Improve ls_files for generating the codecov manifest

[Daverball]

Currently the plugin assumes it's either being run from the project base directory or inside a git repository with the optional GitPython dependency installed to generate the manifest for the coverage results.

There's two improvements that should be made here:

1. Without GitPython it should be possible to manually set the project root using a command line option or environment variable, e.g. --codecov-project-root
2. Whenever coverage is measured across a subfolder in the project using --cov=subdir or equivalent config file options we should filter the output of ls_files according to this sub directory, the manifest should still list these files relative to the project root however, because otherwise codecov.yaml would need to contain path fixes.