chore: address CodeRabbit follow-up findings

[ypriverol]

Summary

Acts on the actionable findings from a CodeRabbit --agent review of the branch. Each item was verified against current code before fixing.

• docs/use-cases.md:262 (major) — replace non-portable grep -oP (PCRE lookbehind, GNU-only) with sed -E so the per-chromosome ENSEMBL example works on default macOS / BSD grep. Also handles the .vcf.gz variant in one pass.
• pgatk/commands/gencode_downloader.py:69 (minor) — also catch subprocess.CalledProcessError from gffread. Matches what ensembl_downloader.py:139 and ncbi_downloader.py already do; previously a gffread failure during --generate-transcripts would bubble up as an uncaught traceback.
• pgatk/commands/ensembl_downloader.py:130 (minor) — when no genome matches a GTF's prefix, the loop silently fell back to next(iter(genome_map.values())). Now warns with the missing prefix and the fallback assembly name so users can spot a GRCh38-GTF / GRCh37-genome mismatch.
• pgatk/testdata/clinvar/mini_clinvar.vcf:8-10 (minor) — add a header comment documenting that the two records at 1:69550 G>A are intentional: rs00002 (Benign, missense) exercises CLNSIG filtering and rs00004 (Pathogenic, synonymous) exercises consequence filtering. Both assertions live in test_clinvar_service.py / test_clinvar_integration.py.

Skipped

• pgatk/commands/cbioportal_to_proteindb.py:99 — CodeRabbit suggested changing if workers > 1 to if workers is not None. The click option defaults to 1 and CancerGenomesService also defaults to 1 when WORKERS is unset (cgenomes_proteindb.py:411), so --workers 1 and "no flag" produce identical behaviour. The guard is not a user-visible bug.

Test plan

• python -m pytest pgatk/tests/ -q — 315 passed
• python -m unittest discover -s pgatk/tests -p "*_tests.py" — 20/20 passed

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