CleanCache causes incorrect paths to CSS/JS files
After running php cleanCache.php all, none of the CSS or JavaScript files on my Magento site were loading, both on the site itself and in the admin site.
Looking at the generated source code, I saw that the links looked something like this:
/var/www/skin/frontend/default/mystuff/css/bootstrap.css
They should properly look like this:
http://example.com/skin/frontend/default/mystuff/css/bootstrap.css
Following this StackOverflow answer got the site working again - just changing the two *merge* options and clearing the cache again did the trick.
Any idea why this happens? The original script had a comment describing the same issue, where it is suggested that there is a permissions problem. However, that is certainly not the case on my machine where all commands are run by the same user that owns the files (and the webserver runs as that same user too).
What else could be going on here?
Just used this script and confirm that this bug still exist.

This is how console reports all missing js and css and how backend looks like
+1 and not a permissions problem
Also cleanDataCache wouldn't work so I swapped that with Mage::app()->getCacheInstance()->flush();