Latex

LaTeX Document Compilation

Default compilation skill for all LaTeX documents. Compiles with autonomous error detection and resolution (up to 5 iterations), runs a citation audit on clean builds, and produces a quality score.

When to Use

• Default method for all LaTeX compilation
• Any .tex file that should compile to PDF
• When compilation fails and you want automatic diagnosis and repair
• When you want a post-compilation citation audit

When NOT to Use

• Markdown documents — use plain markdown, not LaTeX
• Quick notes or drafts — LaTeX overhead not worth it
• Documents that don't need citations, equations, or precise formatting
• Documents with exotic custom classes that need manual debugging

Quality Scoring

Apply numeric quality scoring using the shared framework and skill-specific rubric:

• Framework: ../shared/quality-scoring.md — severity tiers, thresholds, verdict rules
• Rubric: references/quality-rubric.md — issue-to-deduction mappings for this skill

Start at 100, deduct per issue found, apply verdict. Include the Score Block in the final report.

Critical Rules

1. Build artifacts go to out/, PDF stays in the source directory. Ensure .latexmkrc exists with $out_dir = 'out' and an END {} block to copy the PDF back (see pre-flight below). For VS Code builds, .latexmkrc in subdirectories is not picked up — see "VS Code Integration" section for the required .vscode/settings.json config.
2. NEVER write BibTeX entries from memory. Always verify against web sources (CrossRef, Google Scholar, DOI lookup) before writing. See the /literature skill.
3. Check document class before adding packages. Some classes load packages internally (e.g., elsarticle loads natbib — adding \usepackage{natbib} causes errors).
4. Maximum 5 fix iterations. If the document still has errors after 5 auto-fix cycles, stop and report the unresolved errors to the user.
5. Never silently swallow errors. Every fix must be reported: what was wrong, what was changed, and which file was edited.
6. Preserve user intent. Auto-fixes should be minimal and conservative. Add packages or overrides — never remove user content.
7. Citation audit requires clean compilation. Only run the \cite{} vs .bib cross-check after zero errors.
8. Run /bib-validate when new citations were added. The citation audit only checks key cross-references. When .bib entries were added or modified since the last validation, also run /bib-validate for full metadata quality checks (preprint staleness, DOI presence, required fields, author formatting). This is mandatory.

Protocol

Phase 1: Pre-flight

1. Locate the .tex file. Resolve the path (absolute or relative to CWD).
2. Identify the project directory — the folder containing the .tex file.
3. Ensure .latexmkrc exists in the project directory with at minimum:

   $out_dir = 'out';
   # Copy PDF back to source directory after build
   END { system("cp $out_dir/*.pdf . 2>/dev/null") if defined $out_dir; }
   

   If a .latexmkrc already exists, verify it sets $out_dir = 'out' and has the END {} block. If either is missing, add it. Do not overwrite other settings.
4. Create out/ directory if it doesn't exist: mkdir -p <project-dir>/out.
5. Identify the .bib file(s) referenced in the document (scan for \bibliography{}, \addbibresource{}, or \bibinput{}). Note their paths for Phase 5.

Phase 2: Compile-Fix Loop

Run up to 5 iterations. Each iteration:

Step 2a — Compile

cd <project-dir> && latexmk -interaction=nonstopmode <filename>.tex 2>&1

Capture the full output. The log file will be at out/<filename>.log.

Step 2b — Read the log

Read out/<filename>.log in full. Parse for errors and warnings.

Step 2c — Classify errors

Check the log against the known error patterns below. If an error matches, apply the fix and go to Step 2a. If no known pattern matches, record the error as unresolved and stop the loop.

Same-error circuit breaker. Independent of the 5-iteration cap: if the same error (same line family, same pattern signature) survives 3 consecutive fix attempts, stop the loop early. Continued attempts on a stuck error compound damage rather than resolve it. Report what was tried, quote the log line, and ask the user how to proceed. A common signature: Illegal parameter number jumping between line numbers as you edit — that is the diagnostic for a parameterized TikZ style defined inside a Beamer frame; see skills/shared/tikz-rules.md Rule 11.

Known Error Patterns & Auto-Fixes

Check the log against these patterns. Full fix instructions: references/known-errors.md

If an error matches, read the full fix from the reference and apply it. If no pattern matches, record as unresolved and stop the loop.

2.4 PDF backup (paper directories only)

Only run if the compile-fix loop above ended with a successful compilation (PDF exists).

If the .tex file is inside a paper-{venue}/paper/ structure (where paper/ is a symlink to Overleaf):

1. Identify the paper wrapper — the parent of the paper/ symlink (e.g., paper-jbdm/).
2. Create the backup directory: mkdir -p <paper-wrapper>/backup
3. Copy the PDF:

   cp <paper-wrapper>/paper/<filename>.pdf <paper-wrapper>/backup/<wrapper-name>_vcurrent.pdf
   

Detection logic:

• The project directory containing the .tex file is a symlink named paper.
• Its parent directory name starts with paper-.
• If either condition is false, skip this sub-step silently.

Phase 3: Final Report

After the loop ends (either clean compilation or max iterations reached), report:

Compilation Status

How to extract page count

grep -o "Output written on .* ([0-9]* page" out/<filename>.log | grep -o "[0-9]* page"

How to count warnings and boxes

Warnings and typographic boxes are separate — box messages are not Warning-tagged, so a single Warning grep misses every overfull/underfull box. Report both, using the recipes in ../shared/overfull-boxes.md:

# LaTeX/package warnings (refs, fonts, packages)
grep -c "Warning" out/<filename>.log
# Overfull/underfull boxes (the thing the Warning grep cannot see)
grep -cE 'Overfull \\[hv]box \([0-9.]+pt too (wide|high)\)' out/<filename>.log
grep -cE 'Underfull \\[hv]box \(badness [0-9]+\)' out/<filename>.log

Box report (typographic quality)

Extract the top offenders by overflow magnitude and report each box ≥ 1 pt with its location, width, and a remediation tier per the severity gradient + ladder in ../shared/overfull-boxes.md:

awk -F'[()]' '/Overfull \\[hv]box/ {
    split($2, a, "pt"); w = a[1] + 0;
    loc = $0; sub(/.*too (wide|high)\) */, "", loc);
    printf "%7.1f pt  %s\n", w, loc
}' out/<filename>.log | sort -rn | head -20

Report only — do not silently reword prose to close a box (rules/manuscript-edit-budget.md). The only safe auto-fix is inserting \usepackage{microtype} when genuinely absent.

Breadcrumb: Append to .planning/state.md (if exists) or .context/current-focus.md:

### [/latex] Compilation complete [YYYY-MM-DD HH:MM]
- **Done:** [Clean/Errors remaining, N iterations, N pages, N fixes applied]
- **Outputs:** [PDF at <path>]
- **Next:** [Citation audit (if clean) or manual error resolution]

Phase 4: Visual-Fragility Source Lint (clean builds only)

Only run if Phase 2 ended with zero errors. Sits between the final report (Phase 3) and the citation audit (Phase 5). Catches LaTeX source patterns that compile clean but produce visually fragile output — the failure class the title-page incident (2026-06-19) exposed.

Full detector catalogue with regex signatures, severity tiers, remediation, and false-positive caveats: references/source-pathologies.md.

What to run

1. Nine grep-based source-pathology detectors against main.tex plus any \input/\include'd files:

   #	Pattern	Tier
   1	Spacing hacks fighting global spacing (\onehalfspacing + local \\[-Xcm] / \vspace{-…})	Major
   2	Manual vertical-rhythm surgery (repeated \vspace/\vskip/\pagebreak in body)	Moderate–Major
   3	Line breaks as layout engine (\\ / \newline / \linebreak inside \section/\caption)	Moderate–Major
   4	Forced-float carpet bombing ([H]/[!h] pinning, \FloatBarrier overuse)	Moderate
   5	Shrink-to-fit tables/figures (\resizebox{\textwidth}{!}{…}, \adjustbox{width=\textwidth})	Major
   6	Tiny-table typography hacks (\scriptsize/\tiny in tables; negative \tabcolsep; \arraystretch<0.9)	Moderate–Major
   7	Absolute / overlap positioning (\raisebox, \makebox[0pt], \llap, \rlap, \smash, \hspace*) outside math	Major
   8	Fixed-width layout assumptions (p{Xcm}, \begin{minipage}{Xcm}, \parbox{Xcm})	Moderate
   9	Label-before-caption inside floats (\label{…} precedes \caption{…} in a figure/table block)	Major

2. chktex if installed: chktex -q -n8 -n44 main.tex 2>&1 | grep -v "^$". Advisory only — collect warnings; deduct -1 each, capped at -10. Skip if chktex not on PATH.

3. latexindent -k if installed: latexindent -k main.tex 2>&1; echo "Exit: $?". Source-cleanliness smoke test. Non-zero exit → -3 once. Skip if latexindent not on PATH.

Output

Append a Source pathologies subsection to the Phase 3 report:

### Source pathologies

| Pattern | Location | Detail | Tier |
|---------|----------|--------|------|
| 1 Spacing-hacks | titlepage, line 56 | `\\[-0.3cm]` under global `\onehalfspacing` (line 43) | Major |
| 9 Label-before-caption | tab:results, line 412 | `\label` at L410 precedes `\caption` at L413 | Major |

If no findings: "No source pathologies detected." If chktex or latexindent ran, note their PASS/N-warnings status.

Auto-fix scope

Phase 4 is report-only, with one exception: Pattern 1 ("Spacing hacks fighting global spacing") has a deterministic remediation (wrap the affected block in \begin{singlespace}…\end{singlespace}, delete the negative kerns). The skill offers this as an opt-in fix in the final report; the user accepts or declines per case. Do not auto-apply.

For Patterns 2–9 and tool findings: report only.

When to skip

• Compile failed in Phase 2 (pathology lint is meaningless without a build).
• User explicitly invoked /latex --no-lint.

Phase 5: Citation Audit (clean builds only)

Only run this phase if Phase 2 ended with zero errors.

1. Extract all \cite keys from the .tex file (and any \input/\include files):
   • Match \cite{...}, \citep{...}, \citet{...}, \textcite{...}, \parencite{...}, \autocite{...}, and multi-key variants like \cite{key1,key2}.
2. Extract all bib entry keys from the .bib file(s): match @<type>{<key>,.
3. Cross-reference:

4. Report the results as a table. Do not modify any files during the audit — report only.

Phase 6: Quality Score

After all phases complete, compute the quality score:

1. Read references/quality-rubric.md for deduction mappings.
2. Log every issue from Phases 2-5 (unresolved errors, remaining warnings, overfull/underfull boxes from the Phase 3 box report, citation mismatches). The rubric deducts per box by severity (>10pt: -5, 1-10pt: -2, underfull: -1) — feed it the box report, not a Warning count.
3. Compute score (100 - total deductions), apply verdict per ../shared/quality-scoring.md.
4. Append the Score Block to the compilation report:

## Quality Score

| Metric | Value |
|--------|-------|
| **Score** | XX / 100 |
| **Verdict** | Ship / Ship with notes / Revise / Revise (major) / Blocked |

### Deductions

| # | Issue | Tier | Deduction | Category |
|---|-------|------|-----------|----------|
| 1 | [description] | [tier] | -X | [category] |
| | **Total deductions** | | **-XX** | |

6.1 Output verification (before commit)

When the compile produced a PDF (and any backup copy), emit an outputs manifest and run the shared verifier per _shared/verify-outputs.md:

1. Write manifest to <project>/.Codex/state/outputs-manifest-<UTC-timestamp>.json listing every file written this invocation (PDF, backup PDF if 2.4 ran, log files).

2. Run:

   python3 "$HOME/.Codex/skills/_shared/verify_outputs.py" \
       --manifest "$MANIFEST" \
       --project-root "$PROJECT_ROOT"
   

3. If the verifier exits non-zero, do not commit. Surface the missing-files list and stop.

Closes the "hallucinated outputs" failure class (commit b2cff75, 2026-04-18).

Configuration Reference

Output Directory

All LaTeX build artifacts (.aux, .log, .bbl, .fls, etc.) go to an out/ subfolder relative to the source file. The PDF is copied back to the source directory after each successful build, so it lives alongside the .tex file for easy access.

The PDF-copy convention is enforced in two places — keep them in sync when making changes:

1. .latexmkrc (per-project) — Perl END {} block copies PDF after terminal/Codex builds
2. VS Code .vscode/settings.json (per-workspace) — explicit latexmk args in LaTeX Workshop tool definition

VS Code integration, engine auto-detection (pdfLaTeX/XeLaTeX/LuaLaTeX), manual override configs, reference checking scripts, and manual compilation commands:

references/latex-configs.md

Overleaf-Synced Projects

When a project is synced to Overleaf (via Dropbox or Git):

• The out/ directory will sync to Overleaf but Overleaf ignores it — this is fine
• Always use .latexmkrc to enforce out/ — Overleaf ignores this file too
• Overleaf compiles independently on its server; local compilation is for verification only
• The .bst file (e.g., elsarticle-harv.bst) lives in the source directory, not out/

Local-Only Projects (No Overleaf)

Not all projects sync to Overleaf. For local-only projects:

• The same out/ and .latexmkrc conventions apply — this keeps the working directory clean regardless of sync method
• There is no paper/ symlink — .tex files live directly in the project root or a subdirectory

Templates

See references/templates.md for working paper template location, files, citation style toggle, bibliography file naming conventions, and bibliography command reference.

Related Skills

Examples

Basic usage

"Compile my paper at ~/papers/mcdm-survey/main.tex"

Runs the full protocol: pre-flight → compile-fix loop → report → citation audit → quality score.

After fixing a known issue

"Recompile — I added the missing package manually"

Runs from Phase 2 directly (pre-flight can be skipped if .latexmkrc and out/ already exist).

Targeted fix

"My paper won't compile — something about Bbbk"

Identifies as Pattern 2 (font conflict), applies the \let\Bbbk\relax fix, recompiles.