In the lines 192,193 of project I have following lines are in the original template given by department (I did not touched them they are as it is)
\usepackage[bookmarksnumbered,pdfpagelabels=true,plainpages=false,colorlinks=true,
linkcolor=black,citecolor=black,urlcolor=blue]{hyperref}
and lines 85 to 88 is what I added to break long urls in bibliography.
\usepackage{url}
\usepackage{breakurl}
\usepackage{hyperref}
\def\UrlBreaks{\do\/\do-}
The problem is now I get option clash for package hyperref.I am doing this in overleaf.
The package is defined two times.
In this case what should I do so that in bibliography I can get the URLs in next line without any problem.
If I comment line 193 with % and then I generate the pdf then the problem is that all table of contents,table of figures and lists have red color square boxes around them.
Here is a screenshot

The template which department gave me can be seen here on this link full.
So that if some thing I should have mentioned but I did not then you can see thesis.tex file,
on above link.