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The problem with precompiled headers in a project that includes both C and C++ code using CMake is that precompiled headers are language-specific and cannot be shared between C and C++. This means that if a project includes both C and C++ code, separate precompiled headers must be created for each language, which can lead to longer build times and increased complexity in the build system. Additionally, CMake does not have built-in support for creating precompiled headers, so it may require custom scripts or build rules.