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Seems I forgot to add a link to the docs: http://www.klocwork.com/products/documentation/current/Replacing_the_path_to_your_source_files
A fully working commandline argument for a dummy test project:
kwbuildproject -j auto --tables-directory /tmp/test_tables --project testproject --replace-path /home/users/billiett/tmp/myproject/=/ klocwork.kwinject