Disable/change parts of com.arbortext.dita application?
I'm using Arbortext for DITA and, by and large, I'm really satisfied, but some of the pieces don't work quite right for my workflow. For example, some of the check completeness messages warn the writers of things that aren't, for us, problems.
If I copy the entire com.arbortext.dita application into my own custom directory so I can customize it, do I need to delete the default one that comes with Arbortext?
The DITA application is ingrained quite deeply into Arbortext, so I wouldn't mess with it too much if you can avoid it.
If you want to do a few tweaks then making a copy of the folder like you suggest may be the best bet. There is an environment variable APTAPPLICATION which can redirect where Arbortext looks for its "application" folder. That would allow you to work on your own copy of the DITA application without having to move or remove the default application folder.
I don't know what the best way would be to then roll out your DITA application customisations for production use. That would probably depend on the nature of the customisations.
You can copy the DITA application files into your custom directory to tweak them, and you don't need to nuke the versions in $ARBORTEXT/application/com.arbortext.dita to do so.
However, to minimize the impact of your customization, rather than just copying everything over wholesale, I would recommend trying to identify what specific files you need to customize and just move those. If you copy everything, you'll probably start running into problems next time you upgrade Arbortext. The less of the standard code you copy this way, the more likely it is that you'll be able to port your customizations to future upgrades of Arbortext.