Scipion-em-aretomo

Users:
- Add aretomo2 1.1.2
- Fix backwards compatibility.
- Add an option to specify AlignZ per TS.
- fix dose weighting bug related to the tilt angle file (aretomo2 only)
Developers:
- The tests now use the Test Centralization Layer update and expansion of the used test set definition
from em-tomo v3.6.0.
- Update the acquisition order in the CTFTomo objects (field added to that class in scipion-em-tomo v3.7.0).

Users:
- The protocol form now present CTF-related parameters, to choose if estimate it or
not and phase plate acquisition related params (estimate the phase shift).
- Generates the output SetOfCtfTomoSeries if the CTF files are found
- Add dataimport module to parse the CTF generated so it can be called from the
centralized protocol for importing CTFs.
- Fix the origin set by Scipion to the generated tomograms.
- Outputs are not stored in case the are not correctly generated.
- If dose-weighting active, the accumulated dose of the interpolated TS is set to zero to avoid double dose
correction if using the interp TS for the PPPT.
Developers:
- Rewrite tests using the TCL from em-tomo and the reliontomo test dataset.

- add aretomo2 1.0.0
- fix output aln file parsing during local alignment
- add extra output option