I have installed Netbeans on both my Windows 8 machine, and a Ubuntu VM to see if the errors were consistent and they are. After I install Netbeans, I can run a short script and everything is fine. If I add a file to the program, Netbeans breaks and becomes unusable. My Cygwin is set up correctly with all the appropriate plugins (as far as I know). Also, my libraries are not being loaded correctly. "Cannot find include file " or any other one.
"/usr/bin/make" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory '/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++'
"/usr/bin/make" -f nbproject/Makefile-Debug.mk dist/Debug/Cygwin_4.x-Windows/c__.exe
make[2]: Entering directory '/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++'
mkdir -p dist/Debug/Cygwin_4.x-Windows
g++ -o dist/Debug/Cygwin_4.x-Windows/c__ build/Debug/Cygwin_4.x-Windows/main.o build/Debug/Cygwin_4.x-Windows/test.o
build/Debug/Cygwin_4.x-Windows/test.o: In function `main':
/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++/test.cpp:9: multiple definition of `main'
build/Debug/Cygwin_4.x-Windows/main.o:/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++/main.cpp:15: first defined here
collect2: error: ld returned 1 exit status
nbproject/Makefile-Debug.mk:63: recipe for target 'dist/Debug/Cygwin_4.x-Windows/c__.exe' failed
make[2]: *** [dist/Debug/Cygwin_4.x-Windows/c__.exe] Error 1
make[2]: Leaving directory '/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++'
nbproject/Makefile-Debug.mk:60: recipe for target '.build-conf' failed
make[1]: *** [.build-conf] Error 2
make[1]: Leaving directory '/cygdrive/c/Users/Sean/Documents/NetBeansProjects/C++'
nbproject/Makefile-impl.mk:39: recipe for target '.build-impl' failed
make: *** [.build-impl] Error 2
BUILD FAILED (exit value 2, total time: 479ms)