irudik/repo-template

review-tex

Run the LaTeX review protocol on manuscripts and slides. Reviews prose around changed dynamic values, detects hardcoded numeric results, and auto-fixes unambiguous issues.

review-tex

Run the LaTeX review protocol on manuscripts and slides. Reviews prose around changed dynamic values, detects hardcoded numeric results, and auto-fixes unambiguous issues.

proofread

Run expert proofreading on academic documents. Checks grammar, typos, overflow risks, citation consistency, and academic quality for LaTeX, Quarto, and directly provided text-based files. Produces a report without editing files.

review-domain

Run the substantive domain review on manuscripts, slides, or lecture materials. Checks identification, derivations, citations, code-theory alignment, and logical consistency. Produces a report without editing files.

review-julia

Run the Julia code review protocol on Julia scripts. Checks code quality, type stability, performance, and professional standards. Produces a report without editing files.

review-makefile

Run the Makefile review protocol. Checks conventions, dependency correctness, script coverage, and build system quality. Produces a report without editing files.

review-matlab

Run the MATLAB code review protocol on MATLAB scripts. Checks code quality, solver configuration, derivative correctness, and optimization patterns. Produces a report without editing files.

review-r

Run the R code review protocol on R scripts. Checks code quality, reproducibility, domain correctness, and professional standards. Produces a report without editing files.

review-stata

Run the Stata code review protocol on Stata scripts. Checks code quality, reproducibility, data-state safety, and professional standards. Produces a report without editing files.

resume-custom

Recover context after compression or a new session. Reads MEMORY.md, recent plans, session logs, and git state to reconstruct working context.

resume-custom

Recover context after compression or a new session. Reads MEMORY.md, recent plans, session logs, and git state to reconstruct working context.

learn

Save a durable, project-specific lesson to MEMORY.md in a structured [LEARN] format.

trace

Trace an ambiguous result or failure back to its most likely cause using competing hypotheses and evidence. Produces a diagnostic report rather than a code change by default.

learn

Save a durable, project-specific lesson to MEMORY.md in a structured [LEARN] format.

trace

Trace an ambiguous result or failure back to its most likely cause using competing hypotheses and evidence. Produces a diagnostic report rather than a code change by default.

commit

Stage, commit, create PR, and merge to main. Use for the standard commit-PR-merge cycle.

compare-branches

Compare script outputs between two git branches. Uses worktrees to run scripts on both branches and checksums to detect differences.

data-analysis

End-to-end R data analysis workflow from exploration through regression to publication-ready tables and figures

matlab-optim-derivatives

Audit MATLAB optimization derivatives and KNITRO integration with finite-difference validation

proofread

Run expert proofreading on academic documents. Checks grammar, typos, overflow risks, citation consistency, and academic quality for LaTeX, Quarto, and directly provided text-based files. Produces a report without editing files.

refactor

Verify-refactor-verify loop for safe code style changes. Records baseline checksums, applies style-only transformations, then verifies identical output.

review-comments

Review and clean up comments, docstrings, and documentation across specified files or directories

review-domain

Run the substantive domain review on manuscripts, slides, or lecture materials. Checks identification, derivations, citations, code-theory alignment, and logical consistency. Produces a report without editing files.

review-julia

Run the Julia code review protocol on Julia scripts. Checks code quality, type stability, performance, and professional standards. Produces a report without editing files.

review-makefile

Run the Makefile review protocol. Checks conventions, dependency correctness, script coverage, and build system quality. Produces a report without editing files.

review-matlab

Run the MATLAB code review protocol on MATLAB scripts. Checks code quality, solver configuration, derivative correctness, and optimization patterns. Produces a report without editing files.

review-pr

Review and address unresolved PR comments. Implements fixes, commits modularly, replies with commit hashes, and resolves threads.

review-r

Run the R code review protocol on R scripts. Checks code quality, reproducibility, domain correctness, and professional standards. Produces a report without editing files.

review-stata

Run the Stata code review protocol on Stata scripts. Checks code quality, reproducibility, data-state safety, and professional standards. Produces a report without editing files.

setup-makefile

Generate a Makefile for a code directory by scanning scripts for output paths and building dependency rules.

verify-outputs

Checksum script outputs before and after changes. Establishes baseline checksums, re-runs scripts, and compares to detect regressions. Uses CSV as the gold standard.

commit

Stage, commit, create PR, and merge to main. Use for the standard commit-PR-merge cycle.

compare-branches

Compare script outputs between two git branches. Uses worktrees to run scripts on both branches and checksums to detect differences.

data-analysis

End-to-end R data analysis workflow from exploration through regression to publication-ready tables and figures

matlab-optim-derivatives

Audit MATLAB optimization derivatives and KNITRO integration with finite-difference validation

refactor

Verify-refactor-verify loop for safe code style changes. Records baseline checksums, applies style-only transformations, then verifies identical output.

review-comments

Review and clean up comments, docstrings, and documentation across specified files or directories

review-pr

Review and address unresolved PR comments. Implements fixes, commits modularly, replies with commit hashes, and resolves threads.

setup-makefile

Generate a Makefile for a code directory by scanning scripts for output paths and building dependency rules.

verify-outputs

Checksum script outputs before and after changes. Establishes baseline checksums, re-runs scripts, and compares to detect regressions. Uses CSV as the gold standard.