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According to REP 103, all coordinate frames are right-handed. The "standard" base_link setup actually has x forward, y left, and z up. That's what I would suggest transforming your frames to.

AFAIK, tf has no support for left-handed frames. Some of the libraries with geometry support that are common in ROS (bullet, Eigen, transformations.py, KDL, etc.) may have some support for transformations with rotations not strictly in SO(3) (such as mirroring transformations), but unless you really have some good reason for getting into this, I think it's best to avoid.