Keep only one doxygen file. We keep the file build by Regis as it works both with Eclipse and with perl script, however we rename it to have a config file name that match the script name.
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# Doxyfile 1.6.1
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# Doxyfile 1.5.5
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# This file describes the settings to be used by the documentation system
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# This file describes the settings to be used by the documentation system
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# doxygen (www.doxygen.org) for a project
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# doxygen (www.doxygen.org) for a project
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