I also have this issue.
I'm using IDE 1.6.7, on Windows 10
I get the following error message:-
C:\Users\blah\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.15\cores\arduino/Arduino.h:48:17: fatal error: sam.h: No such file or directory
#include "sam.h"
I have seen others with the same issue are able to resolve it by removing the samd directory and then re-installing. I have tried this but not got any further.
I've tried both early and later versions of code - same issue
Google has shown that others have had this issue, but the solutions nearly always seem to be that of re-installing the board in Board Manager.
I can see the MKR1000 in the Com port list, so I know that at least that bit works.
Any ideas, anyone?