Bugfix: Correct statistics for overlapping backup sources

A user reported that restic's statistics and progress information during backup
was not correctly calculated when the backup sources (files/dirs to save)
overlap. For example, consider a directory `foo` which contains (among others)
a file `foo/bar`. When `restic backup foo foo/bar` was run, restic counted the
size of the file `foo/bar` twice, so the completeness percentage as well as the
number of files was wrong. This is now corrected.

https://github.com/restic/restic/issues/3232
https://github.com/restic/restic/pull/3243