I am getting, what I think a permission error. What should the roundcube 
permissions be set to? Right now,
they are set as root, which should work, right?
Or, should I set them to have the same permissions as the apache "user"?

Right now I am getting this error..
Symbolic link not allowed or link target not accessible: 
/var/lib/roundcube/program, referer: https://mail.example.com/

Don't set the entire directory to the apache user. Any web exploit will allow 
an attacker to change the source files embedding things in your pages to then 
attack visitors to the site. Roundcube will work with files owned by root. You 
only need to give apache access to the temp directory.

    drwxr-xr-x  2 root   root    4096 Aug  5 13:25 bin
    drwxr-xr-x  2 root   root    4096 Aug 19 17:22 config
    -rw-r--r--  1 root   root   90022 Aug  5 21:56 favicon.ico
    -rw-r--r--  1 root   root   11214 Aug 28 16:11 index.php
    drwxr-xr-x 38 root   root    4096 Aug  6 19:00 plugins
    drwxr-xr-x  8 root   root      94 Aug  5 13:25 program
    drwxr-xr-x  3 root   root      83 Aug  5 13:25 public_html
    drwxr-xr-x  3 root   root      21 Aug  5 13:25 skins
    drwxr-xr-x  2 apache apache    23 Aug 23 20:12 temp
    drwxr-xr-x 14 root   root    4096 Aug  5 13:25 vendor

I have no idea what symlink is trying to be created inside the program 
directory, if that is what that error is about.

    drwxr-xr-x  7 root root   76 Aug  5 13:25 actions
    drwxr-xr-x  2 root root 4096 Aug 11 12:27 include
    drwxr-xr-x  3 root root 4096 Aug  5 13:25 js
    drwxr-xr-x  3 root root   23 Aug  5 13:25 lib
    drwxr-xr-x 89 root root 4096 Jul 23 16:17 localization
    drwxr-xr-x  3 root root  128 Aug  5 13:25 resources

Or is it complaining because your program directory is missing or denied by 
permission?
Compare your directories and permissions to mine above to see if anything 
stands out.
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