refactor: update Console::run() to allow it be called in command() function

[paulbalandan]

Description
This refactors Console::run() so that it can accept a list of tokens to parse (defaulting to $_SERVER['argv'] if empty) when run() is called. This consequently allows it to be called inside the command() function so that the latter can also enjoy the enhancements to command line parsing.

A behavior break that I am seeing is that command() now receives the $params as a merge of arguments and options, instead of the previous how-it-was-parsed order. However, since getting the params passed to a command by this function is not an intended use, I believe its impact is minimal.

Checklist:

• Securely signed commits
• Component(s) with PHPDoc blocks, only if necessary or adds value (without duplication)
• Unit testing, with >80% coverage
• User guide updated
• Conforms to style guide

[michalsn]

Looks good - thanks!

[paulbalandan]

I reverted the deprecation on Boot::initializeConsole() as I figured there may be users who modified the Console class. The previous deprecation will no longer give the chance to provide a user's own Console class which is too much of a break.