.gitignore

# Build artifacts and generated files
.ccache/
*.cached
*.deb
*.rpm
*.pyc
*.swp
# Temporary files generated during the unit tests have $NAME.tmp.$EXTENSION pattern
*.tmp.*
*.tmp

*.user
**/.DS_Store
_CPack_Packages
_deps
/bin
/lib

#These are the typical build directories
/build
/build-*/
/OpenMS-TOPP-GUI-build/

DartConfiguration.tcl
install_manifest.txt
Makefile
moc_*.cxx*

qrc_resources.cxx
qrc_resources.cpp
resources.qrc.depends

# Autogenerated files and directories (an in-source build)
/src/openms_gui/*_autogen
/src/tests/class_tests/openms_gui/*_autogen
/src/openms_gui/include/OpenMS/VISUAL/OpenMS_GUIConfig.h
/src/openms_gui/qrc_resources.cpp
/src/tests/class_tests/*/include/OpenMS/test_config.h

# Various test outputs
/src/tests/toppas/TOPPAS_out/
/src/tests/toppas/*.trf
/src/tests/class_tests/Testing/
/Testing/

thirdparty_licenses.txt

# Generated CMake files
cmake-*-build
cmake-build-*
cmake_install.cmake
CMakeCache.txt
CMakeDoxyfile.in
CMakeDoxygenDefaults.cmake
CMakeFiles
CPackConfig.cmake
CPackSourceConfig.cmake
CTestTestfile.cmake
OpenMSGUIConfig.cmake
OpenMSGUIConfigVersion.cmake
OpenMSGUITargets.cmake
# An in-source build copies cmake/Modules/ to the build root
/Modules/

# IDE and editor files
*.code-workspace
.cache/*
.clion.*
.idea
.qt/
.vs
.vscode

# Documentation build outputs (an in-source build)
/doc/html-gui/
/doc/doxygen/Doxyfile
/doc/doxygen/doxygen-error.log
/doc/doxygen/parameters/output/
Tutorial_ParamEditor_out.ini

# Log files
TOPP.log
TOPPAS.log

# Security - Credentials, tokens, and secrets
.env
.env.*
.env.local
.env.*.local
*.pem
*.key
*.p12
*.pfx
*.crt
*.cer
*.der
!*.crt.example
!*.key.example
credentials.json
credentials.yaml
credentials.yml
secrets.json
secrets.yaml
secrets.yml
secrets.toml
**/secrets/
**/credentials/
.secrets
.credentials
*.secret
*.secrets

# AWS
.aws/
aws_credentials
.boto

# SSH keys
id_rsa
id_rsa.pub
id_dsa
id_dsa.pub
id_ecdsa
id_ecdsa.pub
id_ed25519
id_ed25519.pub
*.ppk

# API tokens and keys
.npmrc
.pypirc
.netrc
.htpasswd
.htaccess
*.token
api_key*
apikey*
auth.json
auth.yaml
auth.yml

# Docker secrets
docker-compose.override.yml
docker-compose.*.yml
!docker-compose.example.yml

# Kubernetes
kubeconfig
*.kubeconfig
kube/config

# OAuth
oauth_token*
oauth-token*
client_secret*
client-secret*

# GPG
*.gpg
secring.*
pubring.*
trustdb.*

# Terraform
*.tfstate
*.tfstate.*
*.tfvars
!*.tfvars.example
.terraform/

# Ansible
*.vault
vault.yml
vault.yaml
group_vars/*/vault*
host_vars/*/vault*

# IDE credential storage
.idea/**/dataSources/
.idea/**/dataSources.ids
.idea/**/dataSources.xml
.idea/**/dataSources.local.xml

# Shell history (may contain credentials)
.bash_history
.zsh_history
.sh_history

# Local configuration that may contain secrets
config.local.*
settings.local.*
*.local.json
*.local.yaml
*.local.yml
*.local.toml

# Jupyter notebooks checkpoints (may contain credentials in outputs)
.ipynb_checkpoints/

# GitHub tokens
.github_token
github_token*

# Claude/AI tokens and session files
.claude_token
.anthropic_key
.claude/scheduled_tasks.lock

# Link checker cache
.lycheecache

# Lock files from external tools
*.fasta.lock