ctt.toml

[template]
src_path = "."
vcs_ref = "HEAD"

[config]
output_dir = ".ctt"
cleanup = false

[defaults]
project_name = "Test Project"
short_name = "test-proj"
description = "A test project"
author_name = "Test User"
author_email = "test@example.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "None"
data_versioning = false
data_validation = false
github_actions = false
pre_commit_hooks = false
include_publication_templates = false
include_jujutsu = false
include_fossil = false

# ====== EXISTING TESTS (BACKWARDS COMPATIBILITY) ======

# Test 1: Full Academic Project (default configuration)
[output."full-academic"]
[output."full-academic".answers]
project_name = "Test Academic Project"
short_name = "test-academic"
description = "A comprehensive academic research project"
author_name = "Dr. Test Researcher"
author_email = "test@university.edu"
project_type = "Full Academic Project (analysis + writeup)"
programming_language = "Both"
experiment_tracking = "MLflow"
data_versioning = true

# Test 2: Analysis Only Project
[output."analysis-only"]
[output."analysis-only".answers]
project_name = "Data Pipeline Project"
short_name = "data-pipeline"
description = "Data science analysis pipeline only"
author_name = "Data Scientist"
author_email = "datascientist@company.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
experiment_tracking = "Weights & Biases"
data_versioning = true
include_ml_components = true

# Test 3: Manuscript Only Project
[output."manuscript-only"]
[output."manuscript-only".answers]
project_name = "Research Paper"
short_name = "research-paper"
description = "Academic manuscript writing project"
author_name = "Prof. Writer"
author_email = "writer@academic.org"
project_type = "Manuscript Only (writing and publications)"
programming_language = "R"
documentation_format = "Quarto"
include_publication_templates = true

# Test 4: Package Development Project
[output."package-dev"]
[output."package-dev".answers]
project_name = "Scientific Package"
short_name = "sci-package"
description = "Python/R package for scientific computing"
author_name = "Package Developer"
author_email = "dev@packages.io"
project_type = "Package Development (software/library)"
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false
github_actions = true
pre_commit_hooks = true

# Test 5: Custom Configuration - Minimal Setup
[output."custom-minimal"]
[output."custom-minimal".answers]
project_name = "Minimal Project"
short_name = "minimal"
description = "Minimal custom project setup"
author_name = "Minimalist"
author_email = "minimal@example.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = false
include_misc = false
include_notebooks = true
include_scripts = false
include_data_pipeline = true
include_testing = false
include_packages = false
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false

# Test 6: Custom Configuration - Maximum Setup
[output."custom-maximal"]
[output."custom-maximal".answers]
project_name = "Comprehensive Project"
short_name = "comprehensive"
description = "Full-featured custom project with all components"
author_name = "Power User"
author_email = "power@research.edu"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = true
include_infrastructure = true
include_misc = true
# Analysis subcomponents
include_notebooks = true
include_scripts = true
include_data_pipeline = true
include_testing = true
include_packages = true
# Writeup subcomponents
include_manuscript = true
include_presentations = true
include_grants = true
include_abstracts = true
include_posters = true
include_reports = true
include_blog = true
# Infrastructure subcomponents
include_docker = true
include_cloud_deployment = true
include_virtualization = true
include_automation = true
# Other settings
programming_language = "Both"
experiment_tracking = "Neptune"
data_versioning = true
documentation_format = "Quarto"
github_actions = true
pre_commit_hooks = true

# Test 7: Bioinformatics Specialized Project
[output."bioinformatics"]
[output."bioinformatics".answers]
project_name = "Genomics Analysis"
short_name = "genomics"
description = "Bioinformatics project for genomic data analysis"
author_name = "Bioinformatician"
author_email = "bio@genomics.edu"
project_type = "Full Academic Project (analysis + writeup)"
programming_language = "Both"
experiment_tracking = "MLflow"
data_versioning = true
include_eda_templates = true
include_statistical_analysis = true
include_ml_components = true
documentation_format = "Quarto"
include_publication_templates = true

# Test 8: Minimal Starter Project (Beginner-Friendly)
[output."minimal-starter"]
[output."minimal-starter".answers]
project_name = "My First Analysis"
short_name = "first-analysis"
description = "A beginner-friendly data science project"
author_name = "New User"
author_email = "newuser@example.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "None"
data_versioning = false
data_validation = false
github_actions = false
pre_commit_hooks = false
include_publication_templates = false
include_jujutsu = false
include_fossil = false

# Test 9: Quick Manuscript Project
[output."quick-manuscript"]
[output."quick-manuscript".answers]
project_name = "Conference Paper"
short_name = "conf-paper"
description = "Quick manuscript for conference submission"
author_name = "Research Fellow"
author_email = "fellow@university.edu"
project_type = "Manuscript Only (writing and publications)"
programming_language = "R"
documentation_format = "RMarkdown"
include_publication_templates = true
github_actions = false
pre_commit_hooks = false

# ====== NEW COMPREHENSIVE TESTS ======

# === PROGRESSIVE ENHANCEMENT TESTS ===

# Test 10: Progressive - Minimal with Tracking
[output."progressive-minimal-tracking"]
[output."progressive-minimal-tracking".answers]
project_name = "Enhanced Minimal Project"
short_name = "enhanced-minimal"
description = "Minimal project with experiment tracking"
author_name = "Beginning Researcher"
author_email = "beginner@research.edu"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "MLflow"
data_versioning = true
data_validation = true
github_actions = false
pre_commit_hooks = true

# Test 11: Progressive - Minimal with Writeup
[output."progressive-minimal-writeup"]
[output."progressive-minimal-writeup".answers]
project_name = "Minimal with Writing"
short_name = "minimal-write"
description = "Minimal project enhanced with writing tools"
author_name = "Student Researcher"
author_email = "student@university.edu"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Quarto"
include_publication_templates = true
github_actions = true
pre_commit_hooks = true
data_validation = false

# Test 12: Progressive - Full Upgrade
[output."progressive-full-upgrade"]
[output."progressive-full-upgrade".answers]
project_name = "Full Featured Project"
short_name = "full-featured"
description = "Complete academic project with all features"
author_name = "Senior Researcher"
author_email = "senior@research.edu"
project_type = "Full Academic Project (analysis + writeup)"
programming_language = "Both"
documentation_format = "Quarto"
experiment_tracking = "Neptune"
data_versioning = true
data_validation = true
include_eda_templates = true
include_statistical_analysis = true
include_ml_components = true
include_docker = true
include_cloud_deployment = true
include_virtualization = true
include_automation = true
github_actions = true
pre_commit_hooks = true
include_publication_templates = true

# === DOCUMENTATION FORMAT COVERAGE ===

# Test 13: Markdown Documentation
[output."docs-markdown"]
[output."docs-markdown".answers]
project_name = "Markdown Documentation Project"
short_name = "markdown-docs"
description = "Project using Markdown for documentation"
author_name = "Documentation Writer"
author_email = "docs@example.com"
project_type = "Manuscript Only (writing and publications)"
programming_language = "R"
documentation_format = "Markdown"
include_publication_templates = true
github_actions = false
pre_commit_hooks = false

# Test 14: RMarkdown Focus
[output."docs-rmarkdown"]
[output."docs-rmarkdown".answers]
project_name = "R-Centric Analysis"
short_name = "r-analysis"
description = "R-focused project with RMarkdown"
author_name = "R Developer"
author_email = "r.dev@stats.org"
project_type = "Analysis Only (data science pipeline)"
programming_language = "R"
documentation_format = "RMarkdown"
experiment_tracking = "None"
data_versioning = false
include_statistical_analysis = true

# === VERSION CONTROL VARIATIONS ===

# Test 15: Jujutsu VCS
[output."vcs-jujutsu"]
[output."vcs-jujutsu".answers]
project_name = "Jujutsu VCS Project"
short_name = "jj-project"
description = "Project using Jujutsu version control"
author_name = "VCS Explorer"
author_email = "vcs@example.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
include_jujutsu = true
include_fossil = false
documentation_format = "Jupyter Notebooks"

# Test 16: Fossil VCS
[output."vcs-fossil"]
[output."vcs-fossil".answers]
project_name = "Fossil VCS Project"
short_name = "fossil-project"
description = "Project using Fossil version control"
author_name = "Archive Keeper"
author_email = "archive@research.edu"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "R"
include_jujutsu = false
include_fossil = true
documentation_format = "RMarkdown"

# Test 17: Hybrid VCS
[output."vcs-hybrid"]
[output."vcs-hybrid".answers]
project_name = "Hybrid VCS Project"
short_name = "hybrid-vcs"
description = "Project using both Jujutsu and Fossil"
author_name = "VCS Master"
author_email = "vcsmaster@example.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = true
include_infrastructure = true
include_misc = false
programming_language = "Both"
include_jujutsu = true
include_fossil = true
use_hybrid_vcs = true
documentation_format = "Quarto"

# === EXPERIMENT TRACKING COVERAGE ===

# Test 18: Weights & Biases with Python
[output."tracking-wandb"]
[output."tracking-wandb".answers]
project_name = "WandB Experiment Tracking"
short_name = "wandb-exp"
description = "Python project with Weights & Biases tracking"
author_name = "ML Experimenter"
author_email = "ml@experiments.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "Weights & Biases"
data_versioning = true
data_validation = true
include_ml_components = true

# Test 19: Neptune with R
[output."tracking-neptune-r"]
[output."tracking-neptune-r".answers]
project_name = "Neptune R Analysis"
short_name = "neptune-r"
description = "R project with Neptune experiment tracking"
author_name = "R ML Researcher"
author_email = "rml@research.edu"
project_type = "Analysis Only (data science pipeline)"
programming_language = "R"
documentation_format = "RMarkdown"
experiment_tracking = "Neptune"
data_versioning = false
data_validation = true
include_statistical_analysis = true

# === INFRASTRUCTURE COMBINATIONS ===

# Test 20: Docker Only
[output."infra-docker-only"]
[output."infra-docker-only".answers]
project_name = "Docker-Only Project"
short_name = "docker-proj"
description = "Project with Docker containerization only"
author_name = "Container Developer"
author_email = "docker@dev.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = true
include_misc = false
include_docker = true
include_cloud_deployment = false
include_virtualization = false
include_automation = false
programming_language = "Python"
documentation_format = "Jupyter Notebooks"

# Test 21: Cloud Deployment Focus
[output."infra-cloud"]
[output."infra-cloud".answers]
project_name = "Cloud Deployment Project"
short_name = "cloud-deploy"
description = "Project focused on cloud deployment"
author_name = "Cloud Engineer"
author_email = "cloud@engineering.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = true
include_misc = false
include_docker = true
include_cloud_deployment = true
include_virtualization = false
include_automation = true
programming_language = "Python"
experiment_tracking = "MLflow"
include_deployment_templates = true

# Test 22: Virtualization Focus
[output."infra-virtualization"]
[output."infra-virtualization".answers]
project_name = "VM-Based Development"
short_name = "vm-dev"
description = "Project using virtualization for development"
author_name = "VM Administrator"
author_email = "vm@sysadmin.org"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = true
include_misc = false
include_virtualization = true
include_docker = false
include_cloud_deployment = false
include_automation = false
programming_language = "Both"
documentation_format = "Quarto"

# === ACADEMIC WRITING SUBCOMPONENTS ===

# Test 23: Presentations Only
[output."writeup-presentations"]
[output."writeup-presentations".answers]
project_name = "Conference Presentations"
short_name = "conf-present"
description = "Project focused on presentations"
author_name = "Presenter"
author_email = "present@conferences.org"
project_type = "Custom (choose components manually)"
include_analysis = false
include_writeup = true
include_infrastructure = false
include_misc = false
include_manuscript = false
include_presentations = true
include_grants = false
include_abstracts = false
include_posters = false
include_reports = false
include_blog = false
programming_language = "Python"
documentation_format = "Quarto"

# Test 24: Grants Focus
[output."writeup-grants"]
[output."writeup-grants".answers]
project_name = "Grant Applications"
short_name = "grant-apps"
description = "Project focused on grant writing"
author_name = "Grant Writer"
author_email = "grants@funding.org"
project_type = "Custom (choose components manually)"
include_analysis = false
include_writeup = true
include_infrastructure = false
include_misc = false
include_manuscript = false
include_presentations = false
include_grants = true
include_abstracts = true
include_posters = false
include_reports = false
include_blog = false
programming_language = "R"
documentation_format = "Quarto"

# Test 25: Posters and Abstracts
[output."writeup-posters-abstracts"]
[output."writeup-posters-abstracts".answers]
project_name = "Conference Materials"
short_name = "conf-materials"
description = "Project for conference posters and abstracts"
author_name = "Conference Participant"
author_email = "conference@research.edu"
project_type = "Custom (choose components manually)"
include_analysis = false
include_writeup = true
include_infrastructure = false
include_misc = false
include_manuscript = false
include_presentations = false
include_grants = false
include_abstracts = true
include_posters = true
include_reports = false
include_blog = false
programming_language = "Python"
documentation_format = "Quarto"

# Test 26: Reports and Blog
[output."writeup-reports-blog"]
[output."writeup-reports-blog".answers]
project_name = "Technical Communication"
short_name = "tech-comm"
description = "Project for technical reports and blogging"
author_name = "Technical Writer"
author_email = "techwriter@communications.org"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = true
include_infrastructure = false
include_misc = false
include_manuscript = false
include_presentations = false
include_grants = false
include_abstracts = false
include_posters = false
include_reports = true
include_blog = true
programming_language = "Both"
documentation_format = "Quarto"

# === DATA MANAGEMENT VARIATIONS ===

# Test 27: Data Validation Focus
[output."data-validation"]
[output."data-validation".answers]
project_name = "Data Quality Project"
short_name = "data-quality"
description = "Project focused on data validation"
author_name = "Data Quality Engineer"
author_email = "dataquality@engineering.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
data_versioning = false
data_validation = true
experiment_tracking = "None"
include_eda_templates = true
include_statistical_analysis = true
documentation_format = "Jupyter Notebooks"

# Test 28: DVC Without Validation
[output."data-versioning-only"]
[output."data-versioning-only".answers]
project_name = "Data Versioning Project"
short_name = "dvc-project"
description = "Project using DVC for data versioning"
author_name = "Data Engineer"
author_email = "dataeng@pipeline.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
data_versioning = true
data_validation = false
experiment_tracking = "MLflow"
include_data_pipeline = true
documentation_format = "Jupyter Notebooks"

# === PACKAGE DEVELOPMENT SCENARIOS ===

# Test 29: R Package Development
[output."package-dev-r"]
[output."package-dev-r".answers]
project_name = "Statistical R Package"
short_name = "stats-r-pkg"
description = "R package for statistical analysis"
author_name = "R Package Developer"
author_email = "rpkg@cran.org"
project_type = "Package Development (software/library)"
programming_language = "R"
github_actions = true
pre_commit_hooks = false
documentation_format = "RMarkdown"
include_testing = true
data_versioning = false

# Test 30: Multi-Language Package
[output."package-dev-multilang"]
[output."package-dev-multilang".answers]
project_name = "Multi-Language Scientific Package"
short_name = "multi-sci-pkg"
description = "Scientific package supporting both Python and R"
author_name = "Multi-Language Developer"
author_email = "multilang@science.org"
project_type = "Package Development (software/library)"
programming_language = "Both"
github_actions = true
pre_commit_hooks = true
documentation_format = "Quarto"
include_testing = true
include_deployment_templates = true

# === CI/CD AND AUTOMATION VARIANTS ===

# Test 31: GitHub Actions Only
[output."ci-gha-only"]
[output."ci-gha-only".answers]
project_name = "GitHub Actions Project"
short_name = "gha-project"
description = "Project with GitHub Actions CI/CD only"
author_name = "CI/CD Engineer"
author_email = "cicd@automation.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
github_actions = true
pre_commit_hooks = false
experiment_tracking = "None"
data_versioning = false
documentation_format = "Jupyter Notebooks"

# Test 32: Pre-commit Only
[output."ci-precommit-only"]
[output."ci-precommit-only".answers]
project_name = "Pre-commit Hooks Project"
short_name = "precommit-proj"
description = "Project with pre-commit hooks only"
author_name = "Code Quality Engineer"
author_email = "quality@code.org"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
github_actions = false
pre_commit_hooks = true
experiment_tracking = "None"
data_versioning = false
documentation_format = "Jupyter Notebooks"

# === ANALYSIS COMPONENT COMBINATIONS ===

# Test 33: Scripts Without Notebooks
[output."analysis-scripts-only"]
[output."analysis-scripts-only".answers]
project_name = "Production Scripts Project"
short_name = "prod-scripts"
description = "Analysis project using scripts instead of notebooks"
author_name = "Production Engineer"
author_email = "prod@engineering.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = false
include_misc = false
include_notebooks = false
include_scripts = true
include_data_pipeline = true
include_testing = true
include_packages = false
programming_language = "Python"
experiment_tracking = "MLflow"
data_versioning = true

# Test 34: EDA Templates Focus
[output."analysis-eda-focus"]
[output."analysis-eda-focus".answers]
project_name = "Exploratory Data Analysis"
short_name = "eda-focus"
description = "Project focused on exploratory data analysis"
author_name = "Data Analyst"
author_email = "analyst@data.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Both"
include_eda_templates = true
include_statistical_analysis = true
include_ml_components = false
experiment_tracking = "None"
data_versioning = false
documentation_format = "Quarto"

# Test 35: ML Components Focus
[output."analysis-ml-focus"]
[output."analysis-ml-focus".answers]
project_name = "Machine Learning Pipeline"
short_name = "ml-pipeline"
description = "Project focused on machine learning workflows"
author_name = "ML Engineer"
author_email = "mlengineer@ai.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
include_eda_templates = true
include_statistical_analysis = false
include_ml_components = true
experiment_tracking = "Weights & Biases"
data_versioning = true
data_validation = true
documentation_format = "Jupyter Notebooks"

# === EDGE CASES AND MINIMAL COMBINATIONS ===

# Test 36: Absolutely Minimal
[output."absolutely-minimal"]
[output."absolutely-minimal".answers]
project_name = "Bare Minimum Project"
short_name = "bare-min"
description = "Absolutely minimal project configuration"
author_name = "Minimalist User"
author_email = "min@example.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = false
include_misc = false
include_notebooks = true
include_scripts = false
include_data_pipeline = false
include_testing = false
include_packages = false
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false
data_validation = false
github_actions = false
pre_commit_hooks = false
documentation_format = "Jupyter Notebooks"

# Test 37: Maximum Everything (Stress Test)
[output."maximum-everything"]
[output."maximum-everything".answers]
project_name = "Maximum Feature Project"
short_name = "max-features"
description = "Project with every possible feature enabled"
author_name = "Feature Maximalist"
author_email = "max@features.org"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = true
include_infrastructure = true
include_misc = true
# Analysis components
include_notebooks = true
include_scripts = true
include_data_pipeline = true
include_testing = true
include_packages = true
include_eda_templates = true
include_statistical_analysis = true
include_ml_components = true
# Writeup components
include_manuscript = true
include_presentations = true
include_grants = true
include_abstracts = true
include_posters = true
include_reports = true
include_blog = true
include_publication_templates = true
# Infrastructure components
include_docker = true
include_cloud_deployment = true
include_virtualization = true
include_automation = true
include_deployment_templates = true
# Settings
programming_language = "Both"
documentation_format = "Quarto"
experiment_tracking = "Neptune"
data_versioning = true
data_validation = true
github_actions = true
pre_commit_hooks = true
include_jujutsu = true
include_fossil = true
use_hybrid_vcs = true

# ====== MIGRATION TASK TESTING SCENARIOS ======
# These scenarios test automatic cleanup during copier update
# They simulate projects that start with features enabled, then disable them

# === FOLDER REMOVAL TESTS ===

# Test 38: Migration - Remove Analysis Folder
[output."migration-remove-analysis"]
[output."migration-remove-analysis".answers]
project_name = "Remove Analysis Test"
short_name = "rm-analysis"
description = "Test removing analysis folder during update"
author_name = "Migration Tester"
author_email = "migrate@test.com"
project_type = "Manuscript Only (writing and publications)"
programming_language = "R"
documentation_format = "Quarto"
include_publication_templates = true
# This should trigger removal of analysis/ folder since project_type excludes it

# Test 39: Migration - Remove Writeup Folder  
[output."migration-remove-writeup"]
[output."migration-remove-writeup".answers]
project_name = "Remove Writeup Test"
short_name = "rm-writeup"
description = "Test removing writeup folder during update"
author_name = "Migration Tester"
author_email = "migrate@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
experiment_tracking = "MLflow"
data_versioning = true
# This should trigger removal of writeup/ folder since project_type excludes it

# Test 40: Migration - Remove Infrastructure Folder
[output."migration-remove-infrastructure"]
[output."migration-remove-infrastructure".answers]
project_name = "Remove Infrastructure Test"
short_name = "rm-infra"
description = "Test removing infrastructure folder during update"
author_name = "Migration Tester"
author_email = "migrate@test.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
# This should trigger removal of infrastructure/ folder for minimal starter

# Test 41: Migration - Custom Folder Removal
[output."migration-custom-folders"]
[output."migration-custom-folders".answers]
project_name = "Custom Folder Removal Test"
short_name = "custom-rm"
description = "Test removing specific folders in custom configuration"
author_name = "Custom Tester"
author_email = "custom@test.com"
project_type = "Custom (choose components manually)"
include_analysis = false
include_writeup = true
include_infrastructure = false
include_misc = false
include_manuscript = true
include_presentations = false
include_grants = false
include_abstracts = false
include_posters = false
include_reports = false
include_blog = false
programming_language = "Python"
documentation_format = "Quarto"
# Should remove analysis/, infrastructure/, misc/, and most writeup subdirectories

# === TOOL-SPECIFIC CLEANUP TESTS ===

# Test 42: Migration - Remove Docker Files
[output."migration-remove-docker"]
[output."migration-remove-docker".answers]
project_name = "Remove Docker Test"
short_name = "rm-docker"
description = "Test removing Docker files during update"
author_name = "Docker Tester"
author_email = "docker@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false
# Docker should be removed since infrastructure is not included in Analysis Only

# Test 43: Migration - Remove DVC Files
[output."migration-remove-dvc"]
[output."migration-remove-dvc".answers]
project_name = "Remove DVC Test"
short_name = "rm-dvc"
description = "Test removing DVC files when data versioning disabled"
author_name = "DVC Tester"
author_email = "dvc@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
experiment_tracking = "MLflow"
data_versioning = false
data_validation = false
# DVC files should be removed since data_versioning is false

# Test 44: Migration - Remove CI/CD Files
[output."migration-remove-cicd"]
[output."migration-remove-cicd".answers]
project_name = "Remove CI/CD Test"
short_name = "rm-cicd"
description = "Test removing CI/CD files during update"
author_name = "CI/CD Tester"
author_email = "cicd@test.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
github_actions = false
pre_commit_hooks = false
# Should remove .github/workflows and .pre-commit-config.yaml

# Test 45: Migration - Remove Experiment Tracking
[output."migration-remove-tracking"]
[output."migration-remove-tracking".answers]
project_name = "Remove Tracking Test"
short_name = "rm-tracking"
description = "Test removing experiment tracking files"
author_name = "Tracking Tester"
author_email = "tracking@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false
# Should remove MLflow, W&B, Neptune config files

# === LANGUAGE-SPECIFIC CLEANUP TESTS ===

# Test 46: Migration - Python Only (Remove R)
[output."migration-python-only"]
[output."migration-python-only".answers]
project_name = "Python Only Test"
short_name = "python-only"
description = "Test removing R files when switching to Python-only"
author_name = "Python Tester"
author_email = "python@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "MLflow"
data_versioning = true
# Should remove R-specific files: renv.lock, DESCRIPTION, .Rprofile, *.Rproj

# Test 47: Migration - R Only (Remove Python)
[output."migration-r-only"]
[output."migration-r-only".answers]
project_name = "R Only Test"
short_name = "r-only"
description = "Test removing Python files when switching to R-only"
author_name = "R Tester"
author_email = "r@test.com"
project_type = "Analysis Only (data science pipeline)"
programming_language = "R"
documentation_format = "RMarkdown"
experiment_tracking = "None"
data_versioning = false
# Should remove Python-specific files: requirements.txt, uv.lock, .python-version

# === VERSION CONTROL CLEANUP TESTS ===

# Test 48: Migration - Remove VCS Files
[output."migration-remove-vcs"]
[output."migration-remove-vcs".answers]
project_name = "Remove VCS Test"
short_name = "rm-vcs"
description = "Test removing alternative VCS files"
author_name = "VCS Tester"
author_email = "vcs@test.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
include_jujutsu = false
include_fossil = false
# Should remove .jjconfig.toml, _FOSSIL_, .fslckout

# === SUBCOMPONENT CLEANUP TESTS ===

# Test 49: Migration - Analysis Subcomponent Cleanup
[output."migration-analysis-subcomponents"]
[output."migration-analysis-subcomponents".answers]
project_name = "Analysis Subcomponent Test"
short_name = "analysis-sub"
description = "Test removing specific analysis subcomponents"
author_name = "Analysis Tester"
author_email = "analysis@test.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = false
include_misc = false
# Enable only some analysis components
include_notebooks = true
include_scripts = false
include_data_pipeline = false
include_testing = false
include_packages = false
programming_language = "Python"
experiment_tracking = "None"
data_versioning = false
# Should remove analysis/scripts/, analysis/data/, analysis/tests/, analysis/packages/

# Test 50: Migration - Writeup Subcomponent Cleanup
[output."migration-writeup-subcomponents"]
[output."migration-writeup-subcomponents".answers]
project_name = "Writeup Subcomponent Test"
short_name = "writeup-sub"
description = "Test removing specific writeup subcomponents"
author_name = "Writeup Tester"
author_email = "writeup@test.com"
project_type = "Custom (choose components manually)"
include_analysis = false
include_writeup = true
include_infrastructure = false
include_misc = false
# Enable only manuscript and reports
include_manuscript = true
include_presentations = false
include_grants = false
include_abstracts = false
include_posters = false
include_reports = true
include_blog = false
programming_language = "Python"
documentation_format = "Quarto"
# Should remove most writeup subdirectories except manuscript/ and reports/

# Test 51: Migration - Infrastructure Subcomponent Cleanup
[output."migration-infrastructure-subcomponents"]
[output."migration-infrastructure-subcomponents".answers]
project_name = "Infrastructure Subcomponent Test"
short_name = "infra-sub"
description = "Test removing specific infrastructure subcomponents"
author_name = "Infrastructure Tester"
author_email = "infra@test.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = true
include_misc = false
# Enable only Docker
include_docker = true
include_cloud_deployment = false
include_virtualization = false
include_automation = false
programming_language = "Python"
experiment_tracking = "None"
# Should remove infrastructure/cloud/, infrastructure/virtualization/, infrastructure/automation/

# === PROGRESSIVE DOWNGRADE TESTS ===

# Test 52: Migration - Downgrade from Full to Minimal
[output."migration-full-to-minimal"]
[output."migration-full-to-minimal".answers]
project_name = "Full to Minimal Test"
short_name = "full-to-min"
description = "Test downgrading from full academic to minimal starter"
author_name = "Downgrade Tester"
author_email = "downgrade@test.com"
project_type = "Minimal Starter (notebooks + basic writeup)"
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "None"
data_versioning = false
data_validation = false
github_actions = false
pre_commit_hooks = false
include_publication_templates = false
include_jujutsu = false
include_fossil = false
# Should remove infrastructure/, most tools, and complex features

# Test 53: Migration - Analysis to Manuscript Only
[output."migration-analysis-to-manuscript"]
[output."migration-analysis-to-manuscript".answers]
project_name = "Analysis to Manuscript Test"
short_name = "analysis-to-ms"
description = "Test switching from analysis-only to manuscript-only"
author_name = "Switch Tester"
author_email = "switch@test.com"
project_type = "Manuscript Only (writing and publications)"
programming_language = "R"
documentation_format = "Quarto"
include_publication_templates = true
experiment_tracking = "None"
data_versioning = false
# Should remove analysis/ folder and add writeup/ components

# === COMPREHENSIVE CLEANUP TESTS ===

# Test 54: Migration - Comprehensive Cleanup Test
[output."migration-comprehensive-cleanup"]
[output."migration-comprehensive-cleanup".answers]
project_name = "Comprehensive Cleanup Test"
short_name = "comprehensive-cleanup"
description = "Test comprehensive cleanup from maximum to minimal configuration"
author_name = "Cleanup Tester"
author_email = "cleanup@test.com"
project_type = "Custom (choose components manually)"
include_analysis = true
include_writeup = false
include_infrastructure = false
include_misc = false
include_notebooks = true
include_scripts = false
include_data_pipeline = false
include_testing = false
include_packages = false
programming_language = "Python"
documentation_format = "Jupyter Notebooks"
experiment_tracking = "None"
data_versioning = false
data_validation = false
github_actions = false
pre_commit_hooks = false
include_deployment_templates = false
include_jujutsu = false
include_fossil = false
# Should remove: writeup/, infrastructure/, misc/, most analysis subdirs, all tool configs