Revert two-pass transcript selection - #21

The two-pass system was introduced to ensure all selected transcripts overlap the primary (longest) transcript, and also added more strict validation.
The overlap check is now handled downstream (in produce_genes).

In practice, the revalidation causes unintended drops of valid transcripts due to the asymmetry of is_valid_alternative.
An accepted transcript (compared to seed) may fail against the new primary, even if it is a legitimate isoform.

It's now reverted to single-pass selection:

• Seed with earliest-start/highest-score candidate
• Collect valid alternatives in score order (need to be valid against all already selected calls)
• Sort by CDS length and return up to max_transcripts calls (first = longest call is primary)

This ensures that if there are multiple groups of structurally similar transcripts per locus, the best calls are kept per structural group.