I think there is not the best way how to do it. My experience is that if you firstly write software requirements, i.e. WHAT it should do (not HOW), in exact details, choosing proper technologies, data organization and coding become more clear.
Btw, your folder structure is good, in my opinion. - If it fullfils your requirements :>) You can inspire with Bugzilla project, also using CGI scripts and HTML::Template.
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