More changes to size_t and int64_t types

[rboston628]

Description of work

Summary of work

NexusClasses was originally written to work with napi,h, which uses standard int for all integer quantities. However, some of these quantities are better expressed as size_t. Some are better expressed as size_t but can't due to some compatibility expectations for negative numbers, and must be int64_t.

It seems some places in code were constrained by this limitation of NexusClasses to use ints. Several of these places were fixed by resetting types to a more appropriate type.

This should improve the overall code quality of Mantid, by allowing for easier setting of whole counting numbers with unsigned int types, or at least with double width ints.

Part of #38332

Compare and/or combine with #38805

Further detail of work

There should be no changes in this PR, except for:

1. int changed to size_t or int64_t
2. places with size_t and a <0 check fixed to avoid compiler and CppCheck warnings

This does not require release notes because it is an internal change invisible to users.

To test:

Make sure all existing tests pass.

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[github-actions]

👋 Hi, @rboston628,

Conflicts have been detected against the base branch. Please rebase your branch against the base branch.

[github-actions]

👋 Hi, @rboston628,

Conflicts have been detected against the base branch. Please rebase your branch against the base branch.

[peterfpeterson]

Fairly mechanical changes to follow what has happened in NexusClasses