The build of our Java 7 application failed today. Someone had referenced an internal Java implementation class within our code, namely com.sun.xml.internal.txw2.output.IndentingXMLStreamWriter. We use Eclipse, and this reference compiled and ran fine within the IDE. However, the PDE build would fail saying cannot find symbol. The difference can be explained when one realizes that the IDE compiles using the Eclipse compiler, but the PDE build uses javac.
However, one might still be stumped as IndentingXMLStreamWriter can be found within rt.jar. It turns out that javac does not actually compile directly against rt.jar. Instead, it references the file lib/ct.sym. This file is essentially a zip archive containing all of the "blessed" classes. IndentingXMLStreamWriter is not in that file.
It is best to avoid using internal implementation classes, but there is a work-around if one insists. The undocumented compiler argument -XDignore.symbol.file will use rt.jar directly.
The details of this mechanism can be found by inspecting the OpenJDK source files com.sun.tools.javac.main.RecognizedOptions and com.sun.tools.javac.file.JavacFileManager.