Here's an attempt to clean things up a bit. More could be done, but I think this modifies the worst features of the original template.
\documentclass[12pt,letterpaper]{article}
\usepackage{mathtools,amssymb}
\usepackage{graphicx,xcolor}
\usepackage{verbatim}
\usepackage{fancybox}
\usepackage{ulem}
\usepackage{enumitem}
% \usepackage{subfigure}% obsolete! use subfig or, better, subcaption
\usepackage{bbm}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{textcomp}
\newlength\normalparindent
\setlength\normalparindent\parindent
\usepackage{parskip,setspace}
\setstretch{1.3}
\usepackage[textwidth = 6.5in, textheight = 8.5in, marginparwidth=0pt, marginparsep=0pt, headheight=0pt, headsep=0pt, left=1in, top=1.2in]{geometry}
\usepackage{titling}
\newcommand{\Comment}[1]{{}}
\definecolor{MyDarkBlue}{rgb}{0.15,0.15,0.45}
\usepackage[linktocpage=true]{hyperref}
\hypersetup{
colorlinks=true,
citecolor=MyDarkBlue,
linkcolor=MyDarkBlue,
urlcolor=MyDarkBlue,
pdfauthor={John Smith},
pdftitle={SUBJECT},
pdfsubject={hep-th}
}
% use align rather than eqnarray
\newcommand{\nn}{\nonumber}
\newcommand{\gmu}{\gamma^\mu}
\newcommand{\gnu}{\gamma^\nu}
\newcommand{\glmu}{\gamma_\mu}
\newcommand{\gf}{\gamma^5}
\newcommand{\Tr}{\text{Tr}}
\newcommand{\qb}{\mathbf{q}}
\newcommand{\pb}{\mathbf{p}}
\newcommand{\kb}{\mathbf{k}}
\newcommand{\xb}{\mathbf{x}}
\newcommand{\pd}{(2\pi)^d}
\newcommand{\intx}{\int d^d \mathbf{x}\ }
\newcommand{\la}{\langle}
\newcommand{\ra}{\rangle}
\newcommand{\lb}{\left[}
\newcommand{\rb}{\right]}
\newcommand{\half}{\frac{1}{2}}
\newcommand{\pf}{(2\pi)^4}
\newcommand{\intkd}{\int \frac{d^Dk}{(2\pi)^D}\ }
\newcommand{\intpd}{\int \frac{d^Dp}{(2\pi)^D}\ }
\newcommand{\intpdo}{\int \frac{d^{D-1}k}{(2\pi)^{D-1}}\ }
\newcommand{\intl}{\int \frac{d^4l}{(2\pi)^4}\ }
\newcommand{\intld}{\int \frac{d^dl}{(2\pi)^d}\ }
\newcommand{\intle}{\int \frac{d^4l_E}{(2\pi)^4}\ }
\newcommand{\intp}{\int d^d \mathbf{p}\ }
\newcommand{\wsp}{\omega_{\mathbf{p}}}
\newcommand{\intpp}{\int \frac{d^d \mathbf{p}}{\sqrt{\pd 2\wsp}}\ }
\title{SUBJECT\thanks{This is a title.}}
\author{John Smith\textsuperscript{\itshape a,}\thanks{E-mail address: \Comment{\href{mail@mail.edu}}{\url{mail@mail.edu}}}}
\date{}
\pretitle{\begin{center}\LARGE\bfseries}% Note that your original settings do not get bold small-caps and would not do so even if this shape existed in bold for this font. If you want small-caps, change \bfseries to \scshape
\posttitle{\par\end{center}\vskip 10mm}
\preauthor{\begin{center}\large\scshape}
\postauthor{\par\end{center}\vskip 10mm}
\predate{}
\postdate{}
\renewcommand\maketitlehookc{\begin{center}\itshape\textsuperscript{a}Department,\par Address\par\end{center}\vskip 10mm}
\numberwithin{equation}{section}
\begin{document}
\setlength\parindent\normalparindent% Not at all clear this is wise with skip between paragraphs as well, but if you must, you must...
\maketitle\thispagestyle{empty}
\begin{abstract}
Abstract goes in here.
\end{abstract}
\clearpage
\tableofcontents
\clearpage
\section{Introduction}
\section{Conclusions}
\section{Acknowledgements}
\appendix
\section{Appendix 1}
\addcontentsline{toc}{section}{References}
\input{references.tex}
\end{document}

\usepackage{amsmath}– touhami Oct 18 '15 at 18:50\(and\)are working, no matter what I try. Please provide MWE, so we can figure out, where the problem is. – Wamseln Oct 18 '15 at 18:55\renewcommand{\(}{$}and\renewcommand{\)}{$}... But without MWE it's just guessing. – Wamseln Oct 18 '15 at 19:00\makeatletter\DeclareRobustCommand\({% \relax\ifmmode\@badmath\else$\fi}% \DeclareRobustCommand\){% \relax\ifmmode\ifinner$\else\@badmath\fi\else \@badmath\fi}\makeatotherafter\begin{document}– touhami Oct 18 '15 at 19:08\def\({\left(}and\def\){\right)}. I think you should change those in order to get back the usual\(and\)behaviour. – Wamseln Oct 18 '15 at 19:32epsfig,subfigureare obsolete and ought not be used. Page layout dimensions: usegeometryor a similar package rather than manual settings. Tow letter font switches are 20+ years deprecated and ought not be used in LaTeX code. Font switches do not take an argument. Almost never should\centerlinebe used in current LaTeX. Setting\parskipby hand is bad. If you really need this, useparskip. Don't use maths mode for text superscripts - there are better ways these days. If you must change the line spread, usesetspace. – cfr Oct 18 '15 at 19:37eqnarrayshouldn't be used. Usealignfrom amsmath instead. – Bernard Oct 18 '15 at 19:39