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I want Doxygen to ignore, bypass, not search the following directories of my project: */.svn/* */docs/* */Properties/* */bin/* According to the Doxygen FAQ : How can I exclude all test directories from my directory tree? Simply put an exclude pattern like this in the configuration file: EXCLUDE_PATTERNS = */test/* So, my Doxygen file looks like this: # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = */.svn/* \ */docs/* \ */published/* \ */bin/* \ */obj/* The output from Doxygen is: Searching for include files... Searching for example files... Searching for images... Searching for files in directory c:/Test_Fixtures/pc_application/docs Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/prop-base Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/props Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/text-base Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/tmp Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/tmp/prop-base Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/tmp/props Searching for files in directory c:/Test_Fixtures/pc_application/docs/.svn/tmp/text-base Searching for files in directory c:/Test_Fixtures/pc_application/docs/html Sea

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