I wanted to rename one of my files, mypage.php into myprofile.php, but PHPStorm does not find any file references.
In the code, mypage.php is referenced without the file extension. For example:
<a href='../user/mypage/'>
So it has to look for mypage, not mypage.php and rename it myprofile, without file extension.
How can I tell the program to do this?
IDE cannot do that because (as you have mentioned yourself) the file name does not match actual URL reference.
Your only option here is to use ordinary Find & Replace functionality, e.g. Replace in Path to find all occurrences of
/user/mypage/
and replace them into/user/myprofile/
in all files in a project (note; you can limit the scope for this action to a specific folder or custom scope -- check docs)