Hey ashkan
Our live environments are under ubuntu 16.04 + php5. If you can downgrade php until we cover php7 that is fine (it's in our roadmap for next version).
Let me answer question by question below:
1/ Cron indeed looks for missed hashes on VirusTotal. If your API becomes limited at some point it will skip files once you reach the limit (until next cron iteration).
I'm not sure to understand your question regarding VT API v2, we are already using v2.
2/ Yes please look at API documentation, there's a python upload script example. Feel free to reuse and modify:
https://www.adlice.com/documentation/mrf/documentation/#api3/ You need to prepend /mrf to every page in the "leftnav" section and also in "urls/baseurl":
https://www.adlice.com/documentation/mrf/documentation/#config4/ do you have specific error in your apache logs? php.ini would be indeed the place to modify (upload_max_filesize and post_max_size)
5/ same question, do you have any error? Can you show me the config file, especially the "urls/storagePath" ? Make sure this folder exists and is in php available basedir
6/ you can use the search (date field) then bulk select (checkbox in the toolbar) and use "Download ZIP" button (under "Download" multibutton)
7/ can you tell me the purpose of using socks instead of http queries?
Regards,