Remove serialem code and revise context determination

[stephen-riggs]

The SerialEM code has never been used, and if we want to support SerialEM in future it would be better to redo it. This removes all code relating to it.

Also improves and tests the determination of the context in the analyser.

There are some potential difficulties with distinguishing data and metadata. The biggest problem is mdoc files which appear with the same name in both folders.

[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.

Project coverage is 33.28%. Comparing base (344c266) to head (4d926b6).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #632      +/-   ##
==========================================
+ Coverage   32.98%   33.28%   +0.30%     
==========================================
  Files          90       90              
  Lines       11151    11130      -21     
  Branches     1470     1462       -8     
==========================================
+ Hits         3678     3705      +27     
+ Misses       7340     7297      -43     
+ Partials      133      128       -5     

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[tieneupin]

@stephen-riggs , I've added example files for the CLEM workflow to the analyser test, and have realised that the logic for the CLEM workflow can be optimised, as some of it conflicts with the conditions you've put in place for the SPA and Tomo files. I've also merged the main branch into this one so that ISPyB gets installed correctly.

Could you verify that the contents of murfey.client.analyser are as you intended after resolving merge conflicts?

[tieneupin]

Thanks for verifying the merge went ok. Looks good to me now. Feel free to merge to 'main' when you're ready.