There is a directory of files that you want to encrypt it, then simply work with those files and encrypt it again. Is there a simple tool for that? yes encfs is the thing you are looking for.

mkdir -p .encrypted
encfs `pwd`/.encrypted `pwd`/data

This command will ask you a few questions then mount .encrypted into data. you can work with data, copy files and encfs stores encrypted data in .encrypted.

After that run below command to unmount:

encfs -u data

Mount your data directory with this command: (this time it only asks for passphrase)

encfs `pwd`/.encrypted `pwd`/data