augur traits does not export mugration models into the same output directory as traits JSON

[huddlej]

Current Behavior

Running augur traits as follows outputs treecountry.mugration_model.txt and treeregion.mugration_model.txt files in the expected/ subdirectory instead of the same directory where the traits.json is written out.

augur traits \
  --tree expected/tree.nwk \
  --weights config/trait_weights.csv \
  --metadata expected/metadata.tsv \
  --output-node-data traits.json \
  --columns country region \
  --sampling-bias-correction 3 \
  --confidence

This issue results from using the input tree's name as an output prefix for the mugration models instead of the output prefix for the traits file itself.

Expected behavior

All implicit outputs from an augur command should be written to the same directory as the explicit output(s) unless there are explicit options to do otherwise (e.g., a mugration model output prefix).

Possible solution

Determine the full output path of the traits JSON prior to outputting the mugration models and use the prefix of this output path instead of the tree's prefix.