Back up the new directory with the encrypted data:
$ tar c newdir
Discussion Method 1 produces a backup that may be considered fragile: one big encrypted file. If part of the backup gets corrupted, you might be unable to decrypt any of it.
Method 2 avoids this problem. The cp -l option creates hard links, which can only be used within a single filesystem. If you want the encrypted files on a separate filesystem, use symbolic links instead:
Note that a full, absolute pathname must be used for the original directory in this case.
gpg does not preserve the owner, group, permissions, or modification times of the files. To retain this information in your backups, copy the attributes from the original files to the encrypted files, before the links to the original files are deleted:
The Linux Security Cookbook includes real solutions to a wide range of targeted problems, such as sending encrypted email within Emacs, restricting access to network services at particular times of day, firewalling a webserver, preventing IP spoofing, setting up key-based SSH authentication, and much more. With over 150 ready-to-use scripts and configuration files, this unique book helps administrators secure their systems without having to look up specific syntax.