Remove the assumption of a raw directory for processed outputs

[stephen-riggs]

Resolves one of the doppio-live issues, where we assume a raw directory for SPA.

This instead makes it a configurable option, where the raw is added to the path if process_multiple_datasets is True, so that in cases such as eBIC where we send multiple datasets to one location they are still divided up.

Also makes the path construction consistent between SPA and tomo, which will need checking.

[codecov]

Codecov Report

Attention: Patch coverage is 33.33333% with 14 lines in your changes missing coverage. Please review.

Project coverage is 31.86%. Comparing base (2d3e030) to head (f491f06).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #600      +/-   ##
==========================================
+ Coverage   31.77%   31.86%   +0.08%     
==========================================
  Files          90       90              
  Lines       10700    10686      -14     
  Branches     1422     1419       -3     
==========================================
+ Hits         3400     3405       +5     
+ Misses       7187     7168      -19     
  Partials      113      113              

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[tieneupin]

Both the SPA and tomo workflows seem to work fine with the key activated and deactivated. Looks good.