VSCode - Language Server Diagnostics Not Loading Default Libraries

### How are you using the lua-language-server?

Visual Studio Code Extension (sumneko.lua)

### Which OS are you using?

Windows

### What is the issue affecting?

Diagnostics/Syntax Checking

### Expected Behaviour

No errors on the following code:

```Lua
Core = {
Shared = {
Functions = {}
}
}

---Makes a deep copy of a given object.
---Does NOT handle metatables or recursive tables.
---@param Obj any The object to be copied.
---@return any Cpy The copied object.
function Core.Shared.Functions.DeepCopy(Obj)
if Obj then
local Cpy = nil

if type(Obj) == "table" then
Cpy = {}

for K, V in pairs(Obj) do
Cpy[Core.Shared.Functions.DeepCopy(K)] = Core.Shared.Functions.DeepCopy(V)
end
else
Cpy = Obj
end

return Cpy
else
return nil
end
end
```

### Actual Behaviour

Both the `any` annotation type, as well as both the `type()` and `pairs()` functions, display an error through the diagnostics. However, they are still seemingly recognized internally on all other fronts, as hovering works just fine on the functions, and the `any` annotation will be properly recognized for the type it is, displaying an error if missing a return and not displaying an error if all returns are present.

This only seems to affect the `undefined-global` and `undefined-doc-name` diagnostics. Other than that, I have no idea what caused this...

### Reproduction steps

1. Open VSCode.
2. Ensure Sumneko's Lua extension is installed and enabled.
3. Create a new lua file.
4. Attempt to use any built-in functions or annotations. The error should appear.

### Additional Notes

I have spent all 12 hours of my day today trying to figure this out. I'm tired, frustrated, and at a complete loss as to why this is even happening, especially considering it was working just fine as little as last week. My extension has been updated to the most recent version pretty much since the most recent version released.

I'm sure, absolutely positive that I messed something up. But I don't know what. I heard the use of system links can cause issues, but for one the only system links I have are junctions pointing to the install directory of VSCode. Beyond that, from briefly looking at the logs at least, it does not seem like the LS is even using my system links, electing instead to use the full path from my A drive instead of the shortened one on my C drive. Not to mention I've been using system links for well over a year now with absolutely zero issues.

All I did, and I swear all I did, was manually define `Lua.workspace.library` to an LLS-Addon. That's when the issues started happening. I tried restarting VSCode, restarting the language server, restarting my computer, even reinstalling the extension. Made sure it cleanly uninstalled and everything, even cleaned up my entire user data directory for VSCode for good measure. The issue was still there.

Again, I am sure, almost positive I just...changed a setting or something and forgot about it. But I've been through the configuration settings well over a dozen times at this point, and everything to even remotely do with diagnositics or libraries is at it's default setting.

### Log File

[service.log](https://github.com/user-attachments/files/19528644/service.log)

[workspace.log](https://github.com/user-attachments/files/19528650/workspace.log)

Start by reviewing the attached service.log and workspace.log alongside the Lua.workspace.library setting, especially the manually configured LLS-Addon. Reproduce the issue in a new Lua file using type(), pairs(), and the any annotation; done means built-in functions and annotations no longer trigger undefined-global or undefined-doc-name diagnostics.

Written by the indexing model from the issue text.