Add GTF, PAF, GFA to the type allow-list

[jorgeMFS]

Adds three commonly-needed bioinformatics formats that recipes need to declare on their I/O ports but the validator currently rejects:

• GTF — Gene Transfer Format. Used by stringtie, gffcompare. Required column count = 9; attributes column must contain gene_id and/or transcript_id.
• PAF — Pairwise Alignment Format. Used by miniasm, minimap2 output, paftools. 12 mandatory tab-separated columns; numeric position fields validated.
• GFA — Graphical Fragment Assembly. Used by miniasm output, minigraph, gfatools. First character per line must be one of H/S/L/C/P/W/J/#.

Each type gets a representative example in TYPE_DEFINITIONS plus a validator in ALL_TYPES. The examples self-validate against their validators.

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Merge order

Independent. No conflict with sbom-implementation or with any other open PR. Can land in any order.