Missing data when exporting with `Full Collection Hierarchy` + `Active Scene` on

[janhohenheim]

What versions are you using?

Software	Version
OS	Fedora
Blender	5.0.1
Bevy	0.18
bevy_skein (Rust Crate)	irrelevant
Skein Blender Extension	0.1.15

Describe the bug

I find it easier to describe the issue in one section, so forgive me for partially disregarding the bug issue template.

In the Blender file attached below, the export option Data -> Scene Graph -> Full Collection Hierarchy is turned on.
The Blender file has the following setup:

• Main Scene
  • Instance, a collection instance of Collection
• Prefab Scene
  • Collection collection holding a Sensor component
    • Empty holding a ColliderMarker component

What I would expect with this configuration is an export that includes the scenes, and in Main to have a hierarchy containing both the Sensor and further down the descendants the ColliderMarker.
And indeed, that is what I get! That's the part that works well:

glTF 1

{
	"asset":{
		"generator":"Khronos glTF Blender I/O v5.0.21",
		"version":"2.0"
	},
	"scene":0,
	"scenes":[
		{
			"name":"Main Scene",
			"nodes":[
				1
			]
		},
		{
			"name":"Prefab Scene",
			"nodes":[
				4
			]
		}
	],
	"nodes":[
		{
			"name":"Instance"
		},
		{
			"children":[
				0
			],
			"name":"Scene Collection"
		},
		{
			"extras":{
				"skein":[
					{
						"avian3d::collision::collider::backend::ColliderMarker":{}
					}
				]
			},
			"name":"Empty"
		},
		{
			"children":[
				2
			],
			"extras":{
				"skein":[
					{
						"avian3d::collision::collider::Sensor":{}
					}
				]
			},
			"name":"Collection"
		},
		{
			"children":[
				3
			],
			"name":"Scene Collection"
		}
	]
}

The trouble starts when I want to export only Main Scene. Let's turn on Include -> Active Scene and export again:

glTF 2

{
	"asset":{
		"generator":"Khronos glTF Blender I/O v5.0.21",
		"version":"2.0"
	},
	"scene":0,
	"scenes":[
		{
			"name":"Main Scene",
			"nodes":[
				1
			]
		}
	],
	"nodes":[
		{
			"name":"Instance"
		},
		{
			"children":[
				0
			],
			"name":"Scene Collection"
		}
	]
}

As you can see, there's no Skein data in here. Weirdly enough, Empty is also missing?! Am I misunderstanding something here, or is this also a glTF export bug?

Additional context

Repro: repro.zip
sorry for the zip, but GitHub doesn't let me upload the blend file directly.

[ChristopherBiscardi]

Thanks for the repro!

I believe this will end up being a bug in the upstream gltf exporter, but will have to dig in to diagnose and know for sure.