Fix augur index I/O

[huddlej]

Description of proposed changes

Fix a couple of I/O issues with the augur index command including:

• Properly handle missing inputs for augur index, fixing a bug where a FileNotFoundError was not being caught and handled properly (and the exception handler that did exist referenced a variable that did not exist).
• Use standard UNIX-style line endings for index output, for consistency across Augur outputs.

Testing

• Adds functional tests for the index command
• Tested by CI

[codecov]

Codecov Report

Merging #900 (0e164de) into master (002c44f) will increase coverage by 0.00%.
The diff coverage is 33.33%.

@@           Coverage Diff           @@
##           master     #900   +/-   ##
=======================================
  Coverage   34.62%   34.63%           
=======================================
  Files          42       42           
  Lines        6007     6006    -1     
  Branches     1538     1538           
=======================================
  Hits         2080     2080           
+ Misses       3854     3853    -1     
  Partials       73       73           

Impacted Files	Coverage Δ
augur/index.py	65.75% <33.33%> (+0.88%)	⬆️

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