Ruby 1.9
gem install shopify_theme [optional_theme_id]
Generate the config file. Go get a valid api_key and password for your store head to https://[your store].myshopify.com/admin/api and generate a private application. Default it adds the main theme, if you want to edit one of your other themes, add the theme_id.
theme configure api_key password store_url
Download all the theme files
theme download
Upload a theme file
theme upload assets/layout.liquid
Remove a theme file
theme remove assets/layout.liquid
Completely replace shop theme assets with the local assets
theme replace
Watch the theme directory and upload any files as they change
theme watch