When I generate the link directory, I set the file extensions for the generated files to be .tpl.php (as opposed to .php alone). This is because the e-commerce software I'm using places the content of pages into files with those extensions. Link Assistant generates these files with those extensions with no problem.

However, in the e-commerce software I'm using (which is a very well known one) for each .tpl.php file, there is a corresponding file with the exact same name but which only has the .php extension. These are the files that visitors are supposed to navigate to (not the .tpl.php files). This causes a problem in Link Assistant because it creates hyperlinks with the .tpl.php extension (obviously because that is how I configured it when making the template). Navigating to the .tpl.php version of the page gives a dead page though.

Other than manually changing the hyperlinks each time, is there a way to make it so that the generated pages of the link directory keep the .tpl.php extension but all created hyperlinks have the .php extension only?

Unfortunately right now this can not be done with LinkAssistant. However there's a fast way to do that - for instance (on Windows) you can click Start -> Run > "cmd" and then type in the commander

cd YOUR_FOLDER_THE_DIRECTORY_WAS_SAVED_TO

and then when in that directory type

rename *.php *.tpl.php

All the files will be renamed at once.

Actually I just stuck to the easiest way: In the Template Server-Side Settings tab, I simply typed tpl. in front of the php so the extension now reads tpl.php

Link Assistant was capable of this after all. It'd be nice to have the option to add a custom extension in a future version though...

Glad that worked for you as well!