mysql has the following synonyms: my-sql and mysql-query. However, mysql-query seems to still have its own life, questions and followers. Shouldn't the entire tag and its questions and followers be merged into mysql since it's a synonym?
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This just means the tags need to be merged at some point.
It's not a bug.
Regarding, mysql-query & java-api, synonyms process is done by community votes. (batch merging can be done by moderators only, so it moderator didn't involve the tag synonyms process, they won't notice they need to do merging for those tags, right away, isn't it?)
New questions will be automatically mapped, IMHO, but for existing questions, moderators need to merge them instead.