Ensure sub-diagnostic paths are correctly reported by the language server

[micahscopes]

See #1033 discussion for details.

To do:

• Come up with a way to track/lookup an InputFile's corresponding InputIngot so that we can get its correct absolute path.
• Ensure that InputFile paths are correctly set up in the language server (they should be relative to their corresponding ingot root)

[Y-Nak]

• Ensure that each InputFile is located within the root InputFile's directory. For example, if the root input file is my_lib/src/lib.fe, then all input files belonging to my_lib should be placed under my_lib/src.