Switch to createCompilerDiagnostic for an invalid root file

Instead of reporting a file diagnostic when the user specifies a nonexistent file on the command line, we need to report a compiler diagnostic. This was found by the start/length assert in createFileDiagnostic, which was causing the compiler to crash. I think we should take this for release-1.1.
We don't want to report a file diagnostic if we are specifying a file on the command line. File diagnostics are only for ///<reference> or require in this case