[CI/CD](GITIGNORE): Update .gitignore to include the new file extensi…

…ons to ignore

.gitignore

@@ -1,15 +1,7 @@
-# Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-# Visual studio code
 .vscode
-#Python compiled
 *.pyc
-
-# C extensions
-#*.so
-
-# Distribution / packaging
 .Python
 venv/
 env/
@@ -27,99 +19,46 @@ var/
 .installed.cfg
 *.egg
 nohup.out
-# Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
-
-# Unit test / coverage reports
 cover/
 htmlcov/
 .tox/
 .coverage
 .cache
 nosetests.xml
 coverage.xml
-
-# Translations
 *.mo
-
-# Mr Developer
 .mr.developer.cfg
 .project
 .pydevproject
-
-# Rope
 .ropeproject
-
-# Django stuff:
 *.log
 *.pot
-
-# Sphinx documentation
 docs/_build/
-# docs/html/
-# IDEA
-# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
-
-## Directory-based project format
 .idea/
-# if you remove the above rule, at least ignore user-specific stuff:
-# .idea/workspace.xml
-# .idea/tasks.xml
-# and these sensitive or high-churn files:
-# .idea/dataSources.ids
-# .idea/dataSources.xml
-# .idea/sqlDataSources.xml
-# .idea/dynamic.xml
-
-# File-based project format
 *.ipr
 *.iws
 *.iml
-
-# Additional for IntelliJ
 out/
-
-# generated by mpeltonen/sbt-idea plugin
 .idea_modules/
-
-# generated by JIRA plugin
 atlassian-ide-plugin.xml
-
-# generated by Crashlytics plugin (for Android Studio and Intellij)
 com_crashlytics_export_strings.xml
-
-# MACOSX
 .DS_Store
 .AppleDouble
 .LSOverride
-
-# nohup files
 .nohup.out
-
-# Test Files
 test/data/temp_results/
 testworkflow/
 testworkflow*
-
-# Gromacs
 \#*
 mdout.mdp
 traj_comp.xtc
-
-# ipynb checkpoints
 .ipynb_checkpoints
-
-# pycharm
 .idea
-
-# vscode
-.vscode
-
-# Pytest
-__pycache__/
 .pytest_cache/
-
-# MyPy
 .mypy_cache/
-
+reports/
+flake8-badge.svg
+.pytest_cache
+!ref_*.log