This thread is resolved. Here is a description of the problem and solution.
Problem: client gets "It looks like languages per directories will not function" error when tries to enable languages per directories option
Solution: the message is more a notice than an error message. When checking the option, WPML does a quick test to check if everything will work. Sometimes this test says it won't work, but it's a false positive. The only way to be sure they won't work is trying activating them and see what happens.
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