An item with the same key has already been added. Key: res://MainFile.cs

[SyraLessThanThree]

When Godot.Bridge.ScriptManagerBridge.LookupScriptsInAssembly(Assembly.GetExecutingAssembly()); is added to the MainFile all .cs files are also added to the godot filesystem.
So there is gonna be an error
An item with the same key has already been added. Key: res://MainFile.cs
when multiple Mods have Godot.Bridge.ScriptManagerBridge.LookupScriptsInAssembly(Assembly.GetExecutingAssembly());
and .cs files of the same name in the same Location.

In the Templates that specifically happens with MainFile.cs.

Moving them to the folder of the modname would fix that unless they have the same name (in which case we have bigger problems anyway).

[SyraLessThanThree]

The error doesn't change behavior in any way and all the mods still work as intended.
But it shows that mods loaded with errors which can be confusing so this would be a better approach.