X based applications (like Geany, LibreOffice, etc, i.e. with GUI, running via shortcuts in Desktop Apps scope), installed inside libertine, have got access to faked rootfs and to real home dir (/home/phablet). But terminal applications (like mc), installed inside libertine, have got access only to faked rootfs. Why is such difference? What is mechanism for X based applications? How can I grant access for the libertine terminal applications to real home dir?
exec is a hidden subcommand not meant for everyday use - you could use
libertine-launch to properly launch your application from the terminal:
libertine-launch my-container mc
my-container is the id of your container, and
mc is the name of your application.
The syntax has been updated as of libertine-tools version 16.10.20161005-0ubuntu1, where 16.10 is your current distro (15.10 on the current non-desktop devices):
libertine-launch --id my-container mc