fix mugration models output directory

[cwoszczak]

Description of proposed changes

What is the goal of this pull request? What does this pull request change?

Mugration models now output to the directory specified by "--output-node-data". The tree's prefix is no longer used for the trait JSON output path.

Related issue(s)

Fixes #541
Related to #

Testing

What steps should be taken to test the changes you've proposed?
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?

I walked through the Zika tutorial using ./bin/augur and mugration files were added to the same directory as the traits JSON.

Thank you for contributing to Nextstrain!

[codecov]

Codecov Report

Merging #544 into master will decrease coverage by 0.25%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##           master     #544      +/-   ##
==========================================
- Coverage   19.47%   19.22%   -0.26%     
==========================================
  Files          31       31              
  Lines        5073     5072       -1     
  Branches     1284     1288       +4     
==========================================
- Hits          988      975      -13     
- Misses       4062     4074      +12     
  Partials       23       23              

Impacted Files	Coverage Δ
augur/traits.py	7.96% <0.00%> (+0.13%)	⬆️
augur/utils.py	23.07% <0.00%> (-4.56%)	⬇️
augur/tree.py	9.25% <0.00%> (-0.49%)	⬇️
augur/refine.py	5.03% <0.00%> (-0.43%)	⬇️
augur/mask.py	100.00% <0.00%> (ø)
augur/ancestral.py	11.11% <0.00%> (+0.11%)	⬆️
augur/frequency_estimators.py	33.84% <0.00%> (+0.12%)	⬆️
augur/titer_model.py	18.90% <0.00%> (+0.29%)	⬆️

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