The error message about
~/.libreoffice/{3,4}/user/config/javasettings_Linux_*.xml is unrelated,
it is simply telling you libreoffice cannot find a JRE (but it will work
fine without it, for the most part).

What you're seeing is apparmor confinement finally working as intended. The 
package had been shipping apparmor profiles for some time, but they were not 
functional, and they have been fixed.
Those profiles allow reading/writing office documents in $HOME, /mnt and /media 
(that excludes /home2/).

Can you try running the following command in a terminal, and confirm
that this "fixes" your issue:

    sudo apparmor_parser -R

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  libreoffice cannot open a document not within $HOME

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