Fix flake8 staged file paths

Similar to d55a040ba, this is a fallout from changing the signature of
`staged` back to `StagedFile` instances.

I also standardized on the `collect(:path)` syntax to make things more
consistent.

Change-Id: Ic2210fc2508c2bbd277aed8f14521a5b6c428e5f
Reviewed-on: https://gerrit.causes.com/27375
Tested-by: jenkins <jenkins@causes.com>
Reviewed-by: Greg Hurrell <greg@causes.com>