To disable the warning, use the xattr delete command:
xattr -d -r com.apple.quarantine /application/path/here
I downloaded Firefox from Chrome and was presented with the “application downloaded from the internet” warning every time I opened Firefox. To get rid of the warning, I ran the following command from the terminal:
sudo xattr -d -r com.apple.quarantine /Applications/Firefox.app
The xattr command manages attributes on files. The -d flag indicates that the com.apple.quarantine attribute should be deleted. The -r flag indicates that the attribute should be removed recursively from all files in the designated directory.