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The JDT's ..batch.FileSystem() constructor only accepts lowercase .zip and .jar and silently ignores other entries, which affects any such entry on the classpath. (Java and Javac both handle uppercase-suffixed files fine.) Test case checked in, uses libraries tests/bugs/extdirs/lib/uppercase.
This is a bug in the jdt batch compiler. This bug should be raised against org.eclipse.jdt.core. When they fix it we'll pick up their fix.
Done - see bug 50025. If this were resolved as LATER, then after incorporating their fix we'd have a trigger to revive the test, if not to add test cases for the many paths by which classpath entries are added.