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I need help deploying an application on my Amazon Linux server and the remote worker that I'm working with will likely need to be provided with root-level access. I've never provided anyone else access to my server, so am worried about how to track changes that are made.

Monitoring bash / commands:

I've considered using ~/.bash_history to monitor command-line changes, but it doesn't list the directories from which the commands are coming, so I'm not sure it's a complete solution

Monitoring changes to files / directories:

I'm looking for something like git but for the whole system... Is there a way of doing this? From what I've read, running 'git init' at / is not a viable option.

What are good ways of monitoring / logging changes at the user level across the server ?

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    Look into the Linux audit framework and/or /etc/sudoers. bash_history can be easily deactivated, this is not an option at all. Final rule: If you don't trust someone, don't give them root access. – Sven Dec 23 '15 at 1:12
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Running auditd would probably work for you (assuming you configure sudo for the worker to not allow him/her to disable it).

See http://security.blogoverflow.com/2013/01/a-brief-introduction-to-auditd/

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