Feature/st id mapping rework

[jweiser]

Adds StableIdMapping data structure and filter out mis-matches between species in stable id mappings

[adamjohnwright]

Here are some suggestions from claude:

1. Package naming convention - The new package is StableIdMapper (PascalCase), but Java convention is lowercase package names (e.g., stableidmapper or stableid). Consider renaming for consistency.
2. Null safety in StableIdMapping - What happens if an empty list is passed to the constructor? Does getPrimaryId() throw an IndexOutOfBoundsException? Consider adding validation or returning Optional.
3. Test coverage - Are there unit tests for the new StableIdMapping class? The filtering logic in filterOutMismatchedIdentifiers() and species abbreviation extraction would benefit from explicit test cases, especially edge cases (single ID, all mismatched, etc.). 4. Immutability - Consider making StableIdMapping immutable by storing a defensive copy of the input list and making fields final. This prevents subtle bugs if the original list is modified elsewhere.
4. Species abbreviation extraction - The logic extracting the species code (e.g., "HSA" from "R-HSA-12345") should be documented or extracted into a named method for clarity. What happens with malformed IDs that don't follow the expected pattern?
5. The double-negative was confusing - The original condition !(stableIds.size() < 2) (meaning "size >= 2") was hard to read. Good cleanup, but ensure the new logic is semantically identical.

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you can choose to do them or not.