do not index py_binary unless in file mode

[linzhp]

This is yet another implementation of #2822. Based on this:

rules_python/gazelle/python/generate.go

Lines 248 to 252 in 94e08f7

	// Remove the file from srcs if we're doing per-file library generation so
	// that we don't also generate a py_library target for it.
	if cfg.PerFileGeneration() {
	srcs.Remove(name)
	}

The only case when a python file does not exist in py_library is in file mode. Stop indexing py_binary in other mode to avoid ambiguous dependency resolution.

[linzhp]

This PR is ready for review. The failing CI is an infra issue