Niac changes for apm, em, cg, and ms brought back to fairmat assuming that these will be accepted

[mkuehbach]

This PR consolidates the work on definitions for the APM and EM apps and brings back in this process the NIAC changes for the follow sets of definitions:

• NXapm* --> assuming acceptance of fairmat-2024-apm

• NXem* --> assuming acceptance fairmat-2024-em

• NXcg* with supportive NXcs* --> fairmat-2024-computational-geometry

• Assuming acceptance of NIAC non-FAIRmat geometry updates 1532

• NXmicrostructure* just updated planned to stay in contributed_definitions

• NXem_calorimetry just updated planned to stay in contributed_definitions

• After the fairmat branch was merged in all yaml files were recreated firstly via make clean, make nyaml, make nxdl

• Fixes of warnings in the documentation building except for these ...

despite remaining issues review of this PR should start asap cuz this PR is required for composing a consolidated fairmat branch to update pynxtools, I will work on the next issue in parallel

... remaining issues, sorted in order of decreasing implementation priority:
Comments from Lukas,

• mv from applications and base_classes to contributed
• fix inconsistencies in some of the infrastructure files

Furthermore,

• refactor all suffixID to ALLCAPS or use of implicit name via group name="suffixID" type="NXsomething" to group type="NXsomething" or group name="ALLCAPS" type="NXsomething" respectively
• Add ideas from Trieste EM group
• NXcg_primitive to add in cgms-structure.rst
• revert changes on dev_tools/docs/nxdl_index.py to cure that fairmat domain-structure-specific.rst are currently not registered in the index
• using currently a hybrid of the old/new NIAC corporate design and some of our greenish FAIRmat one, use new NeXus logos from Russ from the Autumn 2024 code camp

Further issues remaining that should not block though this PR and on which we should not start working before apm and em examples are working with pynxtools and with examples that work in apps (again):

• Run copyright year script to update all copyright statements, should be done on the final branch (these github accounts will need to be added to the whitelist

  "sherjeelshabih"
  "atomprobe-tc"
  "andreaa93"
  "Tommaso-Pincelli"
  "ca-palma"
  "Marie Yao"

• Move remaining changes from apm, em, cg branches to NIAC
• Check/bug fixing NXem_calorimetry definition pynxtools-em-insitu
• Check/bug fixing NXapm_compositionspace_* CompositionSpace
• Check/bug fixing NXapm_paraprobe_* definition update paraprobe-toolbox

[lukaspie]

So far, the strategy was that we don't move anything to base_classes or applications yet that is not accepted, but to keep everything in contributed_definitions for now (see #329, #338, #349, #350). In this PR, basically everything is moved to these folders. This will be a problem because we are using similar base classes (like NXpeak) and we will have them both in base_classes and contributed_definitions now, which makes it imposssible to see if there are any changes. I suggest to move these files back to contributed until they are accepted by NIAC.

There are also some dev_tools and manual files that need to be reverted back to the state in fairmat, I left comments wherever I detected these.

I have not yet checked any of the actual NXDL files, will do after moving.

[lukaspie]

LGTM. I checked all files, but only ran though them quickly.

The copyrights are significantly changed in many places and are often wrong now, but this can be handled in a follow-up PR.