Move navigation mesh baking to NavigationServer

[smix8]

Moves navigation mesh baking to NavigationServer.

• Moves the 3D NavigationMesh parsing and baking from NavigationMeshGenerator to NavigationServer3D.
• Deprecates the NavigationMeshGenerator singleton.
• Splits the monolithic geometry parsing code into node specific functions.

Fixes #79843.

Requires #79157 to be merged first as a substitute for NavigationMeshGenerator.clear().

The other public functions from the NavigationMeshGenerator can already be found on the NavigationServer3D since Godot 4.1 and #77412.

Updating the NavigationMeshGenerator for further developments is not feasible as the NavigationServer needs to be in full control of the navigation mesh baking process going forward. E.g. for internal threading support or the change to a navmesh instance system as part of the server, or better agent sizes support. The old NavigationMeshGenerator also had nothing but problems from init chain to extendibility and required workarounds and extra functions like #79137.

[smix8]

EDIT
Removed the parsers, nothing but problems with both init and certain platform builds with them, not worth the trouble.

[smix8]

Made the node parsers more readable by splitting them into their own functions.

Now the Editor NavigationMeshEditor (should be renamed NavigationRegion3DEditor because that is what it is) uses the same function as the NavigationRegion3D for consistent bake behavior. Changed that the NavigationRegion3D did entire NavigationMesh resource duplicates for each bake. This not only drained performance on large meshes but also made the bake behavior different in the Editor as compared to baking at runtime. For the future duplicating the resource all the time would also make the resource RID change / invalid all the time as soon as instances get added so it needs to change anyway at some point.

[smix8]

Added a fix for the CSGShape3D collision and changed some functions due to changes in a subsequent pr.

[akien-mga]

Thanks!