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Exclude the directories in .gitignore from clang-formatting

Bas van der Tol requested to merge exclude-gitignored-files-from-formatting into master

The run-clang-formatting.sh script excludes certain directories, but it does try the format files in for example the build subdirectory. This directory is in the .gitignore file. It seems sensible to exclude the directories that are ignored by git from formatting as well.

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