Make regenerating rewrite rules more user-friendly

* Throw a warning if the user is trying to regenerate `.htaccess` without the special declaration.
* Add directions on how to resolve the problem in the usage docs for each relevant command.
When scaffolding a theme or plugin, create the `themes` or `plugins` directory if it doesn't exist

For developers who use the scaffolding commands on brand new projects, this can save a moment of d'oh.
Important bugfix
Merge pull request #1151 from johnbillion/capital_p_dangit

capital_p_dangit
Merge pull request #1149 from wp-cli/create-themes-dir

When scaffolding a theme or plugin, create the `themes` or `plugins` directory
Merge pull request #1147 from wp-cli/flush-notice

Make regenerating rewrite rules more user-friendly
Fuller PHPdoc coverage for `WP_CLI\Dispatcher\Subcommand`
Document `WP_CLI\Dispatcher\get_path()`
PHPdoc and explicit method definitions for `WP_CLI\Dispatcher\RootCommand`
PHPdoc coverage for `\WP_CLI\Dispatcher\CompositeCommand`
PHPdoc for `\WP_CLI\Dispatcher\CommandFactory`
More PHPdoc for `\WP_CLI\Runner`
`WP_CLI` and `WP_CLI\Configurator` also got some PHPdoc coverage
Merge pull request #1152 from wp-cli/internal-docs

PHPdoc coverage for `\WP_CLI\Dispatcher` and friends
Remove unused `check_verbose()` method

Added in 32402827d8e738c7c4e6025b7b3bbc6d7a1a45d2 but doesn't appear to be used. aa542585aeeef589b1ce1e18edf3d4aa30a06786 removed the verbosity argument
Merge pull request #1161 from wp-cli/rm-verbose

Remove unused `check_verbose()` method