I put the file inside a folder which is a symlink to another folder arm-linux-androideabi-gcc cannot find the file while regular cygwin gcc can.
Please ignore error from compilation on hello world.c with arm-linux-androideabi-gcc. Its just to illustrate that cygwin can find the files.
rjagannath@rjagannath /cygdrive/c/android-ndk-r8b
$ ls -al scratch
lrwxrwxrwx 1 rjagannath Domain Users 20 Aug 21 16:18 scratch -> /cygdrive/c/scratch/
=====================GCC Works ===========================
rjagannath@rjagannath /cygdrive/c/android-ndk-r8b
$ gcc hello_world.c
rjagannath@rjagannath /cygdrive/c/android-ndk-r8b
$ gcc scratch/hello_world.c
================arm-linux-androideabi-gcc DOES NOT WORK================
rjagannath@rjagannath /cygdrive/c/android-ndk-r8b
$ ./toolchains/arm-linux-androideabi-4.6/prebuilt/windows/bin/arm-linux-androideabi-gcc hello_world.c
In file included from hello_world.c:1:0:
c:\android-ndk-r8b\toolchains\arm-linux-androideabi-4.6\prebuilt\windows\bin\../lib/gcc/arm-linux-androideabi/4.6.x-google/include-fixed/stdio.h:50:23: fatal error: sys/cdefs.h: No such file or directory
compilation terminated.
rjagannath@rjagannath /cygdrive/c/android-ndk-r8b
$ ./toolchains/arm-linux-androideabi-4.6/prebuilt/windows/bin/arm-linux-androideabi-gcc scratch/hello_world.c
arm-linux-androideabi-gcc.exe: error: scratch/hello_world.c: No such file or directory
arm-linux-androideabi-gcc.exe: fatal error: no input files
compilation terminated.