This can't be the problem, because even if I don't set a font on my
config, the font which selected automatically by emacs is also rendered
disjointed. But to make sure this isn't the case, I removed two
compatible fonts that are automatically selected (namely, Vazir and
Noto, both of which have great Persian support). The default font is now
DejaVu
Mono, which is again rendered disjointed.

On Fri, 31 Jul 2020 at 09:44, Eli Zaretskii <eliz@gnu.org> wrote:

> > From: Sineau Gh <sineaugh@gmail.com>
> > Date: Fri, 31 Jul 2020 00:35:13 +0430
> > Cc: 42562@debbugs.gnu.org
> >
> > Here's some more info I have gathered. If I haven't set the default font
> in my config file, `M-x set-frame-font`
> > only works if there's already an open buffer in the frame. And if I
> visit a new file, the ligatures are rendered
> > broken again, although the font is the same. So I have to change the
> font again.
>
> If the problem comes and goes as you change fonts, then the problem is
> not with Emacs, it is with the fonts you are using: they should
> support Arabic shaping.  Emacs by default chooses suitable fonts for
> the Arabic script, but if you force Emacs to use certain font, you can
> disrupt the automatic font selection algorithm and choose a font that
> doesn't support Arabic shaping.
>
> The problems reported earlier existed with any font, and didn't
> disappear when a font was changed.
>