Best practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects
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Expert guidance for organizing project directories, establishing file naming conventions, and maintaining clean, navigable project structures for research and development work.
Creates isolated Git worktrees for feature branches with prioritized directory selection, gitignore safety checks, auto project setup for Node/Python/Rust/Go, and baseline verification.
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Dispatches parallel agents to independently tackle 2+ tasks like separate test failures or subsystems without shared state or dependencies.
Expert guidance for organizing project directories, establishing file naming conventions, and maintaining clean, navigable project structures for research and development work.
Use the structure matching your project type. Full templates in project-structures.md.
Research/Analysis: data/{raw,processed,external}, notebooks/, src/, scripts/, tests/, docs/, results/, config/
Development: src/package_name/, tests/, docs/, examples/, .github/workflows/
Bioinformatics: data/{raw,reference,processed}, workflows/, config/, scripts/, results/, logs/
Data Analysis with Notebooks: notebooks/, figures/, data/, tests/, scripts/, docs/, archives/
Add MANIFEST.md files for token-efficient navigation (see manifest-system.md).
Detailed conventions in naming-conventions.md. Key rules:
process-telomere-data.py not script.pyreport-2026-01-23.pdf01-exploration.ipynb, 02-analysis.ipynbsession-saves/ directoryDO commit: Source code, documentation, config files, small test data (<1MB), requirements files, READMEs
DON'T commit: Large data files, generated outputs, environment dirs, logs, temp files, API keys/secrets
# Claude Code
.claude/
# Python
__pycache__/
*.py[cod]
.venv/
venv/
# Jupyter
.ipynb_checkpoints/
# Data
data/raw/
data/processed/
*.fastq.gz
*.bam
# Outputs
results/
outputs/
*.png
*.pdf
# Logs & Environment
logs/
*.log
.env
.DS_Store
data/raw/ (read-only if possible)raw/ -> interim/ -> processed/ -> external/Avoid these patterns:
notebook1.ipynb, test.ipynb, analysis_new.ipynbsrc/ directoryDeprecate rather than delete to maintain history and recovery options. Full guide in deprecation-guide.md.
Key pattern:
deprecated/ subdirectory with descriptive namedeprecated/Full systematic guide in reorganization-guide.md. Critical steps:
grep -r "\.json\|\.csv\|\.png" --include="*.ipynb" --include="*.py".bak, .ipynb_checkpoints)Full guide in documentation-organization.md. Key points:
documentation/ directoryToken-efficient project navigation system. Full documentation in manifest-system.md.
/update-manifestDetailed process in deprecation-guide.md (section "Project Cleanup"). Summary:
deprecated/ with descriptive subdirectory namesMINIMAL_ESSENTIAL_FILES.md# Create standard research project structure
mkdir -p data/{raw,processed,external} notebooks scripts src tests docs results config
touch README.md .gitignore environment.yml
| File | Contents |
|---|---|
project-structures.md | Detailed directory templates for all project types |
naming-conventions.md | File naming rules, patterns, and session notes storage |
reorganization-guide.md | Step-by-step reorganization, path updates, verification |
deprecation-guide.md | Deprecation strategy, consolidation, essential file identification |
documentation-organization.md | Documentation standards, change summaries, doc directory structure |
manifest-system.md | Complete MANIFEST system: templates, commands, workflows, best practices |