.keystore and .jks are just file extensions: it's up to you to name your files sensibly. Some application use a keystore file stored in $HOME/.keystore: it's usually implied that it's a JKS file, since JKS is the default keystore type in the Sun/Oracle Java security provider. Not everyone uses the .jks extension for JKS files, because it's implied as the default. I'd recommend using the extension, just to remember which type to specify.