Update deprecations

[stephprince]

Motivation

Fix #2008. Upgrades PendingDeprecationWarnings to DeprecationWarnings and upgrades DeprecationWarnings to raise ValueErrors when creating new objects or UserWarnings on read. Also removes functions previously marked for deprecation.

Here is a summary of the classes and methods updated:

• ProcessingModule.add_container will be replaced by ProcessingModule.add
• ProcessingModule.get_container will be replaced by ProcessingModule.get
• ProcessingModule.add_data_interface will be replaced by ProcessingModule.add
• ProcessingModule.get_data_interface will be replaced by ProcessingModule.get
• ScratchData.notes will be replaced by ScratchData.description
• Clustering will raise an error when creating a new object.
• ClusterWaveforms will raise an error when creating a new object.
• /intracellular_ephys/filtering will raise an error when creating a new object.
• NWBFile arg ic_electrodes will be replaced by arg icephys_electrodes
• NWBFile ec_electrodes property is replaced by electrodes
• NWBFile.add_ic_electrode, NWBFile.create_ic_electrode, and NWBFile.get_ic_electrode will be removed
• NWBFile.add_epoch_metadata_column will be removed
• SweepTable will raise an error when creating a new object and functions that interacted with the SweepTable will be modified
• ImageSeries.bits_per_pixel will be removed
• ImageSeries.format changed to external, default value for format should raise Value error
• ImagingPlane.manifold will raise an error when creating a new object
• ImagingPlane.conversion will be deprecated in favor of origin coords and grid_spacing
• IndexSeries.unit is fixed
• Indexed_timeseries replaced by indexed_images
• _get_resources was removed
• NWBFile.modules is replaced by NWBFile.processing

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

Attention: Patch coverage is 83.33333% with 7 lines in your changes missing coverage. Please review.

Project coverage is 92.33%. Comparing base (a63387d) to head (7b4e197).

Files with missing lines	Patch %	Lines
src/pynwb/core.py	20.00%	3 Missing and 1 partial ⚠️
src/pynwb/file.py	88.23%	2 Missing ⚠️
src/pynwb/image.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2011      +/-   ##
==========================================
+ Coverage   91.88%   92.33%   +0.45%     
==========================================
  Files          27       27              
  Lines        2711     2702       -9     
  Branches      707      708       +1     
==========================================
+ Hits         2491     2495       +4     
+ Misses        144      134      -10     
+ Partials       76       73       -3     

Flag	Coverage Δ
integration	73.09% <16.66%> (+0.24%)	⬆️
unit	83.27% <83.33%> (+0.42%)	⬆️

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