When building a project in Atmel Studio, and if you get an error like the one as follows
<some file>.o: No such file or directory
during the linking stage, then it could be because of the number of characters in the command line. Windows expects that the command line be less than 8192 characters. But when Atmel studio executes the build using Make.exe then there are chances that the number of include directories could be more and hence the command executed by make file has length > 8192 characters. The workaround is to rename the folder(s) so that things works smoothly (or) use mapped letters for include directories.
We are aware of it and would be getting this fixed in the future. J Until then we are sorry for the inconvenience.
Have a good time with studio