Due to two old TokuDB issues and different data formats/sizes for temporal types between 5.5 and 5.6, there is no supported in-place procedure to migrate across MySQL variants and versions. Unfortunately, the only safe and supported way to move to Percona Server 5.6 or 5.7 is a logical dump and reload.
All future TokuDB/PerconaFT bug fixes and new features will be introduced only in Percona Server 5.6/5.7. MariaDB 10.1 is also maintaining a branch of the Percona Server TokuDB storage engine much like they do with Percona XtraDB (InnoDB replacement).
Bugs for TokuDB/PerconaFT can currently still be reported at https://tokutek.atlassian.net or on launchpad at https://launchpad.net/percona-server