I have found the solution which solves my purpose. Hope this helps somebody. Bugzilla now, does not create auto-link for protocols which are not in its list of safe protocols.
Since I was trying to link a file, the 'file' protocol needs to be added to the list of safe protocols. So, I added it to the list which is in the file 'Bugzilla/Constants.pm'.
Now, when I type 'file://', Bugzilla creates the auto-link.
(All this is done in the 'Comments' section).