Now I have another issue: unless I put full file path of font description xml (like "c:/temp/msmincho.xml"), FOP cannot find it. I thought that baseDir in userconfig.xml must set the folder to search for fonts, but it doesn't. What's the directory for FOP to search for files?
There is none. This is a known deficiency. The baseDir is used for the config files itself and for resolving relative URIs, as they occur in external-graphics.