Validate pipeline inputs.

[sdhutchins]

Fixes issue

Fixes #222

Changes proposed in this pull request:

• Add Pydantic models that validate pipeline configuration before managers consume it.
• Simplify NCBI BLAST database management around the current metadata manifest and database format.
• Remove obsolete WindowMasker database scaffolding and version-selection options.
• Update tests, documentation, and standalone examples for the validated configuration and current BLAST database interface.

Tests

• .venv/bin/python -m pytest -q: 235 passed, 3 skipped.
• uv run great-docs build --no-refresh: succeeded.
• uv build --quiet: succeeded.
• git diff --check: passed.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.59%. Comparing base (40b4470) to head (273ef54).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #227      +/-   ##
==========================================
+ Coverage   69.61%   72.59%   +2.97%     
==========================================
  Files          66       68       +2     
  Lines        4245     4316      +71     
==========================================
+ Hits         2955     3133     +178     
+ Misses       1290     1183     -107     

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