Since commit 328c0f65 (Simplify cmVisualStudio10TargetGenerator source classification, 2012-03-19) the VS 10 generator uses the cmGeneratorTarget source classification instead of directly getting the list of source files from the target. This accidentally dropped the CMakeLists.txt files from generated projects because they are added too late for cmGeneratorTarget. All generator-specific source files must be added to targets prior to cmGeneratorTarget construction. Refactor addition of the CMakeLists.txt files with CMake re-run custom commands to take place before normal generation begins, and therefore early enough to be included in the cmGeneratorTarget classification.
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