annotate-latex

name	annotate-latex
description	Inject Proofreader audit findings as comment-only annotations into the paper's LaTeX source so the author can review them in their editor next to the actual proof text. Output is plain `%` comments that do NOT affect the rendered PDF and do NOT require any new packages. Produces a unified diff for review before applying. Triggers on "annotate my LaTeX with the findings", "add audit comments to my .tex", "patch my source with the audit results".
version	0.1.0

Skill: Annotate LaTeX

Role

You take Proofreader audit findings (and optionally counterexample / stress-test / writeup outputs) and inject them into the paper's .tex source as comment-only annotations. The author sees the findings in their editor next to the affected proof text, can address them in a normal revision pass, and can git diff to track what changed.

This is the opposite end of prepare-paper-context: that one reads source in, this one writes annotations back out.

Inviolable rules

1. Comments only. Every annotation begins with % and is a single line. No \todo{}, no \marginpar, no custom macros, no \textcolor, no anything that would render in the compiled PDF.
2. No package additions. Never insert \usepackage{...} lines. Never modify the preamble.
3. No content edits. Never rewrite proof text, theorem statements, or any non-comment lines. The author writes the paper; this skill annotates it.
4. Diff first, apply on consent. Always present a unified diff and ask the user before writing the file.
5. Compile-safe. A LaTeX file that compiled before this skill ran will compile identically after — the rendered PDF is byte-identical except for the missing annotations.

These rules are not preferences; they are hard constraints. The author may be using this skill mid-draft and any unintended LaTeX-level change risks polluting their build artifacts.

Why this exists

Markdown audit reports are good for one-shot review but poor for revision. When the author opens their .tex source in their editor, they want to see "this proof has a problem" near the proof itself, not in a separate document. LaTeX comments are the cleanest way to achieve that without changing what the compiler sees.

Inputs

Required:

1. Paper source — path to the .tex file (or main file of a project) you want to annotate.
2. Audit findings — output of audit-proof (or /proofread's findings list). One result per audit.

Optional: 3. Counterexample report — to annotate the proof with the counterexample summary. 4. Stress-test verdict — to suppress annotations for false_positive findings (the user has decided these aren't real). 5. Writeup briefs — so each annotation can reference the corresponding writeup filename.

Annotation format

Every annotation line begins with % PROOFREADER so the entire set can be removed mechanically with a single sed invocation.

% PROOFREADER [<severity>] [<type>]: <one-line summary>
% PROOFREADER:   <continuation, indented two spaces>
% PROOFREADER:   See <finding-brief-filename> for the full audit.

Severities: minor / moderate / serious / critical. Types: the issue's type field from the audit (incorrect_formula, missing_precondition, dependency_error, etc.).

A typical annotation block is 2–4 lines. Keep them tight — verbose annotations clutter the source and make git diff noisy.

Example

\begin{theorem}\label{thm:foo}
% PROOFREADER [moderate] [missing_precondition]: theorem statement is missing the "continuously backlogged" precondition.
% PROOFREADER:   Proof of Lemma 6 requires continuous backlog; current statement only requires backlog.
% PROOFREADER:   See finding-thm-foo.md.
For any task set $\tau$ satisfying ...
\end{theorem}
\begin{proof}
% PROOFREADER [serious] [incorrect_formula]: load-bearing step on line 4 substitutes R^- where R^+ is required.
% PROOFREADER:   Inductive chain uses lower bound where upper bound was established. See finding-thm-foo.md.
... proof body ...
\end{proof}

For a labeled equation:

\begin{equation}\label{eq:bound}
% PROOFREADER [moderate] [incorrect_formula]: constant gamma assumed = 1; Table 2 shows gamma reaches 1.095.
R_i \leq C_i + \sum_j B_j
\end{equation}

Placement rules

Place each annotation immediately after the \begin{...} line of the environment it applies to, or immediately after the labeled equation's \begin{equation} / \begin{align} line. This keeps git diff minimal — annotation lands one line above the affected content.

For findings that target the whole environment (e.g., a theorem with multiple issues), group all related annotations into one block immediately after \begin{theorem}. Do not interleave annotations with the theorem statement.

For findings that target a specific equation within a proof, place the annotation immediately above the equation. If the equation is inline (no \begin{equation}), place the annotation on the line before the surrounding paragraph and reference the inline location verbally in the annotation text.

Process

Step 1: Match findings to source locations

For each audit finding, look up the targeted result's label and find the corresponding \label{} in the .tex source.

If the audit was done on a PDF (no LaTeX label available), you'll have a result number ("Theorem 3") and a verbatim statement. Search for \begin{theorem} blocks; match by:

• Statement-text similarity (preferred — exact phrase matches).
• Ordinal count (the third \begin{theorem} in document order if numbering is plain).

If matching is ambiguous, list the candidates and ask the user once.

Step 2: Compose annotations

For each finding:

• One header line: % PROOFREADER [<severity>] [<type>]: <one-line summary>. ≤ 100 characters total. State the what, not the why.
• 1–3 continuation lines: % PROOFREADER: <detail> for the why and any quantitative detail.
• One trailing reference line if a finding brief exists: % PROOFREADER: See <brief-filename>.

Step 3: Produce a unified diff

Present the diff. Do not apply yet.

--- a/paper.tex
+++ b/paper.tex
@@ -141,6 +141,8 @@
 \begin{theorem}\label{thm:foo}
+% PROOFREADER [moderate] [missing_precondition]: theorem statement omits "continuously backlogged".
+% PROOFREADER:   See finding-thm-foo.md.
 For any task set $\tau$ satisfying ...

Ask: "Apply this diff to paper.tex? (yes / no / show full diff)". On yes, apply with Edit. On no, do nothing; the diff itself is the deliverable.

Step 4: Index file

After applying, write annotations-index.md next to the paper:

# Proofreader annotations on <paper>

Applied <ISO date>. All annotations are LaTeX comments (`% PROOFREADER ...`)
and do not affect the rendered PDF.

| Location | Severity | Type | Finding brief |
|---|---|---|---|
| `\label{thm:foo}` (paper.tex:141) | moderate | missing_precondition | finding-thm-foo.md |
| `\label{eq:bound}` (paper.tex:167) | moderate | incorrect_formula | finding-eq-bound.md |

To remove ALL Proofreader annotations from this file:
    sed -i '/^% PROOFREADER/d' paper.tex

The sed removal pattern is anchored to the start of the line (^%) to avoid touching any % PROOFREADER substring that happens to appear inside a verbatim environment or string literal.

What this skill does not do

• Compile the paper. No pdflatex invocations.
• Rewrite proofs. Annotations point at issues; the author rewrites.
• Modify the rendered PDF. All annotations are LaTeX comments.
• Add packages. No \usepackage insertions, ever.
• Touch files the user didn't authorize. Always diff-first.

Removing annotations

After a successful revision pass, the author should remove annotations they've addressed. The single sed line in the index file removes all annotations at once. For selective removal, git diff shows every annotation that was added; the author can revert individual hunks.