Yes, I have rewrite rule which assures that links without index.php work properly. But now I want ez to generate links without index.php suffix. Modifying templates (menus, links to content views, etc.) is an easy task - i just use ezroot operator instead of ezurl. But links to content that are generated through eznode protocol in ezxml datatype are handled somewhere deeply. Anyone who has a clue where?
Override content/datatype/view/ezxmltags/link.tpl, ask for a copy of the original (not a blank file), then edit that template and bingo, you can customize all links inside XML blocks.
What you want is done by changing ezurl with ezroot, but you can think of more advanced uses, such as explicitly marking external links (that lead off-site).