Scipion-em-emantomo

Users:
- Small fixes regarding the register of the tilt series acquisition attributes.
- Fix the template matching output register reported by Ricardo Righetto (thanks!).
- Fix the classic subtomo refine transformation matrices assignment when generating the output.
- Fix the particles order in the registered output of protocol extract particles from TS.
- Protocol 'extract particles from TS' is now semi-streamified.
- Protocol 'tilt series alignment and tomo reconstruction':
* Fix the sampling rate of the set of tilt series interpolated.
* Fix the generation of tomograms when not requested.
* The interpolated tilt series is now generated applying the transformation matrix in Scipion convention to the
non-interpolated tilt series.
* Input and output convert steps improved.
* Remove form parameter 'Step between tilts' as it can now be read from the acquisition.
* Add param to correct the XDrift.
* Some other changes in the protocol form.
- Protocol 'average subtomograms' adapted to work with EMAN 3D particles generated from 3D particles (the ones
resulting when using the protocol 'extract particles from TS')
Developers:
- Test for TS alignment & tomo reconstruction updated to the new TCL.

Users:
- Prevent viewers from locking the screen focus.
- Refine new (pppt): set unmasked halves to the resulting average instead of the masked ones.
- Initial model new (pppt): in no. initial volumes requested is one, it generates an AverageSubTomogram instead of a
SetOfAverageSubTomograms, allowing the scheduling with a posterior refine.
- Fix pppt multirefine (bad assigment of the alignments detected).
- Fix protocol extraction from TS: the chainId in the fiducials generation is correct now.
- Update the template 2023_12_emantomo_sta_tutorial_workflow.json.template, so it calls the centralized
CTF import protocol instead of the obsolete corresponding non-centralized protocol.
Developers:
- lstConvert: orders alphabetically the tomograms to prevent data mismatching.
- update tests calls to import CTFs to the new centralized protocol developed for that purpose.

- Hotfix: add templates dir to package_data in setup

- Remove invalid classifier from the setup

- Fix schedule execution
- Fix template

Users:
- Template matching protocol added.
- Clip tomograms protocol added.
- CTF estimation protocol improved.
- Tilt Series alignment and Tomogram reconstruction protocol added, all together as in EMAN. TS alignment converted
to Scipion convention, so they can be used to feed other plugins (interoperability).
- STA per particle per tilt approach protocols added:
> Particle extraction from TS.
> New initial model generation.
> New subtomogram refinment.
> New multi reference alignment and classification.
- Remove some non-used or deprecated protocols: pca classification, tilt refine.
Developers:
- Tests written used the Test Centralization Layer from scipion-em-tomo.