General clean up of unwanted repository files

[rofrano]

There are many binary, metadata, and other duplicate files in this repository that should never have been checked in like:

• Python binaries in multiple __pycache__ folders
• Sphinx _build folders
• Log files *.log
• Database binaries *.db
• Duplicate data folders like aca_db and ontologies
• OS specific metadata like .DS_Store

Once deleted, a proper .gitignore file should be added to keep these files out of the repo for good.