As author of xili-language, I understand your long beginning road. xili-language trilogy is free published since more than 5 years in a contributive approach where I feedback my experience (and long period of works) with WordPress in multilingual context - see this text explaining... -
Flags, for us is a style approach depending of context strategy (flag means country or language ?? ), design and selected theme (from huge available list). The solution is currently in css. In menu or widget, xili-language adds class available for css designing. As in twenty fourteen xili child theme presented as free example, more powerful mechanisms are implemented. (see previous cited link).
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