Instead of using negative lookahead, sometimes it's easier to use the negation outside the regex at the hosting language level. In many languages, the boolean complement operator is the unary !.
So you can write something like this:
! str.hasMatch(/\.php$/)
Depending on language, you can also skip regex altogether and use something like (e.g. Java):
! str.endsWith(".php")
As for the problem with the original pattern itself:
(.*?)(?!\.php)$   // original pattern, doesn't work!
This matches, say, file.php, because the (.*?) can capture file.php, and looking ahead, you can't match \.php, but you can match a $, so altogether it's a match! You may want to use look behind, or if it's not supported, you can lookahead at the start of the string.
^(?!.*\.php$).*$  // negative lookahead, works
This will match all strings that does not end with ".php" using negative lookahead.
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