Assign parameters per context rather than per environment

[stephen-riggs]

This addresses two problems which came up:

1. If find extension fails we should skip the file, and not try and process with the wrong extension. Fixes Database file was treated as a fractions file #605
2. Tomography multigrid currently would trigger with the wrong parameters. Fixes Tomography after SPA processes with the wrong parameters #606

To resolve the multigrid problems I have moved the parameters from the environment to the context.
This also removes some of the client-side parameters which aren't needed such as boxsizes.

[codecov]

Codecov Report

Attention: Patch coverage is 20.25316% with 63 lines in your changes missing coverage. Please review.

Project coverage is 31.82%. Comparing base (041056e) to head (c3e628d).
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #607      +/-   ##
==========================================
- Coverage   31.85%   31.82%   -0.03%     
==========================================
  Files          91       90       -1     
  Lines       10747    10697      -50     
  Branches     1429     1417      -12     
==========================================
- Hits         3423     3404      -19     
+ Misses       7211     7178      -33     
- Partials      113      115       +2     

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[tieneupin]

Any chance json could be replaced with something more indicative of its contents, since it seems to be passed around quite a bit?

[stephen-riggs]

Done this. Might need to check that I haven't broken anything by missing references to it

[tieneupin]

Some comments about variable names, but other than that, no obvious issues. The test runs also seem to work as intended.