Add (post-)processing to remove bad files

[gerritholl]

Where problems persist, make sure some form of post-processing removes bad files, and compiles a list of files removed due to "problems". Analysis needs to also present some statistics on how often this happens, to be added to PUG.

To check:

• [ ] #161
• [ ] #170
• [ ] #171
• [ ] #155
• [ ] #162
• [ ] #281
• [ ] #296