[codex] Add v0.3 assembly gate

[ehsanestaji]

Summary

• Add --gate pipeline for conservative assembly FASTA preflight gating.
• Add machine-readable gate JSON plus TSV, MultiQC, and HTML gate outputs.
• Add provenance.input_sha256 for exact input-file identity.
• Bump the report contract and package metadata to v0.3.0.
• Update docs, examples, release notes, and evidence workflow.

Validation

• python3 -m unittest discover tests/python -v
• cargo fmt --check
• cargo test --locked
• cargo clippy --locked --all-targets --all-features -- -D warnings
• git diff --check
• trailing whitespace scan
• local evidence smoke with scripts/collect_evidence.py --local-only
• pipeline gate CLI smoke on testdata/problem_assembly.fa

Notes

FastaGuard remains FASTA preflight QC. The gate does not replace QUAST, BUSCO,
BlobToolKit, CheckM, annotation, or contamination workflows.

Public NCBI evidence was not copied into the branch because the NCBI Datasets
CLI was not installed locally; local-only evidence smoke passed.