Return breaking changes removing deprecated classes & functions

[rly]

Bring back breaking changes reverted in #1224.

[codecov]

Codecov Report

Attention: Patch coverage is 96.07843% with 2 lines in your changes missing coverage. Please review.

Project coverage is 90.86%. Comparing base (d63e588) to head (44e1ab1).
Report is 1 commits behind head on dev.

Files with missing lines	Patch %	Lines
src/hdmf/backends/hdf5/h5tools.py	90.47%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1227      +/-   ##
==========================================
+ Coverage   89.00%   90.86%   +1.85%     
==========================================
  Files          45       42       -3     
  Lines        9969     9524     -445     
  Branches     2833     2725     -108     
==========================================
- Hits         8873     8654     -219     
+ Misses        774      576     -198     
+ Partials      322      294      -28     

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