Properly handle replacing of files, rerun jobs when file is replaced

[nagem]

Closes #878
Closes #1081

Test fixes and additions yet to come

[nagem]

@gsfr How this affects the reaper:

If a reaper (or anything) sends a file to a container with the same filename:

• If the file object is the same (via hash), the existing file object in the file system and in mongo is unchanged. The file update is ignored.
• If the file object has a different hash, the existing file object is removed from Mongo and a new file is added to Mongo with metadata specified on that upload. All new jobs resulting from rules are run, as well as all old jobs that had this file as input.

Let me know if this is contrary to what you'd expect.