Directory Map:
LoopDetect_2025/
├─ README.md
├─ data/ # shared, read-only inputs for all stacks
│ ├─ raw/
│ └─ interim/ # preprocessed inputs usable by all languages
├─ results/ # only cross-language or final deliverables here
│ ├─ aggregate/ # comparisons (tables/plots) that mix languages
│ └─ reports/ # paper-ready figures, notebooks, PDFs
├─ scripts/ # orchestration only (no language-specific logic)
│ ├─ run_all.sh
│ ├─ collect_artifacts.py # optional: gathers per-language outputs
│ └─ smoke_checks.sh
├─ Python/
│ ├─ src/ # helpers specific to Python evaluations
│ ├─ tests/
│ ├─ scripts/ # Python-only CLIs, notebooks
│ └─ results/ # Python-only artifacts (logs, figs, CSV)
├─ R/
│ ├─ R/ # helpers
│ ├─ tests/testthat/
│ ├─ scripts/
│ └─ results/ # R-only artifacts
├─ MATLAB/
│ ├─ project.prj
│ ├─ tests/
│ ├─ scripts/
│ └─ results/ # MATLAB-only artifacts
└─ env/
├─ python.lock / conda-lock files
├─ renv.lock
└─ matlab-version.txt