A few of the class/javadoc links in the various configuration topics may not yet be updated after the V5 release. Feel free to file Jira issues if you find specific cases.
CommandLines
The bin subdirectory of an IdP installation provides multiple command line utilities. Many (but not all) are a thin veneer over the https://shibboleth.atlassian.net/wiki/spaces/IDP5/pages/3199511365.