If user has netbeans installed on disk D:
and he/she has folder D:/usr (actually "usr" folder at the same disk netbeans is
installed) Parser Settings for C/C++ compilers are wrong: paths are started with
/usr and all system header files are unresolved for all C/C++ projects.



org.netbeans.modules.cnd.makeproject.api.compilers.GNUCCompiler and
org.netbeans.modules.cnd.makeproject.api.compilers.GNUCCCompiler 
use the following code:
   if (platform.getId() == Platform.PLATFORM_WINDOWS) {
            if (new File("/usr/").exists())  // NOI18N
                includePrefix = ""; // NOI18N
            else if (new File("C:/cygwin").exists())  // NOI18N
                includePrefix = "C:/cygwin"; // NOI18N
            else if (new File("D:/cygwin").exists())  // NOI18N
                includePrefix = "D:/cygwin"; // NOI18N
            else if (new File("E:/cygwin").exists())  // NOI18N
                includePrefix = "E:/cygwin"; // NOI18N
            else if (new File("F:/cygwin").exists())  // NOI18N
                includePrefix = "F:/cygwin"; // NOI18N
        }

the value of  new File("/usr/").exists() is true in this particular case (you
run java from the same disk usr folder created at).

you can check with the simple test case that new File("/usr/").exists() will
return true, but new File("/usr/").getCanonicalPath() will return "D:\usr"

P.S. I have spend a half of day trying to understand what is wrong with  my
laptop and I had to debug C/C++ Dev Pack to understand the problem, I am not
sure our users will spend so much time trying to make it work, that's why I have
set priority to P2. The second reason I have set priority to P2 is the algorithm
used to convert system include paths doesn't look correct and will be failed if
we have non standard Cygwin installation for example.