Fix --out vs --output mismatch in extract program help text

[jcurtis2]

All seven extract_* programs registered the long option as --output but advertised --out in their help, causing --out to fail with "unknown option".

Unrelated but related to pass the PR (and probably others), adds a codecov.yml with a 1% project/patch threshold to allow for codecov being flaky about some line coverage. This slight line coverage change disappears and reappears often during a PR's development.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.43%. Comparing base (e6356e7) to head (febe6e2).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #222      +/-   ##
==========================================
- Coverage   77.45%   77.43%   -0.03%     
==========================================
  Files          55       55              
  Lines        9420     9420              
==========================================
- Hits         7296     7294       -2     
- Misses       2124     2126       +2     

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