Do not resolve symbolic links to repositories.

Do not resolve symbolic links to repositories.

When symbolic links under the base repository folder point to repositories
outside the base repository folder, the forming of relative repository
names failed and resulted in NullPointerExceptions.

Create the relative path by not following symbolic links, i.e. the link
name is taken as is and not resolved to the external path.

This also changes the whole `exactPath` method to work on Paths, instead
of Files.

Fixes #891 and fixes #837.