Fix configuration file options being overwritten

[alexcanessa]

Program.js was using its defaults as properties passed, which then overwrote the configuration file.

Fixes #110

[codecov-io]

Codecov Report

Merging #113 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master     #113   +/-   ##
=======================================
  Coverage   86.34%   86.34%           
=======================================
  Files           7        7           
  Lines         293      293           
=======================================
  Hits          253      253           
  Misses         40       40

Impacted Files	Coverage Δ
lib/src/Program.js	82.14% <100%> (ø)	⬆️

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