feat: rename 'gene' to 'cds' in code and public interfaces

[ivan-aksamentov]

Sibling PR in data: nextstrain/nextclade_data#125

Modified input files

The following fields are renamed in the input pathogen.json:

From: aaMotifs[].includeGenes[].gene
To:   aaMotifs[].includeCdses[].cds

From: phenotypeData[].gene
To:   phenotypeData[].cds

From: qc.frameShifts.ignoredFrameShifts[].geneName
To:   qc.frameShifts.ignoredFrameShifts[].cdsName

From: qc.stopCodons.ignoredStopCodons[].geneName
To:   qc.stopCodons.ignoredStopCodons[].cdsName

Modified output files

The following fields are renamed in the output nextclade.json/nextclade.ndjson:

From: results[].missingGenes
To:   results[].missingCdses

The following columns are renamed in the output nextclade.tsv/nextclade.csv:

From: failedGenes
To:   failedCdses

The following fields are renamed in the output nextclade.tree.json:

From: node_atts.missing_genes
To:   node_atts.missing_cdses

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