The problem data is accessible in all plugins.
The problem data contains the (preprocessed) graph, several constraints and further information.
The function SCIPprobdataCreate(), which is called in the reader plugin, parses the input file reduces the graph, initializes the problem data structure and creates the problem in the SCIP environment. See the body of the function SCIPprobdataCreate() for more details.
A list of all interface methods can be found in probdata_stp.h.