filter: Deprecate --output and -o

[victorlin]

Description of proposed changes

--output and -o are aliases to --output-sequences. They will be removed to avoid confusion with other output options.

Related issue(s)

Closes #1607

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs

[codecov]

Codecov Report

Attention: Patch coverage is 85.71429% with 3 lines in your changes missing coverage. Please review.

Project coverage is 71.06%. Comparing base (e1a30ba) to head (e700ea3).

Files with missing lines	Patch %	Lines
augur/filter/io.py	0.00%	1 Missing and 1 partial ⚠️
augur/filter/_run.py	75.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1622      +/-   ##
==========================================
+ Coverage   71.03%   71.06%   +0.03%     
==========================================
  Files          79       79              
  Lines        8258     8268      +10     
  Branches     2005     2007       +2     
==========================================
+ Hits         5866     5876      +10     
  Misses       2101     2101              
  Partials      291      291              

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