Diagnostics can become stale when switching between `<module>.lua` and `<module>/init.lua` structures (such as when going back and forth between git branches)

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

Visual Studio Code Extension (sumneko.lua)

### Which OS are you using?

Linux

### What is the issue affecting?

Diagnostics/Syntax Checking

### Expected Behaviour

Diagnostics should always be performed on the current version of a module that is on disk.

### Actual Behaviour

When switching between two different ways of structuring the same module as described in the title, diagnostics can populate the `Problems` panel in VS Code with information about the version of the module that was on-disk before switching using a mechanism such as `git checkout `

### Reproduction steps

1. Make sure `Runtime Path` includes `?.lua;?/init.lua`
2. Create a module at `foo.lua`, populate it with working Lua code.
3. Create a new `git` branch
4. Refactor `foo.lua` to `foo/init.lua`
5. Various diagnostics will show up in the VS Code Problems Panel, such as duplicate definitions, missing annotations, etc. It almost looks like the LSP is trying to process both files at the same time.

### Additional Notes

_No response_

### Log File

I won't be able to provide logs as this is a proprietary codebase. Apologies.

Reproduce the issue with Runtime Path set to `?.lua;?/init.lua` by switching a git branch from `foo.lua` to `foo/init.lua`, then inspect the VS Code Problems panel for diagnostics from the previous module layout. Compare the diagnostics with the current files on disk; done means only the current module structure is analyzed after the switch.

Written by the indexing model from the issue text.