You can flatten an XML schema that contains multiple includes and redefines to a single schema file from Oxygen XML Author Eclipse plugin by using the main menu action. You can use the equivalent flattenSchema.sh script (found in the scripts subfolder inside Oxygen's installation directory) to flatten an XML schema from the command line.
sh scripts/flattenSchema.sh [-in:inputSchemaURL -outDir:outputDirectory
[-flattenImports:<boolean_value>]
| [-useCatalogs:<boolean_value>]
[-flattenCatalogResolvedImports:<boolean_value>] [-verbose]]