I was looking more at:
core_role_assign_roles and core_role_unassign_roles
core_files_get_files and core_files_upload
All four require the contextid to be passed as a parameter.
I've no problem about abstracting the internals away from the ws, the fewer parameters the better as far as I'm concerned. However trying to write a "complete" Java library to interface with every ws call and then test is challenging because of the contextid's used in the above calls. Currently I have modified the code to include both the new and depreciated calls and am in the process of creating some basic javadoc comments. There is some tidying up as in the original library did not include preferences and custom fields when creating a new user.