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The Meson Build System http://mesonbuild.com/
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meson/test cases/common/106 multiple dir configure .../meson.build

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project('multiple dir configure file')
subdir('subdir')
configure_file(input : 'subdir/someinput.in',
output : 'outputhere',
copy: true)
configure_file(input : cfile1,
output : '@BASENAME@',
copy: true)