I have attached a sample document with problematic Hebrew taken from a 
few of the files.

> Am I to understand that if you type the same exact text into Emacs,
> there's no problem with the display?

Yes, that is correct.

>> gir1.2-harfbuzz-0.0. Is that the correct program?

(xft xfthb x)

> Emacs needs HarfBuzz the library, not the program.  What does the
> following produce inside the latest Emacs you built from Git:
>
>    M-: (frame-parameter nil 'font-backend) RET