Use `get_stylesheet_directory()` instead of `TEMPLATEPATH` when determining where to place a scaffold.

In parent-child theme relationships, `TEMPLATEPATH` will always be the parent theme. We'd like to instead place our CPT/taxonomy in the child theme, as child themes are where the customizations occur.
scaffold: clarify --theme description in docs
Update post type and taxonomy scaffold to support a named theme target
Update man docs
run_mysql_command: use --no-defaults instead of --defaults-file
Merge branch 'scaffold-default-theme' into dev

closes #487
standardize special flags handling
convert InternalFlags class to Sys_Command
Merge branch 'internals-cmd' into dev

closes #489
Merge branch 'theme-version' into dev
Merge branch 'behat-upgradables' into dev
Merge branch 'master' into dev
Only use maintenance mode if a plugin or theme needs updating

When updating plugins (wp plugin update-all) or themes (wp theme update-all) on a WordPress multisite installation, maintenance activated and deactivated even if there are no updates to install.

The Plugin_Upgrader::bulk_upgrade() and Theme_Upgrader::bulk_upgrade() WordPress functions currently don't check that the array passed to it isn't empty, causing maintenance mode to be enabled even if no updates are required.

This bug doesn't affect non multisite installs, because for non multisite installs the code in Plugin_Upgrader::bulk_upgrade() and Theme_Upgrader::bulk_upgrade() only uses maintenance mode if the plugin/theme being updated is activated.

Fixes #491
Change ternary operator to simple if statement
Use empty() check instead of count()

Requested in https://github.com/wp-cli/wp-cli/pull/492#discussion_r4545088.
Merge pull request #492 from om4james/updateall

Only use maintenance mode if a plugin or theme needs updating
Allow capital letters in <value> tokens in @synopsis

Values in @synopsis tags are not matched if they contain capital letters.
This allows for capital letters i.e. --name=<myPropertyValue>
fixes #493
Merge pull request #494 from Future500/master

Allow capital letters in <value> tokens in @synopsis
remove `wp home` command
Merge pull request #496 from wp-cli/no-home

Remove `wp home` command