File behaviour for restarts and diagnostics

[jwallwork23]

File behaviour for restarts and diagnostics

Fixes #935
Fixes #977
Fixes #997
Fixes #898
Merges into #999

Task List

• Defined the tests that specify a complete and functioning change (It may help to create a design specification & test specification)
• Implemented the source code change that satisfies the tests
• Documented the feature by providing worked example
• Completed the pre-Request checklist below

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Change Description

This PR fixes several things related to how restarts and diagnostics are configured with XIOS:

1. Diagnostics are created by averaging all timesteps included in an output file dump.
2. Restart file output frequency and split frequency are aligned so that each output file dump only includes a single timestep's worth of data.
3. Restart files are only read once.
4. Handle file patterns in filenames.

Whilst file patterns are made consistent with what's used elsewhere in nextSIM-DG, the output filenames show the range of datetimes separated by a hyphen.

In this PR, I also overhauled the createFile member function, inlining many of the setters with only a single call site.

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Test Description

Tests are updated to account for the new behaviour.

TODO - to test the diagnostics are written out.

I decided to drop XiosFile_test because it is no longer needed. This meant that we could drop the annoying unittest special case.

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Documentation Impact

TODO

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Pre-Request Checklist

• The requirements of this pull request are fully captured in an issue or design specification and are linked and summarised in the description of this PR
• No new warnings are generated
• The documentation has been updated (or an issue has been created to track the corresponding change)
• Methods and Tests are commented such that they can be understood without having to obtain additional context
• This PR/Issue is labelled as a bug/feature/enhancement/breaking change
• This change conforms to the conventions described in the README