Since you cant change the existing html pages, every time a user clicks on a link in your template, it links to the html page directly, and not through your template.
Avoiding this cannot be one with a server side scripting language anyways.
It depends on the server you are using. You will have to force the server to run your template each time a link, above your template directly is clicked. Then read the url, and include the html page in your template.
Forcing the server to run your template first is server dependant.
If on apache you can use mod rewrite, or forcetype directives. theres alot on the topics on the net.
Your problem is similar to creating search engine friendly urls on dynamic pages.
So one of the existing solutions may work.
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