Filters are ignored in index_userfiles and other index_* methods

[glatard]

Therefore these methods always return all the indexed elements. This is due to the new filtering mechanism in CBRAIN. These methods still use URLs such as "userfiles?id=1457457232&update_filter=filter_hash&clear_filter=filter_hash".

[prioux]

Done for ruby, need to be done with Perl api too.