How to add a subdirectory that runs PHP scripts
In this example, we are adding a blog directory, perhaps to host wordpress.
Edit [eprint install dir]/archives/[archive]/cfg/cfg.d/urls.pl
Amend this line to include the directory you want to make an exception for.
Here we are adding the directory /blog/ to the array.
$c->{rewrite_exceptions} = [ '/cgi/', '/archive/', '/blog/'];
Save and close.
Edit: [eprint install dir]/archives/[archive]/cfg/apachevhost.conf
And add the following.
  Alias /blog/ /path/to/blog/
  <Location "/blog">
     AddHandler php5-script php
     DirectoryIndex index.php
  </Location> 
  <Directory /path/to/blog>
     Order allow,deny
     Allow from all
  </Directory>
