# Build and documentation
docs/build/
Manifest.toml

# OS files
.DS_Store
**/.DS_Store

# Editor files
.vscode/
.idea/

# 3rd party tool directories
.augment/

# Temporary files
*.tmp
*.temp
tmp_output_*.ms
*_output/

# Example outputs
Examples/**/inputs.ms
Examples/**/outputs.ms
Examples/**/*.png
Examples/**/*.pdf

# All image files
*.png
*.jpg
*.jpeg
*.gif
*.bmp
*.svg
*.tiff
*.tif
*.webp
*.ico
*.heic
*.heif

# Exception: Documentation illustration assets
!docs/src/assets/plots/*.png

# Notebooks not ready for public release
Examples/Notebooks/AnisotropicGridComparison.ipynb
Examples/Notebooks/Triple_Graph*.ipynb

# Data outputs
data/figures/

# SSH and server configuration - NEVER COMMIT THESE
*.pem
*.key
*_rsa
*_ed25519
*_ecdsa
id_*
ssh_config
server_config.sh
cluster_config.sh
fileserver_config.sh
.ssh/
ssh_keys/

# Server connection scripts with credentials
*_server_connect.sh
*_cluster_connect.sh
*_fileserver_connect.sh

# Additional security patterns
*password*
*secret*
*token*
*credential*
*.p12
*.pfx
config.ini
settings.ini
.env*
!.env.example

# Node.js dependencies
docs/node_modules/
docs/package-lock.json

# Python cache
__pycache__/
*.pyc
*.pyo
*.pyd
.Python

# Claude Code cache and memory
.cache/
.claudemem
.claude/

# Build artifacts and temporary directories
build_*/
bundle_*/
*_bundle/
*.tar.gz
*.zip

# Log files and job outputs
*.out
*.err
*.log
globtim_*_tests_*.out
globtim_*_tests_*.err

# Temporary Julia scripts and debugging files  
analyze_*.jl
create_*.jl
extract_*.jl
fix_*.jl
!scripts/fix_test_manifest.jl
test_*.jl
!test/test_*.jl
verify_*.jl
debug_*.jl
*_debug.jl
*_validation.jl
*_test.jl
simple_*.jl
investigate_*.jl
hpc_*_debug.jl

# SLURM job files
*.slurm
slurm-jobs/

# Cleanup analysis files (temporary - archive when complete)
*_CLEANUP_ANALYSIS.md
*_WORKFLOW_ANALYSIS.md

# Temporary analysis and collection files
comprehensive_collection_analysis.jl
simple_collection_analysis.jl
actionable_optimization_plan.jl

# Temporary output and result directories (preserve in proper locations)
node_experiments/
*/outputs/
*/results/

# Generated experiment files (auto-generated from templates)
experiments/generated/*.jl

# Result data files (JSON/CSV/PNG outputs)
*_results.json
*_summary.json
*_analysis.csv
*_index.json
*_convergence_analysis.png
*_critical_point_analysis.png

# Archive and backup directories
archives/
backup_*/
archive_*/
*_archive_*/
cluster_results_*/
collected_*_results/
*_comparison_results/

# Experiment results - DEPRECATED legacy directories (use GLOBTIM_RESULTS_ROOT instead)
# These are kept in .gitignore for backward compatibility only
# New experiments should use standardized paths via OutputPathManager
hpc_results/
test_results/
local_results/

# Note: With standardized output system, experiments write to:
#   $GLOBTIM_RESULTS_ROOT/{objective_name}/{experiment_id}_{timestamp}/
# This directory is outside the repository and doesn't need .gitignore
