
### Source: Custom ###
logs/

### Source: Claude ###
docs/to_claude
docs/from_agents
docs/from_user
CLAUDE.md
.claude
mgmt
.mcp.json

### Source: Secrets ###
.git-crypt/keys
**/*secret*

### Source: Development ###
*old*
**/*old*
.old
**/.old
.dev
**/.dev
.playground
**/.playground
**/.legacy
.legacy

# Backup
**/*_back
**/*_backup
**/*_backups

# Renaming
**/.rename_backups

# Logs
*.log
**/*.log
**RUNNING**
**FINISHED**
**/RUNNING
**/FINISHED
**/202?Y-*

# TODO
**/TODO.md

# Memo
GITIGNORED

### Source: Emacs ###
**/*~undo-tree~
**/undohist/*

### Source: Apptainer ###
**/*.sandbox/*
**/*.sif
**/build-temp-*

### Source: LargeFiles ###
data/*

**/*.csv
**/*.mat
**/*.mp4
**/*.npy
**/*.pdf
**/*.pkl
**/*.png
**/*.pth
**/*.pt
**/*.chk
**/*.model
**/*.tiff
**/*.wav
**/*.jpg
**/*.jpeg
**/*.h5
**/*.zip
**/*.tar
**/*.gz
**/*.rar
**/*.7z
**/*.hdf5
**/*.npz
**/*.fits
**/*.avi
**/*.mov
**/*.mkv
**/*.gif
**/*.bmp
**/*.svg
**/*.psd
**/*.tif
**/*.raw
**/*.nii
**/*.dicom
**/*.xls
**/*.xlsx
**/*.doc
**/*.docx
**/*.ppt
**/*.pptx
**/*.txt
**/*.db
**/*.sqlite
**/*.xml
**/*.JNB
**/*.jnb

### Source: Python ###
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Sphinx documentation
docs/_build/
docs/sphinx/_build/
docs/sphinx/api/

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# pdm
.pdm.toml
.pdm-python
.pdm-build/

### Source: Emacs Global ###
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*
.org-id-locations
*_archive
*_flymake.*
/eshell/history
/eshell/lastdir
/elpa/
*.rel
/auto/
.cask/
dist/
flycheck_*.el
/server/
.projectile
.dir-locals.el
/network-security.data

### Source: SQL ###
**/*.db
**/*.sqlite3
*.db-shm
*.db-wal

### Source: GitKeep ###
!.gitkeep
!**/.gitkeep

# Allow doc/branding images and RTD requirements
!docs/**/*.png
!docs/**/*.svg
!docs/**/requirements.txt

# Allow example output artifacts
!examples/**_out/**

### Source: SLURM ###
slurm_logs

# Ruff cache
.ruff_cache/

# Pre-built docs (generated by sphinx-build)
src/*/_docs/
