#430 Reprocessing job misses same named file in same transfer job

[Terry O'Neill]

To reproduce this error follow these steps:

1. Create a transfer job with two files with the same name (different directories)
2. Process this transfer job into the repository
3. Create a reprocessing job
4. Process this job through the Preservation Facility

Now if you look at the pf_data directory that has resulted you will see that only one of the files is still present. This is because when pulling out the original files from the xena files the reprocessing job simply puts them all in the base directory regardless of what directory structure they were in before (even though this directory structure is recorded in the xena file). This needs to be changed to prevent files being overwritten, either by using the same input directory structure or handling file name clashes.