# Target-venue manuscript assembly Read this before choosing the document template, converting a manuscript, or reviewing a format revision. Apply it to the same task and its saved article type, language and formats. A successful export is only the start of the format check. ## Establish the intended format Use the current official instructions and the local learning PDFs from [journal learning](journal-learning.md). First verify that the venue is the saved target or was selected under explicit delegated authority. If it is only a provisional comparator, keep the output venue-neutral and do not label it target-compliant. In the existing working notes, retain the official source/date and the exemplar pages used for decisions. Resolve: - Article type, title page and author information; abstract structure and limit, keywords, section hierarchy, declarations and supplementary files. - Page geometry, columns, fonts, leading and paragraph/heading spacing. - Citation system, marker position relative to punctuation, spacing, consecutive ranges and mixed groups; reference ordering, author initials/truncation, title case, journal abbreviation, volume/pages or article number and DOI display. - Figure/table numbering, captions, panel labels, units and footnotes, editable table requirements, placement, graphical abstract and separate upload files. Do not infer these details from the word "Vancouver" or apply a universal numeric style to every journal. Use an official template/CSL when available and inspect what it actually renders. An old publisher PDF may show a former design; current explicit requirements govern submission. If a requirement remains unavailable, state the specific uncertainty and use a justified observed convention for the draft. Do not claim verified official compliance for that detail. The user's reading PDF should visibly apply the learned page design. If current submission instructions require different column or float placement, produce the appropriate submission files from the same semantic manuscript and identify their purposes clearly. A different reading layout must not silently change the text, references, numbers, selected figures or scientific captions. Keep the scientific caption and accessibility description as separate semantic fields. Some venues require labelled alternative text below legends in the submission manuscript while excluding it from the visible typeset article. Apply that verified rule per output purpose; preserve the description in the required submission files and use supported accessibility metadata in the reading output. Do not remove it indiscriminately from every format, duplicate it in reading captions, or claim a tagged accessible PDF without verifying the emitted file. Do not invent author, affiliation, ethics, funding, journal branding or publication metadata to fill the template. Keep missing submission facts explicit without filling the body with engineering review notes. Before placing manuscript content in a template, apply [publication-surface.md](publication-surface.md). A title-page author note, draft-status field, footer or supplementary page is still reader-facing text. Transfer the scientific manuscript and required declarations; keep task choices, reviewer progress and delivery notes in the local work package. Do not preserve an earlier production-status paragraph as if it were immutable scientific text. ## Verify and actually use official templates Inspect the current venue's author instructions, conference-year paper kit when applicable, and the publisher's author/LaTeX resources. Follow their official template links; if a link is absent or broken, make a focused search of the official venue/publisher resources. Check the requested year, article type, current publisher and review/submission/camera-ready purpose. An older year's class or a generic publisher class is applicable only when the current guidance supports it. Do not infer this from a familiar filename or third-party listing. Download the applicable package locally and actually read its README/instructions, sample source, class options and relevant style settings. Identify its engine, fonts, geometry, title/author macros, anonymity options, bibliography workflow and required assets. Classify what was obtained before selecting a tool: | Asset | Correct use | What it does not establish | |---|---|---| | Raw official LaTeX sample plus `.cls`/`.sty`/bibliography assets | Compile an untouched local copy with its documented build, then fill a working copy through native TeX or a thin adapter. | A complete sample document is **not** a Pandoc template; never pass it directly to `--template`. | | Pandoc LaTeX template | Use `--template` only for Pandoc template syntax that consumes the body (directly or through partials/conditionals) and supplies the metadata/support constructs needed by the emitted TeX. Test with the manuscript's actual metadata and content. | A `.tex` suffix or adding `$body$` alone does not make a raw sample compatible. | | Word template/reference document | Read the official instructions and styles. For Pandoc, prepare a compatible reference DOCX and pass `--reference-doc`; copy styles/section properties from an official Word sample as needed. | A reference DOCX supplies styles/properties, not its sample body, title page, boilerplate or a TeX layout; `.dotx` is not directly a reference DOCX. | When an applicable official template is available, use it. Compile/render its demo first, then a representative manuscript page through the chosen integration. For a thin Pandoc adapter, preserve the official class, options, fonts, geometry and title/abstract structure; translate content insertion and metadata, and add only the support macros/packages actually needed by the writer. Keep the original package beside the adapter and note the small changes. Do not silently replace the class with `article`, overwrite its margins/fonts or discard it because the exporter's stock command is easier. If adaptation conflicts with the class or bibliography system, use its native build and produce the requested Word from the same semantic content. Validate citation/object links in both outputs. Compare the rendered manuscript with the official demo for the applicable mode: title block, fonts, text area/columns, headings, captions and references. Check that our actual text/figures replaced all sample content. Keep source URL/date, package version/year, local assets, applicability decision, actual build command and demo/current page locators in existing layout notes. Downloaded, read, compiled-demo and applied-to-manuscript are distinct observations; only the last with the rendered comparison supports a claim of actual template use. Demo authors, affiliations, ethics and publication identifiers are never our facts. If these sources yield no applicable package, record the actual URLs searched, outcome (not found, inapplicable or inaccessible), remaining uncertainty and the chosen fallback. Stop repeating the same failed lookup; continue with a standard renderer adapted to verified current instructions and the local target PDFs. A build failure with an available template calls for dependency diagnosis or a native build, not a claim that the template does not exist. Report any remaining build limitation and provisional fallback honestly. Normal retrieval, adaptation and repair within the task need no new user approval or template/profile gate. ## Turn the learned format into reusable document assets The host creates or adapts the layout as ordinary document work using the actual target requirements. Do not wait for a developer to supply case-specific commands. Before full assembly, compile a representative working sample containing the real title/abstract structure, one body section, one figure/table caption and references; compare its rendered pages with the learned exemplar pages and correct the source. This sample is part of normal manuscript construction, not a new approval artifact. Reuse a suitable official template first. Otherwise adapt the selected renderer's standard template and reference DOCX using the observations above; do not infer that a stock template already implements the target venue. Use the installed shared manuscript exporter for supported source formats. Inspect its help and existing template/filter arguments before writing a new conversion program. If it has a repeated defect, fix that reusable capability; if a native official TeX workflow is necessary, use its real build system and document that reason. A journal layout is an asset, not a second manuscript compiler or a hardcoded medical-paper generator. Keep the venue layout separate from scientific content: page/section settings, Word styles, TeX template, CSL and only necessary layout filters. Read the actual template's styles and variables before editing. Store these assets and their build invocation with the manuscript so another host can regenerate it. A venue layout may be reused after checking article type and current requirements; never embed a case's title, authors, numbers, conclusions or required figure count in the shared exporter or promote its design into a rule for every field. Apply the observed format in this order: 1. Establish page geometry, body fonts, leading and section/column structure. Handle title/abstract and full-width content as actual sections or layout constructs, keeping the underlying text and object IDs intact. A format-specific filter should handle absent optional metadata instead of assuming every paper supplies the same fields. Prefer the chosen engine/template's native column and float flow. Repeatedly balancing/restarting columns around forced in-place full-width objects can trade a reading-order defect for half-empty pages; changing every float to a fixed position is not a general repair. Check both flow and page occupancy after changing placement, including the title page. 2. Define title, headings, normal prose, captions, bibliography and table text styles. Inspect inherited borders, shading, paragraph spacing and pagination rules; changing the font alone may leave a stock template's decorations or body double-spacing inside tables. Retain editable tables. When applying a Word table style, check its actual `w:styleId` as well as the display name in `word/styles.xml`; the requested style must resolve in the emitted document. For a numbered bibliography, align the hanging indent and any tab stop with the emitted number/separator and the widest labels used. A hanging-indent value alone does not ensure that author text and continuation lines align. Narrow-column headings need appropriate alignment rather than stretched word spacing. Scope keep-with-next/keep-together rules to the smallest meaningful unit; avoid binding long sections or chains of paragraphs into large blocks. 3. Implement article-specific placement: figures inline or at the end, separate figure legends if required, table notes, supplementary material and graphical abstract convention. Derive an end-of-manuscript legend list from the same captions; do not maintain two independently typed caption sets. Verify both figure and legend navigation after a layout transformation. Keep a short table with its caption and notes; for a multipage table, keep its final rows with the notes and apply the venue's continuation convention. Moving all tables to dedicated pages is appropriate only for the intended output's requirements, not a universal cure for pagination failures. 4. Check fonts in the actual PDF and Word render. A requested font family in metadata is not proof that either engine used it; inspect substitutions and glyph coverage and retain the real fonts/dependency notes. Use an available, appropriate font when needed and disclose a material format difference. 5. In a real Word instance or an equivalent faithful editor, update caption and reference fields, repaginate, save the resulting DOCX and export its PDF proof. Use an owned document/application session and close only those resources. Do not pass the separately generated TeX PDF off as a Word rendering. If the venue requests a word count, establish exactly which parts it includes before counting. Calculate from the current complete manuscript, including the specified abstract, captions, tables, references or notes. Exclude running headers, line/page numbers and duplicated layout-only legend copies as the rule requires. Do not treat Markdown tokens or an unexamined Word total as the official count. After substantive edits, refresh the displayed count and inspect the final title page. When the official counting scope is unavailable, label the actual scope used. ### Apply the local published-PDF learning to pages Use the saved target-venue set (three original local PDFs by default, or the user's chosen count), following journal-learning.md's access and version rules. Open each PDF; an author manuscript or HTML printout cannot stand in for the publisher's typography. Identify the relevant publication year/design and article type. For each exemplar, retain concrete page observations and their effect on the current reading layout in the existing notes, for example: | Exemplar file/version and page | Observed design | Adopt/adapt and producing asset, or reason to differ | Current rendered page | |---|---|---|---| | Actual local PDF and page locator | Measured/visually checked font, text width, caption or spacing choice | Template/style/section changed; current official rule if it takes precedence | Page where the change is visible | Across the set, cover title/abstract, normal prose, a dense table when present, main figure/caption, citations/bibliography and final-page rhythm. Record actual font sizes and text/column widths where measurable. Build a small representative page set early and place current and reference page views side by side at the same physical scale; different fit-to-window zooms can conceal tiny text. Every selected PDF must inform a concrete retained or revised layout decision, with any inapplicable observation explained. A list of three papers or screenshots without an applied design decision is not completed learning. Use this comparison to refine the reading PDF's typography, column widths, heading/caption hierarchy, float flow and page density. Use the official demo to check template integration; published pages teach reading design and do not override current submission rules. Keep necessary reading/submission differences explicit. Never copy publisher logos, DOI, volume/issue, page ranges, acceptance dates or other publication identity into an unpublished manuscript. Inspect all finished pages. Fix stranded references, avoidable gaps, crowded table/figure pages and uneven abstract hierarchy in the producing assets. Balance columns/floats where permitted; do not delete references or shrink text to impose an arbitrary page count. A repeated conversion defect belongs in the shared tool; a typography or placement choice belongs in the reusable venue layout. ### Keep figures readable at their final placed size Keeping a figure and its caption on one page is not sufficient acceptance. Check each figure in the actual PDF and faithful Word render independently, including the densest panel, smallest axis/legend label and symbols. Record the final placed width/height and smallest effective label size in the layout notes. For uniform scaling, `effective label pt = source label pt × placed width / source width`, using the same width units; check the real output for cropping or further scaling. For example, an 8 pt label in a 180 mm figure becomes 4.4 pt at 100 mm. Higher image DPI cannot repair that physical text size. For raster-only artwork with unknown source type size, measure the placed lettering and inspect it at physical page scale; do not invent a precise source-font value or approve only a zoomed view. Use the venue's final-size figure lettering rules and the learned page design to set a readable working minimum before placement; if unspecified, choose and record a practical target (often 8–10 pt for ordinary labels), then inspect readability. This is a design target, not an invented journal rule or a fixed score gate. Captions, lines and meaningful internal detail must remain readable too. When figure plus caption does not fit, use an allowed full-width placement or dedicated page, rearrange panels/remove wasted artwork margins, or redraw at the intended size with larger labels. Shorten only redundant caption wording while preserving definitions, units, evidence boundaries and necessary explanations. If still necessary, split at meaningful panel boundaries with consistent IDs and captions, or use an explicitly labelled continued caption where permitted. Keep required separate submission legends derived from the same caption source. Do not keep shrinking the whole figure, remove scientific structure or compress caption text below readability just to satisfy keep-with-next. Rerender affected PDF/Word pages, remeasure the placed figure, and recheck all pages that reflowed. ## Keep one semantic manuscript ### Apply the requested output language Read the same task's `configuration.output_language` and the user's language instructions. For `multilingual` or `other`, use the languages actually specified in the conversation, materials or saved comments. If they remain unspecified, ask only for the missing language choice while continuing language-independent work; do not silently assume a language pair or claim multilingual completion. Produce the complete manuscript in each requested language and requested format, including title, abstract, body, captions, tables, notes and relevant supplements. Use one scientific source with corresponding language versions and stable citation keys/object IDs. Keep numbers, units, equations, evidence boundaries and references equivalent; translations may differ in wording and layout, not findings. Keep a small shared terminology list where ambiguity matters. Preserve bibliographic identity and apply the venue's rules for translated titles instead of inventing new references. Use fonts that cover the actual script. Render and inspect each language's actual PDF/DOCX, checking for missing glyphs, truncation, inconsistent caption labels and omitted passages. The translated manuscript is a user-facing document, not a summary or a translation of internal audit notes. Do not require the historical fixed Chinese audit-file inventory. ### Preserve citations and object references Keep citations as stable bibliography keys and figures/tables/equations as stable IDs. Generate visible numbers in their order of use. Use semantic citation and cross-reference support in the chosen authoring system, such as Pandoc citeproc and cross-reference handling, or native LaTeX citation/label commands. A valid Pandoc citation is not defective merely because its emitted TeX uses `\citeproc` instead of `\cite`. Choose and apply the venue citation style before rendering PDF, DOCX and TeX. Do not fix only one exported file by replacing bracketed text with superscripts, typing reference numbers, or moving citation punctuation with a regex over the whole TeX document. A deliberate citation-style transformation must operate on the citation structure and preserve targets and the surrounding sentence. Each figure and table needs a real caption and ID, plus a body cross-reference to that ID. Preserve LaTeX caption/label/reference semantics. In DOCX, retain editable captions and bookmark/field-based references so the target survives normal editing; when using numbered caption fields, update those fields before the final Word export. Typing "Figure 1" in both places does not create a link or maintain the number when a figure is inserted. Preserve editable tables as tables, not screenshots. Graphical abstracts follow the venue's own convention and need not be forced into the main figure numbering. Apply layout through the venue template and Word styles. Reuse the same source content and bibliography across outputs. Keep the actual build command and the template, CSL, filters, fonts/dependency notes and editable figure assets needed to rebuild. A manuscript-specific layout adjustment may be appropriate; repeated conversion or linking logic belongs in the installed reusable tools. ### Shared Markdown exporter For a Pandoc Markdown source, use the installed `scripts/manuscript_export.py` with its adjacent `scripts/manuscript_refs.lua`. It processes citations once with the selected CSL, then exports the same semantic content to DOCX and TeX and compiles that TeX to PDF. It requires Pandoc 3 or newer and the selected TeX engine. Check these actual executables once; use an available equivalent authoring system when the host has a different toolchain while preserving the semantics. ```text python scripts/manuscript_export.py manuscript.md --bibliography references.bib --csl venue.csl --output-dir export --reference-doc venue-reference.docx --metadata-file venue.yaml --template venue-pandoc.tex --pdf-engine xelatex ``` Here `venue-pandoc.tex` is a compatible Pandoc template, not a raw official sample; `venue-reference.docx` is the prepared style reference. Select the engine actually supported by the template; the example's XeLaTeX is not a venue requirement. The reference DOCX, metadata file and Pandoc template are optional tool arguments; for a venue-specific delivery, supply the appropriate learned layout instead of claiming the default template matches that venue. Run from the working source directory or use full paths. Keep the source, BibTeX, CSL and templates in the editable package along with the resulting files and copied local image assets. For custom `--template` in a TeX/PDF export, the exporter probes Pandoc with the current AST metadata and a unique body marker before writing replacement outputs. This uses Pandoc's native template processing, including partials and conditionals; it does not merely search for a literal `$body$` in the top-level file. A template that drops the body produces a located error and leaves existing manuscript outputs intact. Repair the adapter's body insertion or use the official native TeX build in the same task. Probe success proves body consumption only, not full content integrity or correct layout; compare the real generated manuscript too. The result's `format_inputs` records supplied `template`, `reference_doc`, `metadata_file` and `csl` paths and SHA-256 values, with `applied` indicating use for the requested formats. A TeX template is not applied to DOCX-only export; a reference DOCX is not applied to TeX/PDF-only export. Use these details to check which assets the build actually received. They do not prove official provenance, article/year suitability, visible style fidelity or successful page review, and do not require a new configuration field, user confirmation or JSON dossier. Use `![Caption](figures/overview.png){#fig:overview}` for a numbered figure and `: Caption {#tbl:summary}` for a table caption. Cite these objects in the body as `@fig:overview` and `@tbl:summary`; keep bibliography citations as `[@key]`. For an unnumbered graphical abstract, use a figure ID with `.unnumbered` and `ref-label="Graphical abstract"`. Do not manually repeat "Figure 1" inside a numbered caption. Keep bibliography citations and figure/table references in separate groups. The exporter rejects missing/duplicate/wrong-kind destinations so they can be corrected in the source. Use its repeatable `--lua-filter` option for an article's layout transformations when needed, preserving the shared citation keys, object IDs and source content. Ship any such filter with the editable package. A layout filter must not replace semantic captions or citations with manually numbered prose. The exporter checks both the source and generated manuscript text for production notes. Its result separates `conversion_succeeded`, `publication_surface` and `render_diagnostics`. The final TeX log is checked for missing glyphs; findings include the character/font warning and log location. `word_diagnostics` locates repeated figure prefixes and measures actual image placements and effective DPI. Its label-size result remains unknown without reliable source/render measurement; pixel density is not a legibility pass. Repair repeated prefixes in the producing source or reference label, preserving the valid link and scientific text. Exit 2 means located text, missing glyphs or repeated Word references need review/repair; exit 3 means text extraction was incomplete. Generated paths remain available. Read the report and diagnostics, repair the source, font/notation or extraction problem in the same task, then rerun the affected export. Preserve scientific meaning; these are not new user approval gates. If a match is legitimate research content, preserve it and explain that specific finding in the real review instead of deleting it to make a pattern check pass. Native TeX builds use publication-surface.md's explicit source/output check as well. No-rule-matches does not replace full-page review. After the DOCX writer and layout filters run, the shared exporter resolves a table style's unique display name to its actual table style ID. Valid IDs remain unchanged. If a style is missing, ambiguous or of the wrong type, correct the named style in the reference DOCX/layout and rerun the affected export; do not accept the silently unstyled table or turn a repairable format issue into a new user approval step. Actual appearance still requires the rendering check. Set `figure-title` and `table-title` in the metadata when the venue or language uses different display labels, such as `Fig.`/`Tab.`. The same labels apply to captions and body references in both formats; Word's internal sequence names remain stable. The default labels are `Figure` and `Table`. Place the citation node correctly in the semantic source. For a verified sentence-final superscript convention, `Sentence.[@key]` attaches the marker after the punctuation without an extra word space; the CSL supplies the actual superscript. Other venues and sentence-internal citations can need different placement. Inspect the rendered result rather than assuming the CSL moved the source punctuation automatically. ## Inspect structure, pixels and reader interaction For likely whitespace/column problems, use the existing visual helper directly on each current PDF (including a faithful DOCX proof when available): ```bash python /scripts/visual_readiness_check.py --inspect-pdf --columns 2 --json ``` Choose `--columns 1` for a single-column surface. This read-only path requires PyMuPDF; it reads page pixels and needs no legacy manifest, output directory, form or task-state change. Exit 0 means no heuristic layout signals, 2 means regions require visual review, and 3 means analysis incomplete. It reports the actual PDF hash, pages, normalized regions and source-repair suggestions. It does not prove source/output parity, human viewing or independent approval. Sparse title pages/reference tails may be intentional; assess the actual page and its neighbors instead of treating occupancy as a pass/fail quota. Missing PyMuPDF does not block manual rendering/inspection using an available tool. For an unintended gap, fix the source's float/column/page break, rebuild affected surfaces and compare the same location. Do not shrink type, remove supported content or rewrite an audit note to satisfy a metric. Two unchanged targeted attempts require a different tactic, not a fresh retry count from a new hash. These checks answer different questions and none replaces the others: 1. **Source and output correspondence.** Check all cited keys against the final bibliography, numbering in first-use order, missing/unused entries, and repeated/grouped/range citations. Check body figure/table references against the selected assets and actual captions. Compare PDF and DOCX content with the current source after conversion; counts alone cannot detect a swapped reference, changed number or omitted paragraph. 2. **Destination validity.** Inspect every internal citation and cross-reference destination in the emitted PDF/DOCX. It must identify the intended entry or caption, including entries in different columns on the same page. The mere existence of a hyperlink, or a destination at the beginning of References, is insufficient. For a figure, including an unnumbered graphical abstract, compare the destination position with the rendered visual block: landing below the image on the correct page is still wrong. Preserve a useful target at the block's beginning when moving captions or separating legends. A collapsed range may link only its displayed endpoints; its full cited set must still be correct. Check DOI URLs independently of internal bibliography navigation. 3. **Actual rendering.** Visually read every PDF page and the actual DOCX or a faithful Word rendering. Inspect title/abstract, ordinary body pages, dense tables, equations, all figure/caption pairs and references against the local target PDFs. Check marker size/baseline/punctuation/spacing, wrapping, clipping, float gaps, page density, heading order and final-page composition. In multi-column pages, read each complete column in the document language's normal direction before the next column. Check heading and paragraph continuity across full-width figures/tables and column restarts. A float moved to a later page must not leave separate column groups that appear to reverse the reading sequence; source order or PDF text extraction alone cannot establish this. Repair the layout, preserving content and the applicable template, then inspect the affected pages again. In native Word, inspect bibliography first-line and continuation alignment across different number widths and later pages, not just the first entry. Fix the producing source/template and rerender affected outputs. 4. **Actual reader interaction.** In the user's browser, click a single citation, a citation group/range, an entry in a later reference column/page, a figure or table reference, and a DOI. Verify the intended target and return to the task. Also check the downloaded file in a PDF/Word viewer when needed to distinguish file defects from Web preview defects. A raster page preview can look correct while discarding every PDF link; its appearance is not an interactive check. Fix missing targets, wrong markers, rendering defects and preview defects at their actual source. Reuse unchanged valid analysis and figures. An external site being unavailable is different from a wrong DOI URL; report each accurately. ## Review and package the current revision Give the independent reviewer the current rendered files, semantic source, selected figures and local target-venue PDFs. Request specific findings on the format and editorial criteria that apply, not a generic "all clear". Record what was examined and any remaining concrete gap; do not inherit approval from a different PDF or declare an adopted improvement implemented before it is visible. When a reader identifies a defect in a previously approved file, reopen that specific finding even if the file bytes have not changed. Give a fresh format review the current outputs and representative target-page pairs, without using the old PASS as evidence. Pagination changes can move content throughout a document: inspect all reflowed pages, including tables/notes and the final page, while reusing valid scientific checks and unchanged standalone figure checks. Give one current set: rendered manuscripts, their exact sources, bibliography, each current standalone figure and the scientific supplements, plus the saved research scope and relevant exemplars. Ask for scientific validity, argument and editorial quality, publication-surface cleanliness and actual layout separately. The reviewer reads those files and submits their own real conclusions through the public review entry. A report file alone does not register a review; listing an artifact does not prove it was inspected. Reuse checks of unchanged bytes and review changed or previously uncovered files without restarting all research. After correction, regenerate every affected delivery format and both requested packages. Confirm that their included files match the reviewed revision and that editable dependencies are present. Exercise preview and actual Chrome download through the same task. Separate verified formatting, scientific/editorial quality and missing submission facts in the final report. Do not mark the paper complete while a required or user-rejected figure remains unresolved.