Refactor load_namespaces to return source types, fix registration

[rly]

• Larger breaking change and refactor of load_namespaces (from TypeMap, NamespaceCatalog, and the IO classes) to fix DynamicTableRegion written with hdmf_experimental instead of hdmf_common when using NWB extensions #1347 and improve the code structure for clarity and utility. This change will target HDMF 5.0 and needs to be rebased.
• A separate PR will handle a smaller, non-breaking fix.

TODO:

• Add tests
• Target 5.0 branch

How to test the behavior?

Run tests and pynwb tests

Checklist

• Did you update CHANGELOG.md with your changes?
• Does the PR clearly describe the problem and the solution?
• Have you reviewed our Contributing Guide?
• Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

[codecov]

Codecov Report

❌ Patch coverage is 90.76923% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.41%. Comparing base (a21f308) to head (4302973).

Files with missing lines	Patch %	Lines
src/hdmf/build/manager.py	90.00%	3 Missing and 3 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1372      +/-   ##
==========================================
- Coverage   92.44%   92.41%   -0.03%     
==========================================
  Files          42       42              
  Lines        9762     9764       +2     
  Branches     1982     1985       +3     
==========================================
- Hits         9024     9023       -1     
  Misses        463      463              
- Partials      275      278       +3     

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