Although drag&drop can be very handy, it will not work well in general as ColladaConv does not know the base path to which all resource paths should be relative.
Another thing you could do is creating a small batch file which processes you repository or just a part of it. The following bat file for example, located in Horde's Win32 folder, would compile all models and animations in 'repository' and output them to 'content' where the sample assets are located.
Code:
ColladaConv models -type model -base "../repository" -dest "../content"
ColladaConv animations -type anim -base "../repository" -dest "../content"