Fixup for make.py checks

[pdeiml]

This is a issue which is intended to collect all fixups which are related to 'make.py checks'. It also collects everything which should be but have not been implemented in 'make.py checks'.
Feel free to start a discussion about something!

• @cdeil Please write down a short sentence about issue_123 (close and reference issue_123 afterwards?)
• @cdeil Please write down a short sentence about issue_54 (close and reference issue_123 afterwards?)
• Do all references in /input/sources/ have a corresponding folder and file in /input/data and vice versa
• Printing a table with 'source_id', 'data_entry_status', 'review_required' as columns. 'data_entry_status' and 'review_required' refers to the keywords of the same name.
• Check the name of the folder in /input/data// with the keywords reference_id given in the files in the folders

[cdeil]

Suggest to discuss and do improvements for the scripts one step at a time and to close this issue. That's just pragmatic, given that no-one has a week to do the re-write.

Generally there should be some checks that no old files are around in the input and output folder and all files are in the index files. And then all other checks should start with the index files.

When referencing other GH issues, use th # character, so that a link is created. In this case you mentioned #54 and #123 above.