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When using the batch compiler and access rules on the classpaths entries, they are not flushed between entries. This means that the subsequent entries get all previous access rules.
Created attachment 30619 [details] Proposed fix
Fixed and released in HEAD. No regression tests added since this is internal. The classpaths cannot be accessed from outside the batch package. To verify it, use the test027 in org.eclipse.jdt.core.tests.compiler.regression.BatchCompilerTest. Put a breakpoint line 168 and check the contents of the checkedClasspaths field for the batchCompiler object. You should check that the first entry (ClasspathDirectory) contains two access rules and the other one only one. Before the fix, the second one would contain 3 rules.
Verified for 3.2 M4 using build I20051212-0010