tool setupCommand should run once per tool

[jcollins-g]

@gspencergoog

New ToolDefinitions are created for each ModelElement, so if defined, runSetup will actually execute once for each ModelElement it is referenced in.

Not currently a P1 because the tool definitions for Flutter don't require setups.

[jcollins-g]

Impact of this was reduced significantly as a side effect of #1865. Now it only runs a few times (technically, it runs as many times as the number of subdirectories of where the tool was defined where it is referenced).