Add persistent global configuration via python-dotenv

[Copilot]

• Add python-dotenv as a core dependency in pyproject.toml
• Create src/nwb2bids/_core/_global_config.py with helper functions to load from .env files at global (~/.nwb2bids/.env) and local (.nwb2bids/.env in dataset directory) levels
• Update RunConfig to support loading defaults from .env files via RunConfig.from_dotenv_files()
• Update CLI (_main.py) to use RunConfig.from_dotenv_files() with dotenv-aware sanitization handling
• Add unit tests in tests/unit/test_global_config.py covering dotenv loading logic and priority ordering
• Resolve merge conflicts from main branch (new use_session_labels, probe, silent fields in RunConfig/CLI)
• All 121 non-remote unit + CLI tests pass

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Add configuration file</issue_title>
<issue_description>For persistent global options

This will include

1. default number of jobs to use in parallelization
2. default sanitization level
3. add more here</issue_description>

Comments on the Issue (you are @copilot in this section)

@CodyCBakerPhD The start of this in-memory is in #164

Follow-up will allow setting perment global config on disk</comment_new>
<comment_new>@CodyCBakerPhD
Plan:

• use python-dotenv package for allowing persistent (dataset-specific or system-specific; or local vs. global, in order of priority) files for the RunConfig model
• this also allows environment variables of the specific convention of that package to be used to override items from the persistent files
• the best source of ground truth is still the manually passed flags to the CLI or API </comment_new>

• Fixes Add configuration file #115

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[codecov]

Codecov Report

❌ Patch coverage is 93.10345% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.75%. Comparing base (7252b58) to head (dea88cd).

Files with missing lines	Patch %	Lines
src/nwb2bids/_command_line_interface/_main.py	0.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #352      +/-   ##
==========================================
+ Coverage   85.42%   85.75%   +0.32%     
==========================================
  Files          41       42       +1     
  Lines        1818     1874      +56     
==========================================
+ Hits         1553     1607      +54     
- Misses        265      267       +2     

Flag	Coverage Δ
unittests	85.75% <93.10%> (+0.32%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/nwb2bids/_converters/_run_config.py	96.29% <100.00%> (+0.64%)	⬆️
src/nwb2bids/_core/_global_config.py	100.00% <100.00%> (ø)
src/nwb2bids/_command_line_interface/_main.py	0.00% <0.00%> (ø)

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[CodyCBakerPhD]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Resolved in 7b43fa6. The conflict in _main.py was between main's updated sanitization_config initialization (placed before run_config_kwargs) and the PR's dotenv-aware approach that only adds sanitization_config to kwargs when --sanitization flags are explicitly passed. The merge keeps the dotenv behavior while incorporating main's new use_session_labels, probe, and silent fields. All 121 non-remote tests pass.