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ok - there seems to be a bit of confusion about how to best modify templates. When a module is installed, all defined templates for that module are inserted into the database, where they can be seen in "System" -> "Templates". If you want to modify a template, instead of modifying the files in /modules/<modulename>/templates, you can modify them in the database by:
First. Clone the default template set. Go to "System" -> "Templates" and click [ Clone ] for the default template set.
This template set will hold all our custom changes.
Second. Edit your template. If you click on "[List]" next to "System", you will see a long list of templates. Page templates are displayed at the top, block templates are displayed at the bottom. In your particular example, you want to modify the Main Menu Block - "system_block_mainmenu.html" in the block section.
To add links to your main menu block add the appropriate html code after
<!-- end module menu loop -->
To make them look just like the other modules in the main menu block your code should look like this:
<a class="menuMain" href="yoururl">Your Title Goes Here</a>
Third. Set this new template set as the default.Go to "System" -> "Preferences" -> "General Settings" and change the "Default Template Set" property to our new template set.
If the above seems too daunting for you, I highly recommend downloading the iMenu module, which lets you define Main Menu links in the administration panel.