Fix: rule deprecation warnings did not consider all rules

[not-an-aardvark]

What is the purpose of this pull request? (put an "X" next to item)

[x] Bug fix

Tell us about your environment

• ESLint Version: master
• Node Version: 11.0.0
• npm Version: 6.4.1

What parser (default, Babel-ESLint, etc.) are you using?

N/A

Please show your full configuration:

N/A

What did you do? Please include the actual source code causing the issue.

From within the ESLint repository:

const CLIEngine = require(".").CLIEngine;
const cliEngine = new CLIEngine();

console.log(cliEngine.executeOnFiles(["Makefile.js"]));

Ran eslint Makefile.js --format json in the ESLint repository

What did you expect to happen?

I expected the output to contain a usedDeprecatedRules property indicating that the no-catch-shadow rule (which we enable in eslint-config-eslint) has been replaced by no-shadow.

What actually happened? Please include the actual, raw output from ESLint.

{ results:
   [ { filePath: '/path/to/eslint/Makefile.js',
       messages: [],
       errorCount: 0,
       warningCount: 0,
       fixableErrorCount: 0,
       fixableWarningCount: 0 } ],
  errorCount: 0,
  warningCount: 0,
  fixableErrorCount: 0,
  fixableWarningCount: 0,
  usedDeprecatedRules: [] }

What changes did you make? (Give an overview)

This fixes a bug where rule deprecation warnings would only be generated for rules passed via the --rule flag on the command line, rather for all rules configured in a config file. It also addresses an issue where passing a nonexistent rule on the command line would cause CLIEngine to crash, which broke the eslint-canary build.

Additionally, usedDeprecatedRules was only appearing on the result of CLIEngine#executeOnFiles before. I updated it to also appear on the result of CLIEngine#executeOnText, since the two functions are documented to have the same output format.

Is there anything you'd like reviewers to focus on?

Nothing in particular