feat: StringTie novel transcript discovery + hybrid GTF

[pinin4fjords]

Summary

Adds reference-guided novel-transcript assembly via StringTie (preferring RNA-seq BAMs, falling back to Ribo-seq with tightened defaults) or a user-supplied annotation via --novel_gtf. Either source flows through a common filtering chain (gffcompare class-code filter, optional strand-aware rRNA/repeat blacklist, concat with the canonical backbone) and produces a hybrid annotation at <outdir>/stringtie/hybrid_reference.gtf.

This is the foundation for #165 / #171 / extended ORF discovery. With the default --skip_stringtie true and no --novel_gtf, the new hybrid_gtf workflow channel equals ch_canonical_gtf from #161, so downstream wiring is uniform whether novel discovery is on or off.

Changes

• New local subworkflow NOVEL_TRANSCRIPT_DISCOVERY chaining bam_stringtie_merge (per-sample StringTie + merge) and the upstream gtf_hybridmerge_gffcompare subworkflow (gffcompare + class-code filter + optional blacklist intersect + concat with canonical).
• Install upstream modules: stringtie/stringtie, stringtie/merge, gffcompare, bedtools/intersect.
• Install upstream subworkflows: bam_stringtie_merge, gtf_hybridmerge_gffcompare (PR feat(subworkflows): gtf_hybridmerge_gffcompare modules#11729, merged).
• New params: --skip_stringtie (default true), --novel_gtf, --stringtie_class_codes (default 'u', intergenic only), --rrna_blacklist, --extra_stringtie_args, --extra_stringtie_merge_args, --stringtie_ribo_fallback_args (default '-m 100 -c 5 -j 3 -f 0.05 -g 100' to tighten the Ribo-seq fallback).
• Workflow emits hybrid_gtf from the riboseq workflow.

Caveats

• Ribo-seq StringTie defaults are first-pass empirical, not literature-validated. The pipeline warns when the fallback is active.
• Default --stringtie_class_codes = u keeps only unambiguously intergenic transcripts. Stranded users can opt into 'u,x' to recover antisense; unsafe for non-stranded protocols.
• --rrna_blacklist is silently skipped when not supplied.

Stacked PR notes

Sixth in the stack splitting #174. Targets #181 (feat/162-ribotish-qc-canonical-doc).

Closes #164

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