Orchestration Log: When this skill is activated, append a log entry to outputs/orchestration_log.md: `` ### Skill Activation: Review Engine (Round [N]) **Timestamp:** [current date/time] **Actor:** AI Agent (review-engine) **Input:** [N] review points from [source] (annotated PDF / pasted text / reviewer report) **Output:** [N] changes implemented, paper recompiled, latexdiff generated **Human decisions:** [list of QUESTION items resolved by orchestrator] ``

Review Engine

Core Principle

Academic revision is a structured, repeatable process: extract feedback -> interpret -> classify -> implement -> verify. This engine automates the entire loop. The human orchestrator approves the change plan; the engine executes it.

This skill was derived from 4 actual co-author revision rounds on a real paper (Blask & Funk, 2026). Every step reflects what we learned works — and what fails — when processing human feedback on AI-generated manuscripts.

When to Activate

• User provides an annotated PDF (co-author or reviewer comments)
• User pastes reviewer comments from a journal decision letter
• User says "implement these changes", "process this review", "revision round"
• User says "respond to reviewers", "R&R", "revise and resubmit"
• After self-review (Phase 6) produces a critique that needs implementation

Prerequisites

• paper.tex exists in latex/ and compiles successfully (this is the baseline)
• pdflatex and bibtex are available
• latexdiff is available (for visual change tracking)
• PyMuPDF (fitz) is available for PDF annotation extraction (pip install pymupdf)

Step 1: EXTRACT Review Points

The first step is to get all review points into a structured format, regardless of how the reviewer provided them.

From Annotated PDF (Co-Author Review)

This is the most common case: a co-author annotates the PDF with highlights, sticky notes, and text comments. Use scripts/extract_annotations.py:

import sys
sys.path.insert(0, "scripts")
from extract_annotations import extract_annotations, annotations_to_markdown

annotations = extract_annotations("path/to/annotated.pdf")
print(annotations_to_markdown(annotations))
print(f"\nTotal: {len(annotations)} annotations found")

If scripts/extract_annotations.py is not available, use inline PyMuPDF:

import fitz

doc = fitz.open("path/to/annotated.pdf")
annotations = []

for page_num, page in enumerate(doc, 1):
    for annot in page.annots() or []:
        entry = {
            "page": page_num,
            "type": annot.type[1],  # "Highlight", "Text", "FreeText", "StrikeOut"
            "content": annot.info.get("content", "").strip(),
            "author": annot.info.get("title", ""),
            "highlighted_text": "",
        }

        # Extract highlighted/marked text via quadpoints
        if annot.type[0] in (8, 9, 10, 11) and annot.vertices:  # Highlight, Underline, Squiggly, StrikeOut
            quad_count = len(annot.vertices) // 4
            text_parts = []
            for i in range(quad_count):
                quad = annot.vertices[i * 4:(i + 1) * 4]
                rect = fitz.Rect(
                    min(p[0] for p in quad), min(p[1] for p in quad),
                    max(p[0] for p in quad), max(p[1] for p in quad),
                )
                text_parts.append(page.get_text("text", clip=rect).strip())
            entry["highlighted_text"] = " ".join(text_parts)

        if entry["content"] or entry["highlighted_text"]:
            annotations.append(entry)

doc.close()

Common pitfall: The user may send the wrong PDF (without annotations). If extraction returns 0 annotations, tell the user immediately and ask them to re-send. Do NOT proceed with an empty annotation list.

From Pasted Text (Journal R&R)

Parse reviewer comments by detecting common patterns:

Reviewer 1:
Major Comments:
1. The authors should clarify...
2. The methodology section lacks...

Minor Comments:
1. On page 5, the reference to...

Split into individual review points by:

• Numbered items ("1.", "2.", "-", "a)")
• Reviewer sections ("Reviewer 1:", "Reviewer 2:")
• Category headers ("Major Comments:", "Minor Comments:", "Questions:")
• Page/line references ("page 5", "line 42", "Section 3")

From Self-Review (Phase 6 Output)

Parse the structured self-critique from self_review.md or the Phase 6 output. Each bullet point or numbered item becomes a review point.

Output Format

Every extraction method produces the same structure:

{
  "id": 1,
  "source": "pdf_annotation" | "pasted_text" | "self_review",
  "page": 5,                    # PDF page (if applicable)
  "type": "Highlight",          # Annotation type (if PDF)
  "reviewer": "Burkhardt Funk", # Reviewer name (if known)
  "reviewer_text": "just delete, I think ref to tab 1 is also wrong here",
  "highlighted_text": "Following Hevner et al.'s guidelines, we evaluate in three steps",
  "section_ref": null            # Will be filled in Step 2
}

Step 2: MAP to Source

For each review point, locate the corresponding position in paper.tex.

Mapping Strategy

1. Primary: Text match. Take the highlighted_text (or key phrases from

reviewer_text) and search paper.tex using grep/search. Handle:

• LaTeX commands embedded in text (\textit{...}, \citep{...})
• Line breaks (the PDF renders continuous text that spans multiple LaTeX lines)
• Ligatures and special characters (fi, fl, -- vs. --)

1. Secondary: Page-to-section estimation. If no text match is found, use the

PDF page number to estimate which LaTeX section it corresponds to. Compile the paper, check page breaks, and narrow down the section.

1. Tertiary: Manual flag. If neither works, flag the review point with

mapping_confidence: low and present it to the user for manual location.

Identifying Section Context

For each matched location, also extract:

• The \section{} or \subsection{} it belongs to
• The line number in paper.tex
• 3 lines of surrounding context (for the change plan display)

Output

Each review point is enriched:

{
  ...,
  "tex_line": 256,
  "tex_section": "\\subsection{Pipeline Implementation}",
  "tex_context": "Following Hevner et al.'s guidelines, we evaluate in three steps...",
  "mapping_confidence": "high" | "medium" | "low"
}

Step 3: CLASSIFY Actions

For each review point, determine what the reviewer is asking for and how to respond.

Action Types

Priority Levels

• CRITICAL: Factual error, wrong reference, misattribution, missing content
• MAJOR: Structural change, unclear argument, missing justification
• MINOR: Wording improvements, terminology, formatting
• COSMETIC: Typos, spacing, style preferences

Classification Process

For each review point:

1. Read the reviewer_text in context of highlighted_text
2. Determine intent (what does the reviewer want changed?)
3. Assign action_type and priority
4. For actionable items, draft a proposed_change (1-sentence description)
5. Determine automation_level: can this be done automatically, or does it need

human input or another engine (figure-engine, writing-engine)?

Handling Multilingual Comments

Reviewers may comment in any language (German is common in DACH academia). Interpret the comment in its original language; do not require translation. Common German review phrases:

• "streichen" / "löschen" = DELETE
• "umformulieren" = REPLACE/RESTRUCTURE
• "verschieben nach" = MOVE
• "zu lang" / "kürzen" = SHORTEN
• "passt" / "ok" / "einverstanden" = APPROVE
• "unklar" / "verstehe ich nicht" = needs EXPAND or RESTRUCTURE

Output

Each review point is enriched:

{
  ...,
  "action_type": "DELETE",
  "priority": "MAJOR",
  "automation_level": "full_auto" | "guided" | "needs_approval" | "needs_engine" | "needs_human",
  "proposed_change": "Remove the three-step evaluation paragraph at line 256",
  "depends_on": []  // IDs of other changes this depends on
}

Step 4: PLAN -- Present Change Plan

This is the QUALITY GATE. Do NOT proceed without user approval.

Change Plan Format

Present a structured overview of all review points and proposed changes:

📋 REVISION PLAN -- Round [N]
━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Source: [annotated PDF from Burkhardt Funk / Reviewer 1 report / ...]
Extracted: [N] review points
Actionable: [N] changes | Approved: [N] (no action) | Questions: [N] for you

 #  | Type        | Priority | Section | Reviewer Said               | Proposed Change
----|-------------|----------|---------|-----------------------------|--------------------------
 1  | REPLACE     | MINOR    | global  | "systems -> agents"         | Global replace in 8 locations
 2  | DELETE      | MAJOR    | S4.1    | "just delete"               | Remove eval paragraph (L256)
 3  | MOVE        | MAJOR    | S4.2    | "belongs in conclusion"     | Move scope para to S8
 4  | RESTRUCTURE | MAJOR    | S4.2    | "briefly describe each agent"| Rewrite with phase summaries
 5  | FIX         | MINOR    | S7.3    | "is it 7.1?"               | Fix cross-reference
 6  | FIGURE      | MAJOR    | Fig 1   | "extend orchestrator zone"  | Regenerate via PaperBanana
 7  | APPROVE     | --       | S2.5    | "fine with phases"          | No action -- logged
 8  | QUESTION    | MAJOR    | S4.2    | "do we do that?"            | ⚠️  Need your decision

⚠️  QUESTIONS requiring your input:
  Q1 (#8): Burkhardt asks "do we do that? delete?" about Phase 5/6 descriptions.
           -> Delete entirely, or shorten to one sentence each?

Execution order (respecting dependencies):
  1 -> 2 -> 3 -> 4 -> 5 -> 6

🔄 Approve plan to proceed with implementation.
   -> Override: modify any proposed change before I execute.

Handling Questions

For items classified as QUESTION:

• Present the reviewer's comment with full context
• Offer 2-3 concrete options (not open-ended)
• Wait for user's decision
• Update the change plan with the decision
• Re-present if needed

Dependencies

Some changes depend on others:

• Terminology replacement should happen BEFORE restructuring (so the new text

already uses correct terms)

• Moves should happen BEFORE expansions (so new text goes to the right place)
• Fixes should happen AFTER structural changes (cross-references may shift)

Build a dependency graph and present the execution order.

Step 5: IMPLEMENT Changes

After the user approves the plan, execute changes in dependency order.

Execution Order

1. Global terminology changes (REPLACE with replace_all: true)

• These affect the entire file and should be done first
• Example: replace "research systems" with "research agents" globally

1. Deletions (DELETE)

• Remove content cleanly, leaving a comment marker
• Format: % [R{round}: {brief description} -- deleted per {reviewer}]

1. Moves (MOVE)

• Cut content from source location (leave comment marker)
• Paste at target location with transition sentences
• Fix any cross-references that pointed to the moved content

1. Restructures (RESTRUCTURE)

• These are the most complex changes -- rewrite section flow
• Invoke writing-engine if new text needs to be drafted
• Preserve citation keys and cross-references

1. Shortenings (SHORTEN)

• Condense text while preserving key information and citations
• Leave comment marker noting what was shortened

1. Fixes (FIX)

• Cross-reference corrections: scan all \label{}, fix \ref{}
• Typo corrections
• Formatting fixes

1. Figure changes (FIGURE)

• Invoke figure-engine skill
• Use PaperBanana direct Python API via paperbanana_direct.py
• Copy generated figure to latex/figures/
• Update \includegraphics path if needed

1. Expansions (EXPAND)

• Invoke writing-engine skill for new text
• Place at correct location
• Integrate with surrounding text

Comment Markers

Every change gets a LaTeX comment marker for traceability:

% [R3: Moved scope paragraph to conclusion per Burkhardt]
% [R3-05: Fixed cross-reference Section 6.1 -> \ref{sec:task_redistribution}]
% [R4: Three-step evaluation paragraph deleted per Burkhardt]

Format: % [R{round}: {brief description}] Or with ID: % [R{round}-{change_number}: {description}]

Step 6: VERIFY

After all changes are implemented, verify the paper still compiles and looks correct.

Compilation

Run the full LaTeX compilation cycle:

cd latex/
pdflatex -interaction=nonstopmode paper.tex
bibtex paper
pdflatex -interaction=nonstopmode paper.tex
pdflatex -interaction=nonstopmode paper.tex

Target: 0 errors, 0 undefined references, 0 undefined citations.

If compilation fails:

1. Check the .log file for the error
2. Fix the issue (usually a mismatched brace, missing \end{}, or bad \ref{})
3. Recompile (up to 3 fix-recompile attempts)
4. If still failing after 3 attempts, present the error to the user

Latexdiff

Generate a visual diff against the baseline:

latexdiff <(git show BASELINE_COMMIT:latex/paper.tex) latex/paper.tex > latex/paper_diff.tex
pdflatex -interaction=nonstopmode latex/paper_diff.tex
bibtex paper_diff
pdflatex -interaction=nonstopmode latex/paper_diff.tex
pdflatex -interaction=nonstopmode latex/paper_diff.tex

The baseline commit should be:

• The commit just before the first revision round started
• Or a user-specified commit hash

Sanity Checks

1. Page count: Should be within +/-2 pages of the original. Major deviations

indicate something went wrong (content accidentally deleted or duplicated).

1. References: grep "undefined" paper.log should return 0 matches.
2. Orphans: All figures referenced in text should exist in figures/.
3. Bibliography: All \citep / \citet keys should resolve.

Verification Report

✅ REVISION ROUND [N] COMPLETE
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
📄 paper.pdf -- [N] pages, 0 errors
📊 Changes implemented: [N] of [N] planned
📝 paper_diff.pdf generated against baseline [commit hash]

Compilation:  ✅ Clean (0 errors, 0 warnings)
References:   ✅ All \ref{} and \citep{} resolved
Page count:   [N] pages (was [N] before revision)
Figures:      ✅ All [N] figures present

Review points:
  ✅ Implemented:  [N]
  ℹ️  Approved:    [N] (no action needed)
  ❓ Deferred:    [N] (marked for next round)

Step 7: DOCUMENT

Change Log

Save a detailed change log for each round:

File: outputs/revision_log_r{N}.md

# Revision Log -- Round [N]

**Date:** [ISO 8601]
**Reviewer:** [name]
**Source:** [annotated PDF / pasted comments / reviewer report]
**Review points:** [N] total ([N] implemented, [N] approved, [N] deferred)

## Changes Implemented

### Change 1: [brief title]
- **Type:** REPLACE
- **Reviewer said:** "[exact quote]"
- **Action:** Global replacement of "research systems" with "research agents" (8 occurrences)
- **Files affected:** paper.tex (lines 118, 235, 255, ...)

### Change 2: [brief title]
...

## No Action Required

### Approval 1: [brief title]
- **Reviewer said:** "[exact quote]"
- **Reason:** Positive feedback, no change needed

## Deferred to Next Round (if any)

### Deferred 1: [brief title]
- **Reviewer said:** "[exact quote]"
- **Reason:** Needs empirical data / needs further discussion

Revision Letter (for Journal R&R)

If the review came from a journal, generate a formal revision letter:

File: outputs/revision_letter.md

# Response to Reviewers

Dear Editor,

Thank you for the opportunity to revise our manuscript "[title]" (MS-XXXX).
We have carefully addressed all reviewer comments as detailed below.

---

## Reviewer 1

### Comment 1.1
> [Exact quote of reviewer comment]

**Response:** [How we addressed it]
**Change:** [Specific change made, with section/page reference]

### Comment 1.2
> [Exact quote]

**Response:** ...

---

## Reviewer 2
...

Orchestration Log

Append to outputs/orchestration_log.md:

## Phase 8: Revision (Round [N])
**Timestamp:** [ISO 8601]
**Actor:** AI Agent (review-engine)
**Action:** Processed [N] review points from [reviewer], implemented [N] changes
**Key metrics:** [N] review points, [N] changes, [N] approvals, [N] questions resolved
**Output artifacts:** paper.pdf, paper_diff.pdf, revision_log_r[N].md

**Quality Gate Decision:** [Approved / Redirected]
**Orchestrator Feedback:** "[user's response to change plan]"
**Scope Changes:** [any modifications to proposed changes]

Git Commit

If the user approves:

git add latex/paper.tex latex/paper.pdf latex/paper_diff.pdf outputs/revision_log_r*.md
git commit -m "Round [N]: implement [reviewer] review ([N] changes)

Changes: [1-line summary of each change]

Co-Authored-By: Claude <[email protected]>"

Error Recovery

• PDF has no annotations: Tell the user immediately. Ask if they sent the

correct file. Do NOT proceed with empty annotations.

• Text not found in paper.tex: Flag the review point with low confidence.

Present to user with the reviewer's comment and ask them to locate it manually.

• Compilation fails after changes: Revert the last change, try again.

If persistent, present the error and the problematic change to the user.

• Conflicting reviewer instructions: Present both to the user with options.

Do not make the decision autonomously.

• Figure generation fails: Note it in the change plan, continue with other

changes. Flag the figure change as "deferred" in the change log.

Integration with Other Engines

The review engine orchestrates other skills when needed:

Iteration

This phase is designed to repeat:

Round 1: Major structural feedback  -> implement -> send back
Round 2: Terminology and flow       -> implement -> send back
Round 3: Minor corrections          -> implement -> send back
Round 4: Final approval + cosmetics -> implement -> done

Each round:

• Uses the SAME baseline commit for latexdiff (cumulative changes visible)
• Increments the round number in comment markers (R1, R2, R3, R4)
• Produces its own revision log (revision_log_r1.md, revision_log_r2.md, ...)
• Can handle feedback from multiple reviewers simultaneously (group by reviewer)