Revert "store: pass list of indexes when pruning a subgraph" #9232

Job	Run time
Subgraph Runner integration tests	3m 41s
Run integration tests	5m 20s
Clippy linting	1m 53s
Build in release mode	1m 4s
Check rustfmt style	5s
Run unit tests	7m 41s
	19m 44s

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