Add explicit no-change annotations and batch stats overhaul

[catchambers]

Summary

• Preserve synonymous no-change variants with explicit = markers across annotation and AA aggregation.
• Normalize batch output structure and batch stats reporting, including structured per-stage summaries and final summary metrics.
• Update batch output paths, docs, and release metadata for the 0.1.0 release prep.
• Add and update unit/integration coverage for annotation, sequence parsing, AA aggregation, batch normalization, and summary stats.

Testing

• Added and updated unit tests for annotation, sequence parsing, AA score aggregation, batch normalization, and summary-stat output shape.
• Added an integration-style batch normalization test to cover batch config loading and output generation.

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Accept legacy blank no-change markers in AA classification

This classifier now treats only '=' as “no amino-acid change”, but older score tables (and callers that still use compare_to_reference with its default) represent no-change as ''. In those inputs, aa_seq_diff == '' now falls through to missense_aa, which can corrupt downstream WT/synonymous-dependent stats and normalization when reprocessing legacy outputs or pre-annotated data.

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