> Is this just for your own exploration

Yes

> in which case you might want to avoid Fuseki entirely and just work with TDB

I can issue SPARQL queries directly at TDB2 without using Fuseki?

My original problem still stands tho :) Is "s-put" the only way to replace a 
graph in a TDB2 dataset? Is there any CLI tool (non http) that can manipulate a 
TDB2 dataset to replace a graph with another (eg. replace wikidata with a new 
dump)?

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