refactor: convert devicepreferences command to yargs

[rossiam]

• Added note to CONTRIBUTING.md document about multi-word flags.
• added /node_modules/ to testPathIgnorePatterns config
• slightly cleaned up package.json (reordered some stuff to match order it is documented)
• updated @types/yargs package
• converted api-organization-command.ts to yargs
• converted common-flags.ts command to yargs
• converted devicepreferences-util.ts command to yargs
• converted devicepreferences command to yargs
• fixed variable name in apps-utils.test.ts
• moved some unit tests but actual working unit tests will come in a future pull request
• removed a couple of obsolete TODOs

Checklist

• [x] I have read the CONTRIBUTING document
• [x] My code follows the code style of this project (npm run lint produces no warnings/errors)

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Latest commit: ab368850cda3703bf3b660f3916b1688a50b21b2

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