Release 0.6.0 alpha

1. Strain analysis on by default — --no_strains to disable.
2. Two-stage strain filtering — protal emits a raw MSA (.raw.msa.fna), a post-filter produces .msa.fna; re-filterable without re-running protal. pergene_filtered dropped.
3. New qcmsa post-filter — first release, on by default. Coverage gate → Tukey-IQR multi-allelicity → site cleanup → hcov reapply, with a decision log. Standalone or via --run_qcmsa/--no_qcmsa, --strain_preset, --qcmsa_script. Remove msa related flags in protal
4. SNP filters exposed and fixed — --snp_min_af, --snp_min_mean_qual, --snp_no_strand; quality gate AND → OR; now applied on the MSA path.
5. Simulator rework — strain-sharing datasets, manifest/seed provenance, --from_manifest byte-for-byte replay, flag renames.