Fix inconsistent IsDirectDependency="true" in baseline generation

Baseline generation doesn't seem to consistently choose whether to include `IsDirectDependency="true"` when filtering to `Distinct` usages. I think this causes spurious changes in baseline updates:

```diff
-
+
```

We should do something like use the "maximal" `IsDirectDependency="true"` value (include it if *any* usages are `true`), or just trim this attribute entirely from the baseline. (You have to look at the full annotated usages file to be effective at removing prebuilts anyway.)