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Using M3 and a JDK 1.4 as my default libraries, I get this warning and I cannot get rid of it. Incompatible .class files version in required binaries. Project 'org.eclipse.jdt.core.tests.formatter' is targeting a 1.1 runtime, but is compiled against 'D:JDKs/jdk1.4.1_02/jre/lib/ext/ldapsec.jar' which requires a 1.4 runtime. My compiler settings for this project is to ignore incompatible required binaries.
Cannot reproduce. Once using custom project settings, these go away, no matter whether the preference is enabled on workspace settings.
Reproduced. Problem is induced by dependent projects having this warning enabled.
Side problem: there were 2 occurrences of the complaint about incompatible .classfile versions for rt.jar. This comes from the fact that the validation code was recursing in containers, then re-processing entries one by one and revalidating them (so as to accumulate problems).
Fixed both issues.
Verified.