Remove deprecated methods from NWBFile

[oruebel]

Motivation

This PR removes previously deprecated functions and parameter from NWBFile

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running ruff check . && codespell from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.83%. Comparing base (716e3ce) to head (9ce6ef4).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2033      +/-   ##
==========================================
+ Coverage   91.73%   91.83%   +0.10%     
==========================================
  Files          27       27              
  Lines        2722     2683      -39     
  Branches      710      702       -8     
==========================================
- Hits         2497     2464      -33     
+ Misses        149      144       -5     
+ Partials       76       75       -1     

Flag	Coverage Δ
integration	73.46% <100.00%> (+0.50%)	⬆️
unit	82.25% <100.00%> (-0.04%)	⬇️

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[oruebel]

@stephprince @rly not sure if this should be for 3.0 or 4.0 release

[stephprince]

I think these changes are all covered by #2011, which was merged into the release-3.0.0 branch but has not yet been merged into dev.

[stephprince]

I think these changes are all covered by #2011, which was merged into the release-3.0.0 branch but has not yet been merged into dev.

@oruebel can I close this PR since I think these changes are covered in the release-3.0.0 branch as mentioned above? If there are additional changes here that should be merged, let me know.