The API for FHIR Toolkit is an early prototype that lives on the branch api. Its current capabilities are to create and delete channels and to run server tests against a channel. The file fhirtoolkit.javadoc.zip contains the generated JavaDocs.
There are two integration tests (on branch api) that demonstrate some basic capabilities.
ChannelApiIT - create, get, delete a channel
TestApiIT - run a conformance test against the default channel (integrated HAPI server)
As noted above the API lives on its own development branch for now and is not part of any release. When we have expanded the capabilities to a useful point it will be added to the main development branch and released with the toolkit.