Use file_format and use new FileIO hyperspy metadata

[ericpre]

The PR for hyperspy/hyperspy#3528. These changes are compatible with the release and development version of hyperspy.

Progress of the PR

• Update reference metadata dictionary to support changes in #3528,
• Handle deprecation of reader and extension parameters in the test suite,
• update docstring: replace mentions of reader argument,
• update user guide: replace mentions of reader argument,
• add a changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting of the changelog entry (and eventual user guide changes) in the docs/readthedocs.org:rosettasciio build of this PR (link in github checks)
• update tests,
• ready for review.

[codecov]

Codecov Report

❌ Patch coverage is 40.00000% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.03%. Comparing base (c4aa0b1) to head (73e8a77).
⚠️ Report is 234 commits behind head on main.

Files with missing lines	Patch %	Lines
rsciio/emd/_api.py	14.28%	3 Missing and 3 partials ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #425   +/-   ##
=======================================
  Coverage   88.02%   88.03%           
=======================================
  Files          91       91           
  Lines       11538    11547    +9     
  Branches     2131     2135    +4     
=======================================
+ Hits        10156    10165    +9     
+ Misses        875      872    -3     
- Partials      507      510    +3     

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[ericpre]

The failure on the development branch of hyperspy is fixed in hyperspy/hyperspy#3528.

[jlaehne]

Note that a number of user guide pages and docstrings mention the reader argument and need to be adapted once this is released on the HyperSpy side!