I have a Virtual Private Server and I want to backup all files in these directories:
/etc
/usr/local
/home
Is the best way to accomplish this to run Duplicacy as root, and to make the repository in / (so the Duplicacy config is in /.duplicacy), and to use this filter config:
+etc/*
+usr/local/*
+home/*
Or is there a better way?
I would create a directory in your users home and symlink those locations you want to backup into that folder.
Duplicacy follows first level symlinks.
That said, stuff worth backing up in /etc and /use/local is configuration, that can be saved manually after initial setup. I would not backup those folders.
Does your VPS provider offer instance snapshotting? That would be more useful and atomic way to accomplish way-back machine for your instance.