Standardise CLEM workflow

[tieneupin]

The CLEM workflow was set up years ago, and as the repo has evolved and other workflows have been added over time, it has become clear that the more recent workflows trigger processing and submit messages in a different way.

This PR updates the CLEM workflow API endpoints and workflow recipes so that the behaviour is more consistent across workflows. As a general rule, outbound messages such as the ones to cryoem-services will be constructed directly in the endpoint or the workflow instead of being outsourced to a separate workflow that is loaded by Murfey's feedback_callback function. Database registration tasks will be handled in workflow messages so that they can be reinjected more easily .

• The LIF and TIFF API endpoints will directly submit messages to the processing_recipe service instead of loading up a workflow to do so
• The message for the align_and_merge service will be directly constructed and sent as part of the register_preprocessing_results workflow instead of being sent to a separate align_and_merge workflow

The redundant workflows, endpoints, and modules will be deleted in a subsequent PR.

The actual diff is +178/-59, with the rest being due to the addition and updating of tests.

[codecov]

Codecov Report

❌ Patch coverage is 95.23810% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.96%. Comparing base (a186050) to head (3a0c13b).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #861      +/-   ##
==========================================
+ Coverage   54.65%   54.96%   +0.31%     
==========================================
  Files         104      104              
  Lines       11160    11206      +46     
  Branches     1475     1480       +5     
==========================================
+ Hits         6099     6159      +60     
+ Misses       4741     4727      -14     
  Partials      320      320              

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[stephen-riggs]

Looks fine to me