Refactor __main__.py

Most of the changes are internal, i.e. show no changed behaviour. Instead, the
code should be  more robust and maintainable. This is achieved by:

* Choosing composition over inheiritance
* Leaning even further into static typing, with the different combinations of
  options being encoded in a sum type-like manner, by combining wrapper classes
  with `Union`.
* More consistent typeassert of fields loaded from argparse.NameSpace at the
  point where they are accessed
* The requirements for each command is encapsulated more directly in classes,
  with their invariants clearer, and more enforced

Further, some user-facing stuff have been changed:
* Refactoring of the command-line flags exposed to the user, such that only the
  flags actually used by each command is exposed.
* Changed the grouping of command-line flags to be more sensible
* Added the `--version` flag to all subcommands

.github/workflows/cli_vamb.yml

@@ -42,7 +42,7 @@ jobs:
         cat outdir_vamb/log.txt
     - name: Run TaxVAMB
       run: |
-        vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -t 10 -o C --minfasta 200000
+        vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -pq -t 10 -o C --minfasta 200000
         ls -la outdir_taxvamb
         cat outdir_taxvamb/log.txt
         vamb bin taxvamb --outdir outdir_taxvamb_no_predict --no_predictor --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -e 10 -q -t 10 -o C --minfasta 200000
@@ -53,10 +53,10 @@ jobs:
         cat outdir_taxvamb_preds/log.txt
     - name: Run Taxometer
       run: |
-        vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10
+        vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pq -pt 10
         ls -la outdir_taxometer
         cat outdir_taxometer/log.txt
-        vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pt 10
+        vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pq -pt 10
         ls -la outdir_taxometer_pred
         cat outdir_taxometer/log.txt
     - name: Run k-means reclustering