Review Domain Substance Protocol

Run the substantive domain review protocol for manuscripts, slides, or lecture materials.

Steps

1. Identify files to review:
   • If an argument is a specific filename such as .tex, .qmd, or .md, review that file only.
   • If the argument is all, review all .tex files in latex/ excluding latex/latex_extras/, plus any .qmd files if the project contains them.
2. For each file, follow the domain review protocol:
   • Apply all five lenses.
   • Check literature/ for citation fidelity if that directory exists in the project.
   • Check code/ for code-theory alignment.
   • Check latex/references/references.bib for bibliography cross-referencing.
   • Save the report to quality_reports/[FILENAME_WITHOUT_EXT]_substance_review.md.
3. After all reviews complete, present a summary:
   • Overall assessment
   • Total issues found per file
   • Breakdown by severity
   • Top three most critical issues
4. Do not edit source files. Produce reports only.

The Five-Lens Protocol

Lens 1: Identification and Causal Claims

• Are causal claims supported by the identification strategy?
• Are assumptions stated and plausible?
• Are threats to identification discussed?

Lens 2: Derivations and Mathematical Correctness

• Do derivations follow from stated assumptions?
• Are boundary conditions and edge cases handled?
• Are approximations acknowledged and bounded?

Lens 3: Citation Fidelity

• Do cited claims match the original source?
• Are key methodological references included?
• Are any claims attributed to the wrong paper?

Lens 4: Code-Theory Alignment

• Does the code implement what the paper claims?
• Do variable names and transformations match the model?
• Are estimation commands consistent with the stated specification?

Lens 5: Backward Logic and Internal Consistency

• Do conclusions follow from the reported results?
• Are results contradicted elsewhere in the document?
• Is the narrative consistent from introduction through conclusion?