Performance enhancements, util refactor and and clean up tests

[sygao]

Performance enhancements

• Replace initialization event store read with filename check
• Utilize event index cache in Repo.index_otus()
• Utilize event index cache in Repo.iter_otus()

Fixes

• Repo._iter_events() and .get_source_event_ids() now handle chaff files

Utils refactor

• Move Molecule to virtool_cli.utils.models
• MoveMolType, Strandedness and Topology to utils.models and replace relevant duplicate enums in ncbi.models
• Move utils.console.console, utils.id_generator.generate_random_alphanumeric() and .generate_unique_ids to legacy.utils
  • test_utils_hashing() moved to legacy utils test dir
• Move utils.format, .ncbi, .storage to utils.deprecated submodule

Clean up tests

• Replace test files in src_test with current EventSourcedRepo files
• Move old src_test files to prototype_src_test dir
• Remove prototype test_utils_storage and test_utils_reference

Add larger-scale add test

• Add test_add_bulk
• Add more demo Genbank and Taxonomy files to cache_test

[igboyes]

This deprecated stuff should just be removed. Is there something stopping you?

[sygao]

This deprecated stuff should just be removed. Is there something stopping you?

I just moved the last of the utils, so not anymore.

[virtool-bot]

🎉 This PR is included in version 2.0.0-alpha.31 🎉

The release is available on GitHub release

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