Fix duplicated warnings

[trexfeathers]

Story

• As a
  Iris user
• I want
  To only receive each warning once - the Python default behaviour
• So that
  I do not need to develop specific strategies for working with Iris versus other Python libraries, and so my stdout/stderr is readable, allowing effective development

Notes

Reports of some warnings being raised once per file. I suspect something related to parallelism - warnings are not thread safe by default, but can be made so (from reading Stack Overflow).

From refinement discussion

• Initial work must be to diagnose when 'duplicates' are issued. Is it just once per file? Once per Cube? Is there some thread safety involved?
• Further steps will depend on the results of the diagnosis.

### Tasks
- [ ] https://github.com/SciTools/iris/issues/5463
- [ ] https://github.com/SciTools/iris/issues/5499
- [ ] https://github.com/SciTools/iris/issues/5536