Once you have some sites set up, a basic WordShell command that deals with a single site looks like this:
wordshell <site-nickname> <options>
or if working with a particular plugin:
wordshell <site-nickname> <plugin> <options>
Note that that order always applies; the site is always first (if any), then the plugin (if any), then the options.
Instead of a single site, you can perform an operation upon multiple sites, by comma-separating them:
wordshell <site-nickname>[,<site-nickname2>[,...]] <plugin> <options>
If you want to perform an operation on all known sites, then for the site nickname you use “all”. Similarly if you want to perform an operation on all known plugins on a site, you use “all” as the plugin name.
For example, to list all plugins on a certain site:
wordshell mysite --list
Or to list all plugins on several particular sites:
wordshell mysite,site2,site3 --list
Or to list all sites for which Akismet needs an update:
wordshell all akismet --listupdates
Or to update every plugin to the latest version on a certain site:
wordshell mysite all --update --latest
If no options are given, then the default mode of “update” is assumed. So this line means exactly the same as the previous one:
wordshell mysite all --latest
Note that when referring to a plugin, you refer to its short name, which WordPress calls its “slug”. This means things like “akismet”, “contact-form-7”, “nextgen-gallery”. If you find a plugin in the WordPress plugins directory (http://wordpress.org/extend/plugins) and note its URL, then it will be something like http://wordpress.org/extend/plugins/cimy-user-fields – the last part (cimy-user-fields) is the “slug”.