pandoc-fix

name	pandoc-fix
description	Use when Pandoc compile of the ICONOCRACIA thesis fails — undefined citation keys, LaTeX package errors, Markdown→LaTeX escape issues (underscores, ampersands, unicode), YAML frontmatter errors, missing .csl/.bib, or broken cross-references. Diagnoses the error, applies minimal fix, re-runs compile.
disable-model-invocation	true

pandoc-fix

Diagnose and patch Pandoc compile errors for vault/tese/. Distinct from compilar-tese (which just runs make). Use AFTER a compile fails.

When to invoke

• pandoc: Error producing PDF
• LaTeX Error: File 'X.sty' not found
• Could not find reference '@citationkey'
• ! Undefined control sequence
• YAML parse exception
• citeproc: reference X not found
• Garbled output: unicode chars dropped, footnotes misplaced, tables breaking

Workflow

1. Capture error. Re-run failing command with full log:

   cd vault/tese && make docx 2>&1 | tee /tmp/pandoc-err.log
   # PDF path: add -V debug, or retry with --verbose
   make pdf 2>&1 | tee /tmp/pandoc-err.log
   

2. Classify using the table below. Pick fix category BEFORE editing.

3. Apply minimal fix. One error class per edit — don't bundle.

4. Re-run same target. If new error → repeat. If same error → fix didn't land, inspect.

5. Commit fix with message naming the error class (e.g. fix(tese): escape underscores in capitulo-3 code refs).

Error classes

Symptom	Cause	Fix
reference X not found (citeproc)	@chaveCitacao missing in references.bib	Add BibTeX entry to vault/tese/references.bib. Export from Zotero → BibLaTeX format. Match key exactly.
File 'abntex2.sty' not found	LaTeX package missing	Install: brew install --cask mactex-no-gui OR switch to DOCX: make docx.
! Package inputenc Error: Unicode character	PDF engine lacks UTF-8	Use XeLaTeX: add --pdf-engine=xelatex to PANDOC_PDF in Makefile.
! Undefined control sequence \something	Raw LaTeX in .md not loaded via preamble	Wrap in \newcommand in header-includes, or remove the macro and use Markdown syntax.
YAML parse exception	Bad frontmatter (unquoted colon, stray ---)	Run python -c "import yaml; yaml.safe_load(open('capitulo-N.md').read().split('---')[1])" on indicated file.
Underscores render as subscript in PDF	Unescaped _ in prose	Replace word_with_underscore → word\_with\_underscore OR use backticks for code.
& breaks LaTeX	Unescaped ampersand	Replace & → \& outside code fences.
Quoted text breaks	Fancy quotes "..." in LaTeX context	Use straight "..." or --variable:smart flag.
toc empty / wrong depth	--toc-depth=3 but headings deeper	Either raise depth or reduce heading levels.
Images missing in output	Relative path broken when Pandoc runs from vault/tese/	Use paths relative to Makefile cwd, or --resource-path=.:../.:../..

Citation key repair

Most common thesis failure. Pipeline:

# 1. List all [@key] in chapters
grep -rEho '\[@[a-zA-Z0-9_-]+\]' vault/tese/*.md | sort -u > /tmp/cited.txt

# 2. List all @key in bib
grep -E '^@' vault/tese/references.bib | sed -E 's/@[a-zA-Z]+\{([^,]+),.*/\1/' | sort -u > /tmp/defined.txt

# 3. Diff — keys cited but not defined
comm -23 <(sed 's/\[@\(.*\)\]/\1/' /tmp/cited.txt | sort -u) /tmp/defined.txt

Each missing key → either (a) add to references.bib via Zotero export, or (b) fix typo in chapter.

LaTeX escape cheat

Characters needing \ escape in Markdown prose destined for PDF:

& % $ # _ { } ~ ^ \

Regex to find unescaped underscores in a chapter (skip code fences):

awk '/^```/{f=!f;next} !f' vault/tese/capitulo-3.md | grep -nE '[^\\]_[a-zA-Z]'

Red flags — stop before editing

• About to edit chapter but haven't read the error log verbatim → read log first.
• About to bulk sed escape all _ → will break code blocks and references.bib keys. Use awk with code-fence state.
• About to install LaTeX packages → check DOCX target works first; DOCX rarely blocks on LaTeX.
• Error mentions line number in generated .tex not .md → map back via pandoc --verbose output.

Common mistakes

• Editing output file instead of source. output/tese_completa.tex is generated; fix .md chapters.
• Fixing symptom not cause. If three chapters show same error, fix pattern once via script.
• Skipping make clean between iterations. Stale .aux files mask fixes.
• Committing generated artifacts. output/ should be gitignored.