[ENH] Document GraphDB setup script and other setup clarifications (#180

)

* document how to use graphdb_setup.sh

* add notes on redeploying + changing user permissions

* clarify GraphDB does not need to be downloaded

* shorten descriptions

* indicate path for data-config.ttl

* move setup details into admonitions and remove Stardog instructions

* add new section on updating graph config

* minor section refactoring

* reorder info boxes and add example cases for resetting graph