[digiown]

It is quite hard to do this safely on typical Linux systems, since there is a substantial amount of writable system data (e.g. syslog, /etc, /var). If unencrypted they will leak data, and if encrypted there is little difference from just encrypting the root.

[hparadiz]

You encrypt the entire partition with LUKS. Not individual folders and files.

[ndsipa_pomu]

A typical linux system will have everything in one partition and even if you do like to split up the system (for historical re-enactment?) it wouldn't matter as you'd be encrypting the whole disk anyway.