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It can happen that project or workspace directory differs from actual one where the source files are built. For example make can change actual directory using -C switch like eg. make -C ~/src/myapp all Include directories specified in the makefile are usually relative and the output parsers does not prefix them with whole path. The sequence of commands can look like this cd /my/nice/dir gcc -Dinclude -o output_binary /full/path/to/source.c and it needs to include /my/nice/dir/include instead of the relative one. Only workaround I know is to include absolute paths of these directories to CDT user settings but it would be nice if the parser can deal with this by itself.