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Another way that you can modify the main menu and not affect the way that it does its magic is by modifying the template for it in the XOOPS Admin->System Admin->Templates manager. This template should be under the systems module. This way it will show up the same way under every theme that you have available.
system_block_mainmenu.html is the template that you will need to edit. Just look at the code to match up the css styles and you should be fine. I had to do this to add in a couple custom links to the user block.
le="color: #000000"><?php <table width="100%" cellspacing="0"> <tr> <td id="mainmenu"> <a class="menuTop" href="<{$xoops_url}>/"><{$block.lang_home}></a> <!-- start module menu loop --> <{foreach item=module from=$block.modules}> <a class="menuMain" href="<{$xoops_url}>/modules/<{$module.directory}>/"><{$module.name}></a> <{foreach item=sublink from=$module.sublinks}> <a class="menuSub" href="<{$sublink.url}>"><{$sublink.name}></a> <{/foreach}> <{/foreach}> <!-- end module menu loop --> </td> </tr> </table>
I supplied the original code for the main menu. Just add in your custom links after the last closing tag for the row.
le="color: #000000"><?php <table width="100%" cellspacing="0"> <tr> <td id="mainmenu"> <a class="menuTop" href="<{$xoops_url}>/"><{$block.lang_home}></a> <!-- start module menu loop --> <{foreach item=module from=$block.modules}> <a class="menuMain" href="<{$xoops_url}>/modules/<{$module.directory}>/"><{$module.name}></a> <{foreach item=sublink from=$module.sublinks}> <a class="menuSub" href="<{$sublink.url}>"><{$sublink.name}></a> <{/foreach}> <{/foreach}> <!-- end module menu loop --> </td> </tr> <tr> <td> <a href="<{$xoops_url}>/customlinklocation">custom link</a> </td> </tr> </table>
If you do that you should be good to go with custom links in your main menu.