I finally found what was wrong, and why ECJ couldn't compile like it should. I missed my modifications made to jva.io.VMFile, the native layer between Java files and Amiga files. With this in place, ECJ can now compile correctly. So, no more need to use jikes.
Connecting the dots
However, the file handling is not entirely solved just yet. I'm still pondering on how to solve the dot file, ".", denoting the current directory. I think it's a rather silly little marker; to me as an amigan it serves no real purpose. It just sits there. On unix, a path like "/dev/./././" is really just "/dev/". So, I don't really see the point (pun intended).
Anyhow, I think I have to handle it somehow, since there'll probably be a few applications assuming that it works (amongst them jamvm). The "/dev/" example also leads me to one such unix-amiga inconsistency. In the mauve test suite, a test exists involving files and URI's. The test wants the URI of file "/dev/tmp" to be just "/dev/tmp" (or rather the URI "file://dev/tmp"), whereas the current JAmiga implementation happily tries to make that into "file://SYS:System//dev/tmp/", when I guess it really should be just "file://dev/tmp/" (internally represented as "dev:tmp/"). And where AmigaDOS thinks the path "SYS:System//Utilities", really is "SYS:Utilities", JAmiga thinks its just "SYS:System/Utilities".