-*.c filter=uncrustify
-*.cpp filter=uncrustify
-*.h filter=uncrustify
-src/contrib/* !filter
-nb_kernel_Elec* !filter
+# Generic rules
+*.c filter=uncrustify gmx-doxygen
+*.cpp filter=uncrustify gmx-doxygen
+*.cu filter=uncrustify
+*.h filter=uncrustify gmx-doxygen
+*.cuh filter=uncrustify
+CMakeLists.txt filter=copyright
+*.cmake filter=copyright
+*.cmakein filter=copyright
+*.py filter=copyright
+*.l filter=includesort
+*.y filter=includesort
+*.pre filter=includesort
+*.tex filter=copyright
+*.bm filter=copyright
+# Exceptions: extra files to include
+admin/*.sh filter=copyright
+admin/git-pre-commit filter=copyright
+# Exceptions: files to exclude
+*.pc.cmakein !filter
+cmake/CheckC*CompilerFlag.cmake !filter
+cmake/FindBLAS.cmake !filter
+cmake/FindLAPACK.cmake !filter
+cmake/ThreadMPI.cmake !filter
+cmake/Platform/BluegeneQ*.cmake !filter
+cmake/*.c -filter -gmx-doxygen
+cmake/*.cpp -filter -gmx-doxygen
+cmake/*.c.cmakein !filter
+docs/doxygen/Doxyfile-*.cmakein !filter
+docs/doxygen/*.cpp !filter
+docs/doxygen/examples/*.cpp filter=uncrustify_only
+docs/doxygen/examples/*.c filter=uncrustify_only
+docs/manual/UseLATEX.cmake !filter
+scripts/GMXRC.* !filter
+scripts/make_gromos_rtp.py !filter
+src/contrib/* -filter -gmx-doxygen
+src/external/* -filter -gmx-doxygen
+src/gromacs/gmxlib/nonbonded/preprocessor/gmxpreprocess.py !filter
src/gromacs/linearalgebra/gmx_blas/* !filter
src/gromacs/linearalgebra/gmx_lapack/* !filter
-src/gromacs/selection/parser.cpp !filter
-src/gromacs/selection/parser.h !filter
-src/gromacs/selection/scanner.cpp !filter
-src/gromacs/selection/scanner_flex.h !filter
+src/gromacs/selection/parser.cpp -filter -gmx-doxygen
+src/gromacs/selection/parser.h -filter -gmx-doxygen
+src/gromacs/selection/scanner.cpp -filter -gmx-doxygen
+src/gromacs/selection/scanner_flex.h -filter
+nb_kernel_Elec* filter=copyright -gmx-doxygen
+nb_kernel*pre filter=copyright
+*.eps binary
+*.jpg binary
+*.svg binary
+*.png binary
+*.pdf binary
+*.ogl binary
+*.gif binary
+*.jpg binary
+*.tpr binary
+*.trr binary
+*.tng binary
+*.xtc binary
+*.edr binary
+*.cpt binary