Make canonical paths relative to the repository root

[aeqz]

Clarification and motivation

After the #230 refactor, we will be using a custom FilePath canonicalization that is weaker than System.Directory.canonicalizePath. It currently applies a FilePath.makeAbsolute transformation and we can try to avoid it in order to reduce some filesystem state dependency.

Acceptance criteria

• If possible, replace the FilePath.makeAbsolute transformation in our canonicalizePath function by another transformation that allows us to hold paths relative to the repository root instead of absolute ones.