Complementary functionality doesn't work as expected when using consistency-based methods

[scapella]

I have detected an unexpected behaviour when trimming an alignment based on consistency methods, which compute their scores based on the level of agreement across a set of input alignment.

trimAl doesn't return those columns which are removed when applying -ct parameter. I have detected it using -ct alone or with other methods e.g. -gt

@Vicfero could you please verify to what extend this affect to the new version?