Why are many of my apps now called "<name>.app"
Solution 1:
Finder > Preferences > Advanced > [] Show all filename extensions
This is an interface-wide setting, any display of a filename will display the associated extension.
If desired, a per-file setting is available in that file's Get Info dialog from Finder.
Edit: Adding a screenshot showing what I have Hazel doing as I mentioned above. This runs on both my Documents directory and my Google Drive directory.