From what I understand, Clean URL support in achieved through mod_rewrite using the following rule:
What that means is that URL's of the form http://somesite.com/node/view/1 are rewritten as http://somesite.com/index.php?q=node/view/1
According to RFC 2396 - Uniform Resource Identifiers (URI): Generic Syntax, Page 14, section 3.4,
3.4. Query Component
The query component is a string of information to be interpreted by
query = *uric
Within a query component, the characters ";", "/", "?", ":", "@",
"&", "=", "+", ",", and "$" are reserved.
Which means that the "/" character when it appears in the Query Component has to be escaped!
I read somewhere that Mozilla used to complain when it encountered an unescaped "/" character in the query component, but since IE did not seem to mind, they eventually turned a blind eye toward it too. So, having an unescaped "/" in the query component does not create an immediate problem.
That aside, if my interpretation is correct, then wouldn't the right thing (following standards) to do be escaping the "/" character in the query component, that is, shouldn't url() in includes/common.inc escape $url?