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- Move bgm- and bgmCompare-specific C++ code into src/bgm/ and src/bgmCompare/ - Update build system to support C++ sources in subdirectories - Generate src/sources.mk at configure time to list all .cpp files - Include sources.mk from Makevars.in using portable (CRAN-compliant) rules
- Reorganize remaining C++ files into src/ subdirectories - Include headers relative to src/ and drop per-module -I flags
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This PR reorganizes C++ sources into subdirectories under src/, updates header includes to be path-qualified relative to src/, and simplifies the build configuration to use a single include root. The build remains fully portable and CRAN-compliant.