Known usages/subtypes missing in pkl-doc model version 2

[sin-ack]

It seems #1169 introduced a typo here:

pkl/pkl-doc/src/main/kotlin/org/pkl/doc/RuntimeData.kt

Line 159 in 55eac20

fun perPackageVersion(): RuntimeData = RuntimeData(knownVersions = setOf())

This should be using copy, otherwise all data is dropped. This is preventing pkl-doc from generating known subtypes/usages in class pages.

[sin-ack]

Additionally, there's addKnownUsages missing here which also prevents usages from being included in the JSON file:

pkl/pkl-doc/src/main/kotlin/org/pkl/doc/RuntimeDataGenerator.kt

Lines 211 to 216 in 55eac20

	val (data, _) =
	ref.existingPerPackageVersionRuntimeData.addKnownSubtypes(
	ref,
	newSubtypes,
	descendingVersionComparator,
	)

[sin-ack]

One more, this is causing known usages to be added to known subtypes on subsequent runs of pkldoc on the same output directory:

pkl/pkl-doc/src/main/kotlin/org/pkl/doc/RuntimeData.kt

Line 131 in 55eac20

(this.knownUsages + newLinks).distinctByCommparator(comparator).sortedBy { it.text }.toSet()