tckgen: Update help info to reflect change to initcutoff

Initial FA / FOD cutoff (i.e. required value at streamline seed) used to be twice the standard cutoff.
It was changed by e2757bbe, however the tckgen help page was not updated to reflect this.
revpe_dwicombine: enhancements

Was trying to get this to work on some unique data; ultimately failed, but made some worthwhile updates anyways:
- Use a manual combination of reversed-PE DWI pairs: eddy code currently cannot do least-squares reconstruction.
- Perturb image axes at start and end of script so PE axis is always axis 1 (topup refuses to run if the PE axis is 2).
Fixes #113.
ProgressBar: simplify and fix a few bugs
Merge branch 'master' into C++11