Linter include dirs cache out of date

[gnikit]

Describe the bug
The cache in the linter can be out of date if a file is renamed or deleted. Fundamentally this means that the cache should also allow for directories to be removed

To Reproduce
Change the include dirs in the settings and check what is `included

Build info (please complete the following information):

• OS: Linux x64
• Extension Version 3.0 pre-Release
• Visual Studio Code Version 1.67.0