Well, here are some more thoughts why the way you are shipping your custom portal-ext.properties file in the ROOT folder is NOT a good idea.
If you deploy an EXT plugin, which modifies the Portal Source itself, and you ship portal.properties with it, the portal-ext.properties file will get overridden and all the customization you have done are lost.
If you redeploy an Ext Plugin you will have to delete the whole ROOT Folder and start with a fresh install. This will result in the loss of the portal-ext.properties file as well. You would have to have the foresight, to backup the ROOT folder of your installation. To be honest: I didnt and started swearing.
Wouldn't it be better, if you leave the property files at the location and include the include-and-overwrite directive in there?
Just a few thoughts. No offence intended ;)
And another Thing:
in your portal-ext.properties is the directive:
which leads to the following:
the directory for the document_library would be:
I think this is a slight mistake there ;)