Fix for cygwin compile

Hi,

I need this patch for compiling Simavr on Cygwin.
The patch fixes 2 issues:
- The Linux version is handled in the "else" branch in Makefile.common. I don't know the reason why, so I added an "ifneq" condition to prevent "no avr-libc root dir" failure. Later in the make file Msys is handled correctly.
- In simavr -Werror is turned on and isalpha and isdigit dies. An additional (int) cast is required.

After adding the patches:
make WIN=Msys
works.

Not sure what this "WIN=Msys" means (currently this is how Makefile.common handles Windows builds), but at least it compiles.