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
Merge branch 'master' into dev
Merge branch 'master' into dev
bump version to 0.11.0-alpha
Merge branch 'dev'