[Bug 205093] databases/mysql56-server: First run misplaces my.cnf directly into /usr/local/

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=205093
Bug 205093 depends on bug 216244, which changed state.

Bug 216244 Summary: update mysql56 to the most recent version + use system libs instead of bundled + backport changes of mysql57
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=216244

           What    |Removed                     |Added
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             Status|Open                        |Closed
         Resolution|---                         |FIXED

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