refact: remove bento_lib coupling for config and server

[v-rocheleau]

This PR removes the usage of bento_lib to initialize the FastAPI app and Pydantic Settings.

The aim is to remove user-facing concepts that are specific to Bento, like environment variables prefixes, and service-info extensions.

These changes also allow adopters to use their own GA4GH service-info definitions.

Also includes a refactor that removes the ingestion router, since the ingestion is done from the experiment path.

[codecov]

Codecov Report

Attention: Patch coverage is 97.08738% with 3 lines in your changes missing coverage. Please review.

Project coverage is 81.52%. Comparing base (1c26941) to head (c53ca22).
Report is 10 commits behind head on main.

Files with missing lines	Patch %	Lines
transcriptomics_data_service/service_info.py	88.88%	1 Missing and 1 partial ⚠️
transcriptomics_data_service/main.py	91.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #25      +/-   ##
==========================================
+ Coverage   81.39%   81.52%   +0.12%     
==========================================
  Files          14       14              
  Lines         586      628      +42     
  Branches       30       32       +2     
==========================================
+ Hits          477      512      +35     
- Misses         98      103       +5     
- Partials       11       13       +2     

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[davidlougheed]

out of curiosity, what is the reason for adding duplicate code back in beyond funny BENTO_ prefixes of env vars?

[v-rocheleau]

out of curiosity, what is the reason for adding duplicate code back in beyond funny BENTO_ prefixes of env vars?

Removing the BENTO_ prefixes from the env vars is one of the main reasons.
The Candig team and I are worried that relying on bento_lib for the pydantic Settings and FastAPI base class could become a compatibility issue in the future, since the plan for tds is to be platform agnostic.

[noctillion]

LGTM!