In FeynCalc (like in FORM or Schoonship) there is in principle
no distinction of contra- and covariant indices for gamma-matrices and metric tensors.
It is just the MakeBoxes-rules I once attached such that DiracMatrix[mu]
displays with a superscript. Internally it is just DiracGamma[LorentzIndex[mu]] and contraction is performed on repeated indices.
Of course, with Levi-Civita tensors the story is different, but this
is a different topic.
If you are calculating scalar quantities, it does not matter where you put indices (at least if you have Lorentz covariance...).
Rolf
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