Prepare v1.1.0 reference workflow release

[ehsanestaji]

Scoped change description

Prepare v1.1.0 with Nextflow and Snakemake reference workflow examples, report retention before gate enforcement, and pinned engine CI.

Update source metadata and release notes. Published packages and upstream wrapper pins remain at v1.0.0; no release is published by this PR.

Tests

• Rust: 239 tests passed; formatting and Clippy passed.
• Python: 181 tests and 268 subtests passed with both workflow engines required, zero skips.
• Nextflow, Snakemake and workflow lint passed.
• Packaged macOS Apple Silicon binary passed the reference quickstart; schema, catalogue and archive checksum verified.

Hosted CI and cross-platform release builds are pending.

Contract impact

• No public contract change.
• Public contract changed; JSON, TSV, HTML, schema, and finding catalogue impacts are described above.

Documentation impact

• No documentation change is needed.
• Documentation, examples, or release notes were updated.

Review checklist

• Tests cover changed behaviour or explain why tests are not applicable.
• DCO: every commit includes a Signed-off-by: line.
• Attribution-trace review: the change has no unwanted authorship or tool-provenance traces.
• The contribution stays within FastaGuard's FASTA-level preflight scope.