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Are the resource supposed to be in the classpath? Or are they just extra
files that you had for other purposes but happen to be in the source
directories.
If it is (1), then they need to be copied. If it is (2), they should be
moved out of the source folders to non-source folders in the project.
(There are exclusion filters that can be used to exclude copy certain
files, but if you have a lot of them, the filter could be cumbersome to
create or get over aggressive).
If you want to try out the exclusion patterns, go to the
project->Properties->Java Build Path. Select Source tab, expand the
source folder, you will see (Exclusion filters), click on it and then
the "Edit" button.