Emit a warning if includeInputSubdirs is unintentionally unset

[kmoscoe]

It's easy to forget this, and if you do, you'll likely end up with some impossible-to-debug errors because of references to missing objects.

I think the Java test failures are bogus; just flakiness.

[codacy-production]

Up to standards ✅

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[gemini-code-assist]

Code Review

This pull request adds a warning log in simple/stats/runner.py when an input store is a directory but include_input_subdirs is disabled. The reviewer noted that this implementation will trigger false-positive warnings for standard flat directory imports that do not contain subdirectories, and suggested checking for the actual presence of subdirectories before logging the warning.

[gmechali]

Hey Kara, I dont think this is worth doing tbh, no one will read through those logs...We gotta handle it better right off the bat.
I guess it doesnt hurt either.

[kmoscoe]

Hey Kara, I dont think this is worth doing tbh, no one will read through those logs...We gotta handle it better right off the bat. I guess it doesnt hurt either.

So would it be better to do the Gemini suggestion, and automatically the option to true in this context? I just thought that if (in the rare case) the error was not the missing option but the directories, they could intentionally correct it. But it seems like an unlikely case.