ingest: Switch to 1 metadata TSV + 3 FASTA files

[joverlee521]

Currently, the ingest workflow produces 3 metadata TSV + 3 FASTA files for the L/M/S segments and 1 all metadata + all sequences FASTA.

In discussion on Slack and nextstrain/pathogen-repo-guide#59, the suggested path forward is to switch this to 1 central metadata TSV with 3 FASTA files. This should follow the suggested plan to collapse and dedup strain metadata into a single record.