitations/threats-to-validity,
        and reference placeholders sized to the requested/derived citation
        strategy when verified BibTeX entries are unavailable. Keep the compact package short enough that all
        required sections are visible before any evaluator truncation:
        put the plan and expansion plan before the LaTeX skeleton, and
        keep MANUSCRIPT_TEX under 2,500 words.
      - REPAIR_EXISTING: return a repaired clean LaTeX package focused on
        citation integrity, structure, and removal of process text.
      - COMPILE_ONLY: return a compile handoff package and blockers only;
        do not invent missing manuscript body.

      CITATION CONTRACT (load-bearing):
      - DO NOT invent cite keys. Use ONLY keys that appear verbatim in
        REFERENCES_BIB below.
      - DO NOT cite a key that REFERENCES_BIB does not contain.
      - Every claim that needs evidence MUST cite at least one key from
        REFERENCES_BIB.
      - Distribute citations according to paper_preferences.CITATION_STRATEGY;
        avoid repeatedly citing one key when enough verified sources exist.
      - If REFERENCES_BIB is empty or lacks enough verified entries, do
        not emit \cite{...}. Use visible placeholders such as
        [REF-01 needed: agent benchmark survey] in the LaTeX text and
        list them under REFERENCE_PLACEHOLDERS instead. Placeholder
        references are safer than fabricated BibTeX.

      FIGURE/TABLE CONTRACT:
      - Inline the figure_placeholders block verbatim into Results.
      - Inline the table_placeholders block verbatim into Method or
        Results (split by purpose).
      - Inline the analysis_outline block verbatim into Discussion.
      - Reference figures/tables via \\ref{fig:<id>} and \\ref{tab:<id>}
        where they appear in the body; never reference an id not present
        in the placeholders.

      Paper preferences:
      {{ outputs.paper_preferences | truncate(2000) }}

      Outline:
      {{ outputs.outline | truncate(8000) }}

      Citation plan:
      {{ outputs.citation_plan | truncate(8000) }}

      Figure placeholders (inline this verbatim somewhere in Results):
      {{ outputs.figure_placeholders | truncate(4000) }}

      Table placeholders (inline this verbatim in Method/Results):
      {{ outputs.table_placeholders | truncate(4000) }}

      Analysis outline (inline this verbatim in Discussion):
      {{ outputs.analysis_outline | truncate(4000) }}

      Bibliography (cite keys MUST come from here):
      {{ outputs.refbib | truncate(8000) }}

      CRITICAL OUTPUT CONTRACT (load-bearing — the downstream
      compile_pdf step parses these markers literally):

      - The MANUSCRIPT_TEX section is MANDATORY and MUST come first.
        It MUST start with the literal token `MANUSCRIPT_TEX:` on its
        own line, immediately followed by `\documentclass{article}`
        and end with `\end{document}`. Do NOT wrap in ```latex
        fences. Do NOT prefix with markdown headings.
      - If you find yourself running out of tokens, shorten section
        bodies — DO NOT omit MANUSCRIPT_TEX. A short complete
        \documentclass…\end{document} block is FAR more useful than
        a long MANUSCRIPT_PLAN with no LaTeX.
      - REFERENCES_BIB is the second mandatory section. Use
        `REFERENCES_BIB:` on its own line followed by BibTeX entries.
        If the bibliography is empty, output `REFERENCES_BIB:`
        followed by a single line `% no verified references` (the
        \cite{} keys in MANUSCRIPT_TEX should then be visible
        placeholders, not BibTeX-keyed cites).

      Return EXACTLY in this order (no preamble, no markdown headings):

      MANUSCRIPT_TEX:
      \documentclass{article}
      \usepackage{xeCJK}
      \usepackage{graphicx}
      \usepackage{booktabs}
      \usepackage{amsmath}
      \usepackage{hyperref}
      \title{...}
      \author{...}
      \date{\today}
      \begin{document}
      \maketitle
      \begin{abstract}...\end{abstract}
      \section{Introduction}...
      \section{Related Work}...
      \section{Method}...
      \section{Experiments}...
      (inline the figure_placeholders, table_placeholders, and
      analysis_outline blocks verbatim where appropriate)
      \section{Discussion}...
      \section{Limitations}...
      \section{Threats to Validity}...
      \section{Conclusion}...
      \bibliographystyle{plain}
      \bibliography{references}
      \end{document}

      REFERENCES_BIB:
      <BibTeX entries copied verbatim from the provided bibliography —
      only the entries actually cited in MANUSCRIPT_TEX. If empty,
      output a single `% no verified references` line.>

      MANUSCRIPT_PLAN:
      - (optional) section-by-section plan with target pages and
        contribution. Skip this section if MANUSCRIPT_TEX is already
        tight on tokens.

      TARGET_LENGTH_EXPANSION_PLAN:
      - For COMPACT_SKELETON, list the concrete section expansions,
        extra experiments, figures, tables, and citation work needed
        to grow this package into the user-requested target length.

      REFERENCE_PLACEHOLDERS:
      - (optional) placeholder reference notes if REFERENCES_BIB is
        empty or sparse.

      COMPILE_NOTES:
      - <short note about figure/reference assumptions>
- id: citation_map
  label: "引用映射"
  label_en: "Citation mapping"
  kind: tool_call
  tool: exec_command
  tool_allowlist: [exec_command]
  depends_on: [final_manuscript_package, consistency_pass, assemble_manuscript_tex, refbib]
  when: "'PAPER_MODE: COMPILE_ONLY' not in outputs.paper_contract"
  tool_args:
    # Deterministically parse citations from artifact files instead of
    # sending the full manuscript back through an LLM.
    command: |
      python3 - <<'PY'
      import os, re
      from pathlib import Path

      pkg = os.environ.get('MANIFEST', '')
      m = re.search(r'MANUSCRIPT_PATH:\s*(.+)', pkg)
      b = re.search(r'REFERENCES_PATH:\s*(.+)', pkg)
      tex_path = Path(m.group(1).strip()) if m else Path('paper/paper.tex')
      bib_path = Path(b.group(1).strip()) if b else Path('paper/references.bib')

      tex = tex_path.read_text(encoding='utf-8', errors='ignore') if tex_path.is_file() else ''
      bib = bib_path.read_text(encoding='utf-8', errors='ignore') if bib_path.is_file() else os.environ.get('REFBIB', '')

      cite_counts = {}
      for group in re.findall(r'\\cite\{([^}]+)\}', tex):
          for key in [k.strip() for k in group.split(',') if k.strip()]:
              cite_counts[key] = cite_counts.get(key, 0) + 1

      entries = {}
      for match in re.finditer(r'@\w+\s*\{\s*([^,\s]+)\s*,(.*?)(?=\n@\w+\s*\{|\Z)', bib, re.DOTALL):
          key = match.group(1).strip()
          body = match.group(2)
          title = re.search(r'title\s*=\s*[\{\"]([^}\"]+)', body, re.I)
          url = re.search(r'(?:url|howpublished)\s*=\s*[\{\"]([^}\"]+)', body, re.I)
          doi = re.search(r'doi\s*=\s*[\{\"]([^}\"]+)', body, re.I)
          eprint = re.search(r'eprint\s*=\s*[\{\"]([^}\"]+)', body, re.I)
          locator = (url.group(1) if url else '') or (f'doi:{doi.group(1)}' if doi else '') or (f'arXiv:{eprint.group(1)}' if eprint else '')
          entries[key] = {
              'title': title.group(1).strip() if title else '',
              'locator': locator,
          }

      strong_domains = ('arxiv.org', 'aclanthology.org', 'dl.acm.org', 'openreview.net', 'ieee.org', 'nature.com', 'science.org', 'biorxiv.org', 'pnas.org')
      weak_markers = ('medium.com', 'wikipedia.org', 'github.com', 'stackoverflow.com', 'twitter.com', 'x.com')
      def quality(locator, invalid=False):
          low = locator.lower()
          if invalid:
              return 'INVALID'
          if any(d in low for d in strong_domains) or 'doi:' in low or 'arxiv:' in low:
              return 'STRONG'
          if any(w in low for w in weak_markers):
              return 'WEAK'
          if locator:
              return 'OK'
          return 'WEAK'

      rows = []
      invalid = weak = strong = ok = unused = 0
      all_keys = sorted(set(cite_counts) | set(entries))
      print('CITATION_MAP:')
      print()
      print('| Cite Key | Cited Times | Title | URL / DOI / arXiv | Source Quality |')
      print('|---|---:|---|---|---|')
      for key in all_keys:
          count = cite_counts.get(key, 0)
          entry = entries.get(key)
          invalid_row = entry is None
          q = quality(entry['locator'] if entry else '', invalid=invalid_row)
          if invalid_row:
              invalid += 1
          elif count == 0:
              unused += 1
              q = 'UNUSED'
          elif q == 'STRONG':
              strong += 1
          elif q == 'OK':
              ok += 1
          elif q == 'WEAK':
              weak += 1
          title = entry['title'] if entry else '(MISSING IN BIB)'
          locator = entry['locator'] if entry else '-'
          print(f'| {key} | {count} | {title} | {locator} | {q} |')
      print()
      print(f'SUMMARY: total_cite_keys={len(cite_counts)}, strong={strong}, ok={ok}, weak={weak}, invalid={invalid}, unused={unused}')
      print(f'ARTIFACTS: manuscript={tex_path} references={bib_path}')
      PY
    workdir: "{{ inputs.workspace_dir }}"
    timeout: 30
    env:
      MANIFEST: "{{ outputs.get('consistency_pass') or outputs.get('assemble_manuscript_tex') or outputs.get('final_manuscript_package', '') }}"
      REFBIB: "{{ outputs.refbib }}"
- id: paper_length_gate
  label: "篇幅门禁"
  label_en: "Length gate"
  kind: llm_chat
  depends_on: [final_manuscript_package, consistency_pass, assemble_manuscript_tex]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  with:
    system: "You verify manuscript length requirements before final packaging."
    task: |
      Check whether the manuscript package satisfies the requested paper
      length, section coverage, and compact/skeleton mode constraints.

      Paper preferences:
      {{ outputs.paper_preferences | truncate(4000) }}

      Manuscript package:
      {{ outputs.get('consistency_pass') or outputs.get('assemble_manuscript_tex') or outputs.get('final_manuscript_package', '') | truncate(8000) }}

      Reply with:
      LENGTH_GATE: <pass|warn|block>
      ESTIMATED_WORDS: <int or unknown>
      BLOCKERS:
        - <blocker or none>
      WARNINGS:
        - <warning or none>
- id: citation_integrity_gate
  label: "引用门禁"
  label_en: "Citation gate"
  kind: llm_chat
  depends_on: [final_manuscript_package, consistency_pass, assemble_manuscript_tex, citation_plan, refbib, citation_map, paper_length_gate]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  with:
    system: "You verify LaTeX/BibTeX citation integrity."
    task: |
      Validate citation integrity before LaTeX compilation.

      Requirements (LOAD-BEARING — block compilation if any fails):
      - REFERENCES_BIB and body citations satisfy the user-requested or
        derived CITATION_TARGET from paper_preferences when sources allow it
      - distinct citation keys used/planned in the body match
        paper_preferences.CITATION_STRATEGY; do not enforce a fixed count
      - NO citation keys absent from references.bib (citation_map column
        "INVALID" must be 0)
      - every cited entry MUST have a verifiable URL or DOI or arXiv
        eprint field in REFERENCES_BIB; entries with only howpublished
        text are degraded but acceptable; entries with no URL/DOI/eprint
        at all are blockers
      - no Source Quality == WEAK in citation_map for primary claims
        (introduction headline / method core / results headline);
        warn but do not block for related-work / motivation context
      - every major claim has nearby citation support or an explicit caveat

      Citation plan:
      {{ outputs.citation_plan | truncate(8000) }}

      Bibliography:
      {{ outputs.refbib | truncate(8000) }}

      Citation audit table (read this — do NOT re-derive):
      {{ outputs.citation_map | truncate(4000) }}

      Reply with:
      INTEGRITY: <pass|warn|block>
      INVALID_COUNT: <int>
      WEAK_PRIMARY_COUNT: <int>
      UNUSED_COUNT: <int>
      BLOCKERS:
        - <blocker or none>
      WARNINGS:
        - <warning or none>
- id: latex_sanitizer
  label: "LaTeX 清理"
  label_en: "LaTeX cleanup"
  kind: llm_chat
  depends_on: [citation_integrity_gate]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract or 'PAPER_MODE: COMPILE_ONLY' in outputs.paper_contract"
  with:
    system: "You sanitize LaTeX deliverables and reject process text."
    task: |
      Sanitize the final LaTeX package contract before compilation. Confirm
      that process commentary, markdown fences, chat preambles, debug logs,
      and non-paper text are absent from MANUSCRIPT_TEX and REFERENCES_BIB.
      Preserve valid LaTeX, CJK text, citations, figure references,
      placeholder figure/table blocks (\fbox + tabular), and section content.
      Reply with a concise readiness note and any blocking issue only.

      Citation gate:
      {{ outputs.citation_integrity_gate | truncate(2000) }}
- id: compile_latex
  label: "编译 LaTeX"
  label_en: "Compile LaTeX"
  kind: llm_chat
  depends_on: [latex_sanitizer]
  when: "'PAPER_MODE: COMPILE_ONLY' in outputs.paper_contract"
  with:
    system: "You prepare compile-only handoff notes without invoking LaTeX in this step."
    task: |
      Produce a concise compile handoff note. COMPILE_ONLY is for
      assessing an existing LaTeX manuscript. The full manuscript and
      compact skeleton paths compile a PDF via compile_pdf after quality
      gates pass.

      Sanitizer result:
      {{ outputs.latex_sanitizer | truncate(2000) }}

      Reply exactly:
      COMPILE_READY: <yes|blocked>
      NEXT_STEP: provide or select an existing manuscript package to compile
      BLOCKERS:
        - <blocker or none>
- id: compile_pdf
  label: "编译 PDF"
  label_en: "Compile PDF"
  kind: tool_call
  tool: exec_command
  tool_allowlist: [exec_command]
  depends_on: [latex_sanitizer, consistency_pass, assemble_manuscript_tex, final_manuscript_package]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  tool_args:
    # Runs the actual xelatex × bibtex × xelatex × 2 cycle so the
    # user gets a real PDF, not just LaTeX source. Extracts
    # MANUSCRIPT_TEX / REFERENCES_BIB from the consistency/assembly/final
    # package contract (passed via env var to dodge shell-escape hell).
    command: |
      python3 - <<'PY'
      import os, re, subprocess, sys
      from pathlib import Path

      pkg = os.environ.get('MANUSCRIPT_PKG', '')

      # 1. Try MANUSCRIPT_TEX: / REFERENCES_BIB: contract markers first.
      m = re.search(r'MANUSCRIPT_TEX:\s*(.+?)(?:REFERENCES_BIB:|COMPILE_NOTES:|\Z)', pkg, re.DOTALL)
      tex_body = m.group(1).strip() if m else ''
      mb = re.search(r'REFERENCES_BIB:\s*(.+?)(?:COMPILE_NOTES:|\Z)', pkg, re.DOTALL)
      bib = mb.group(1).strip() if mb else ''

      # 2. Fallback A: maybe LLM wrapped LaTeX in ```latex fences without the marker.
      if not tex_body:
          fenced = re.search(r'```(?:latex|tex)?\s*(\\documentclass[\s\S]+?\\end\{document\})', pkg)
          if fenced:
              tex_body = fenced.group(1).strip()

      # 3. Fallback B: maybe there's a raw \documentclass…\end{document} block.
      if not tex_body:
          raw = re.search(r'(\\documentclass[\s\S]+?\\end\{document\})', pkg)
          if raw:
              tex_body = raw.group(1).strip()

      # 4. Fallback C: artifact-only FULL_MANUSCRIPT path. Read the
      # persisted manuscript and bibliography from disk instead of
      # requiring the full document to be present in the meta context.
      manifest_tex_path = None
      manifest_bib_path = None
      if not tex_body:
          pm = re.search(r'MANUSCRIPT_PATH:\s*(.+)', pkg)
          bm = re.search(r'REFERENCES_PATH:\s*(.+)', pkg)
          if pm:
              manifest_tex_path = Path(pm.group(1).strip())
              if manifest_tex_path.is_file():
                  tex_body = manifest_tex_path.read_text(encoding='utf-8')
          if bm:
              manifest_bib_path = Path(bm.group(1).strip())
              if manifest_bib_path.is_file():
                  bib = manifest_bib_path.read_text(encoding='utf-8')

      # 5. Strip any leftover markdown fences from extracted bodies.
      tex_body = re.sub(r'^```(?:latex|tex)?\s*\n', '', tex_body)
      tex_body = re.sub(r'\n```\s*$', '', tex_body)

      def scrub_placeholder_table_cells(tex):
          """Scrub numeric-looking data cells from placeholder tables."""
          numeric = re.compile(
              r'^\s*(?:\\textbf\{)?[-+]?\d[\d,]*(?:\.\d+)?\s*(?:%|ms|s|x|MB|GB|points?)?(?:\})?\s*$',
              re.I,
          )
          out = []
          in_tabular = False
          after_midrule = False
          for line in tex.splitlines():
              if r'\begin{tabular}' in line:
                  in_tabular = True
                  after_midrule = False
                  out.append(line)
                  continue
              if in_tabular and r'\end{tabular}' in line:
                  in_tabular = False
                  after_midrule = False
                  out.append(line)
                  continue
              if in_tabular and r'\midrule' in line:
                  after_midrule = True
                  out.append(line)
                  continue
              if in_tabular and after_midrule and '&' in line and r'\bottomrule' not in line:
                  suffix = r' \\' if line.rstrip().endswith(r'\\') else ''
                  row = line.rstrip()
                  if suffix:
                      row = row[:-2].rstrip()
                  cells = [cell.strip() for cell in row.split('&')]
                  if len(cells) > 1:
                      cells = [cells[0], *('---' if numeric.match(cell) else cell for cell in cells[1:])]
                      indent = re.match(r'^\s*', line).group(0)
                      line = indent + ' & '.join(cells) + suffix
              out.append(line)
          return '\n'.join(out)

      # 6. If still empty, fail loudly. Quality-first paper generation
      # must not disguise a missing manuscript as a degraded PDF.
      if not tex_body:
          print('COMPILE_FAILED: MANUSCRIPT_TEX block missing; refusing to create degraded PDF')
          print('PACKAGE_PREVIEW:')
          print(pkg[:2000])
          sys.exit(1)

      # 7. Auto-wrap if the LLM gave a body fragment but no \documentclass.
      if '\\documentclass' not in tex_body:
          tex_body = (
              r"\documentclass{article}" "\n"
              r"\usepackage{xeCJK}" "\n"
              r"\usepackage{graphicx}\usepackage{booktabs}\usepackage{amsmath}\usepackage{hyperref}" "\n"
              r"\begin{document}" "\n"
              + tex_body + "\n"
              r"\bibliographystyle{plain}" "\n"
              r"\bibliography{references}" "\n"
              r"\end{document}" "\n"
          )

      # 8. Auto-add xeCJK if the body contains CJK chars but doesn't load it.
      if re.search(r'[一-鿿]', tex_body) and 'xeCJK' not in tex_body:
          tex_body = tex_body.replace(
              r'\documentclass{article}',
              r'\documentclass{article}' + '\n' + r'\usepackage{xeCJK}',
              1,
          )

      tex_body = scrub_placeholder_table_cells(tex_body)

      paper = Path('paper'); paper.mkdir(exist_ok=True)
      (paper / 'paper.tex').write_text(tex_body, encoding='utf-8')
      (paper / 'references.bib').write_text(bib, encoding='utf-8')

      logs = []
      for cmd in (
          ['xelatex','-interaction=nonstopmode','paper.tex'],
          ['bibtex','paper'],
          ['xelatex','-interaction=nonstopmode','paper.tex'],
          ['xelatex','-interaction=nonstopmode','paper.tex'],
      ):
          r = subprocess.run(cmd, cwd='paper', capture_output=True, text=True)
          logs.append(f"--- {' '.join(cmd)} (rc={r.returncode}) ---")

      pdf = (paper / 'paper.pdf').resolve()
      if pdf.is_file():
          log_text = (paper / 'paper.log').read_text(encoding='utf-8', errors='ignore') if (paper / 'paper.log').is_file() else ''
          pm = re.search(r'Output written on .+?\((\d+) pages?', log_text)
          pages = pm.group(1) if pm else '?'
          print(f'PDF_PATH: {pdf}')
          print(f'PDF_PAGES: {pages}')
          print(f'PDF_BYTES: {pdf.stat().st_size}')
          print(f'TEX_BYTES: {(paper / "paper.tex").stat().st_size}')
          print(f'BIB_BYTES: {(paper / "references.bib").stat().st_size}')
      else:
          tail = '\n'.join(logs[-3:])
          # Dump the last 80 lines of paper.log so the failure mode is visible.
          log_text = (paper / 'paper.log').read_text(encoding='utf-8', errors='ignore') if (paper / 'paper.log').is_file() else ''
          log_tail = '\n'.join(log_text.splitlines()[-80:])
          print(f'COMPILE_FAILED:\n{tail}\n\n=== paper.log tail ===\n{log_tail}')
          sys.exit(1)
      PY
    workdir: "{{ inputs.workspace_dir }}"
    timeout: 120
    env:
      MANUSCRIPT_PKG: "{{ outputs.get('consistency_pass') or outputs.get('assemble_manuscript_tex') or outputs.get('final_manuscript_package', '') }}"
- id: publish_pdf
  label: "发布 PDF"
  label_en: "Publish PDF"
  kind: tool_call
  tool: publish_artifact
  tool_allowlist: [publish_artifact]
  depends_on: [compile_pdf]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  tool_args:
    path: "paper/paper.pdf"
    name: "paper.pdf"
    mime: "application/pdf"
- id: deliver_paper
  label: "论文交付"
  label_en: "Paper delivery"
  kind: llm_chat
  depends_on: [final_manuscript_package, compile_pdf, publish_pdf, citation_map]
  when: "'PAPER_MODE: FULL_MANUSCRIPT' in outputs.paper_contract or 'PAPER_MODE: COMPACT_SKELETON' in outputs.paper_contract or 'PAPER_MODE: REPAIR_EXISTING' in outputs.paper_contract"
  with:
    system: "You write a one-paragraph delivery note for a compiled academic paper. Output is concise — no LaTeX source, no markdown fences. Obey USER_LANGUAGE strictly: en means English only; zh means Chinese only."
    task: |
      Produce the user-facing delivery message. Confirm the PDF
      is ready, name its location, page count, citation summary,
      and list any open warnings from the citation audit. Keep
      the message under 200 words.

      USER_LANGUAGE: {{ inputs.get('user_language', 'zh' if (inputs.user_message | contains_cjk) else 'en') }}

      Language rules:
      - If USER_LANGUAGE is en, write English only. Do not include Chinese
        headings, labels, warnings, or bilingual labels.
      - If USER_LANGUAGE is zh, write Chinese only. Do not include English
        headings except literal file paths, artifact IDs, and citation keys.
      - Do not copy warning prose from intermediate audit text; translate
        any warning into the selected USER_LANGUAGE.

      Original request:
      {{ inputs.user_message | xml_escape | truncate(400) }}

      PDF compile result (paths are absolute):
      {{ outputs.compile_pdf | truncate(800) }}

      Artifact publication result:
      {{ outputs.publish_pdf | truncate(800) }}

      Citation audit summary tail:
      {{ outputs.citation_map | truncate(2000) }}

      {% if inputs.get('user_language') == 'zh' or (inputs.user_message | contains_cjk) %}
      Format:
      📄 论文已生成

      - PDF: <absolute path or artifact id>
      - 页数: <N>
      - 引用: <total / strong / weak / invalid / unused>
      - 备注: <one line about figures, tables, analysis dimensions>

      If the audit shows INVALID > 0, prefix the message with
      "⚠️ 注意: <N> 处引用未在 bib 中，建议重新生成" and list the offending
      cite keys.
      {% else %}
      Format:
      📄 Paper compiled

      - PDF: <absolute path or artifact id>
      - Pages: <N>
      - Citations: <total / strong / weak / invalid / unused>
      - Notes: <one line about figures, tables, analysis dimensions>

      If the audit shows INVALID > 0, prefix the message with
      "⚠️ Warning: <N> citation keys are missing from references.bib; regenerate
      or repair the bibliography" and list the offending cite keys.
      {% endif %}

meta-paper-write (Meta-Skill)

Draft a long LaTeX manuscript by orchestrating paper-specific skills and bounded LLM synthesis. The pipeline now leads with explicit experiment design + placeholder figures/tables + citation provenance audit so the deliverable can be reviewed for academic rigor, not just length.

DAG (in order):

1. paper_collect — extracts topic, mode, language, target length, audience, and reference count from the same turn without pausing for a form. Missing facts are marked as assumptions so first-pass paper requests complete inline.
2. paper_preferences — expand the collected facts into a planning contract.
3. search_papers — multi-search-engine query biased toward arXiv / ACL Anthology / ACM DL / OpenReview / IEEE / Nature / Science so the returned URLs translate into real bibliographic identifiers.
4. refbib — paper-refbib-stub now extracts eprint/doi from arXiv/DOI URLs and tags each entry with note = {source: <domain>} so downstream gates can classify provenance without re-fetching.
5. source_pack — curate references and enforce ≥20-source coverage.
6. experiment_design — decides how many figures and tables the paper needs based on RQs, hypotheses, analysis dimensions, and the target page budget. Every figure/table is tied to an RQ or analysis dimension; no decorative artefacts.
7. figure_placeholders — render LaTeX \fbox{\parbox{...}} placeholder figure environments for each entry in FIGURE_PLAN. Zero matplotlib dependency.
8. table_placeholders — render LaTeX \begin{tabular} placeholder tables for each entry in TABLE_PLAN. Cells contain ---/<TBD>; no fabricated numbers.
9. analysis_outline — bind every figure/table id to a Discussion subsection that names potential findings + threats to validity, and covers every ANALYSIS_DIMENSION.
10. outline — paper outline that ties Method to experiment design and Results to the figure/table plan.
11. citation_plan — assigns concrete cite keys from refbib to claims; cannot invent keys.
12. writing_plan + section authors — the explicit FULL_MANUSCRIPT path converts the user's page target into section-level target_words and citation budgets before prose is written; section authors obey that plan.
13. final_manuscript_package — compact / repair modes produce MANUSCRIPT_TEX with the figure/table/analysis blocks inlined verbatim, plus REFERENCES_BIB containing only the entries actually cited.
14. citation_map — strict markdown audit table: Cite Key | Cited Times | Title | URL/DOI/arXiv | Source Quality with INVALID / UNUSED / WEAK detection. Inlined into the final deliverable AND queryable per-run via opensquilla skills meta runs show.
15. citation_integrity_gate — reads citation_map directly; blocks when INVALID > 0 or any primary claim cites a WEAK source.
16. latex_sanitizer — strips process text without rewriting the paper.
17. compile_pdf / publish_pdf / deliver_paper — compile and publish the final PDF for FULL_MANUSCRIPT, COMPACT_SKELETON, and REPAIR_EXISTING. The compiler refuses to create degraded PDFs when MANUSCRIPT_TEX is missing.
18. compile_latex — handoff note (COMPILE_ONLY mode).

Removed from the previous version:

• paper_mode (llm_classify) — superseded by paper_collect
• experiment (skill_exec → paper-experiment-stub, fake CSV) — superseded by experiment_design (real plan, not data). The bundled paper-experiment-stub skill was deleted with this rewrite.
• plot (skill_exec → paper-plot-stub, matplotlib line chart) — superseded by figure_placeholders (zero-dependency LaTeX). The bundled paper-plot-stub skill was deleted with this rewrite.

The default path is COMPACT_SKELETON and ends with a compiled PDF without section-by-section drafting. Explicit full/PDF/long-form requests use FULL_MANUSCRIPT. If the topic is missing, paper_clarify pauses and asks the user before generation continues. The compiler refuses to synthesize a degraded PDF when the manuscript contract is missing.