Arabic charachters are not generated in PDF with latex

Question

I'm using pandoc to generate PDF files and I've installed MiKTeX for latex libraries.

I have a .tex file contains Arabic and English charachters. when I compile the file it generates a PDF file without arabic charachters.
here's the command I execute:

pandoc --latex-engine=xelatex khaled.tex -o khaled.pdf

and here's the tex file content:

\documentclass{article}
\usepackage{fontspec}

\setmainfont[Ligatures=TeX]{Junicode}
\newfontfamily\arabicfont
    [Script=Arabic,        % to get correct arabic shaping
     Scale=1.2]            % make the arabic font bigger, a matter of taste
    {Scheherazade}         % whatever Arabic font you like

\newcommand{\textarabic}[1] % Arabic inside LTR
           {\bgroup\luatextextdir TRT\arabicfont #1\egroup}
\newcommand{\n}         [1] % for digits inside Arabic text
           {\bgroup\luatextextdir TLT #1\egroup}
\newcommand{\afootnote} [1] % Arabic footnotes
           {\footnote{\textarabic{#1}}}
\newenvironment{Arabic}     % Arabic paragraph
           {\luatextextdir TRT\luatexpardir TRT\arabicfont}{}

\begin{document}

English text ``\textarabic{جملة عربية وسط جملة إنجليزية}'' with Arabic in
between. English paragraph left aligned English paragraph left aligned English
paragraph left aligned English paragraph left aligned English paragraph left
aligned English paragraph left aligned English paragraph left aligned English
paragraph left aligned English paragraph left aligned English paragraph left
aligned English paragraph left aligned.

\begin{Arabic}
فقرة عربية محاذاة إلى اليمين فقرة عربية محاذاة إلى اليمين \n{١٢٣٤٥} فقرة عربية
محاذاة إلى اليمين فقرة عربية محاذاة إلى اليمين فقرة عربية محاذاة إلى اليمين
فقرة عربية محاذاة إلى اليمين فقرة عربية محاذاة إلى اليمين فقرة عربية محاذاة إلى
اليمين فقرة عربية محاذاة إلى اليمين فقرة عربية محاذاة إلى
اليمين\afootnote{حاشية عربية.} فقرة عربية محاذاة إلى اليمين.
\end{Arabic}

\end{document}

Answer 1

I'de like to thank @Alan Munn and @ShreevatsaR and @khaled Hosny for putting me on the road. I asked this question with zero knowledge in LaTeX and after 6 days in reading and trial&error, I've gathered enough information to lead the way :)

Solution:
first thing I did is using packages that are compatible with the XeLaTeX enging. I used \usepackage{polyglossia}

and finally passing the parameter lang:ar here is the full command line I've used:
pandoc --latex-engine=xelatex -V mainfont:"Amiri" -V lang:ar -V dir:rtl -H include.tex khaled.md -o khaled.pdf