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I don't know if it is usual practice, but in my current project there are some directories that are not meant to be compiled, although required to be in the project. These directories have java files and eclipse finds errors like "The declared package does not match the expected package". I suggest that there could be some option to select some of those packages and select them not to be compiled.
We are currently working on this issue, see the newsgroup post on workspace structure evolution.
*** Bug 23992 has been marked as a duplicate of this bug. ***
*** Bug 23298 has been marked as a duplicate of this bug. ***
Implementation is planned to be made available for M4 at last (APIs for M3).
Improved API spec for IClasspathEntry.getExclusionPatterns (new for 2.1) JavaCore.newSourceEntry(IPath) JavaCore.newSourceEntry(IPath,IPath[]) (new for 2.1) IPackageFragmentRoot.getNonJavaResources IPackageFragment.getNonJavaResources IJavaProject.getNonJavaResources
JavaModel support got added. Builder is not yet there.
Tag as fixed once we have testcases proving it works.
Actually, this is a duplicate. *** This bug has been marked as a duplicate of 22039 ***