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There is no canonical book that I know of. I'm sure there are some books though if you check Amazon for "Linux System Administration". They might not be a bad place to start.

I use rsync for backups. Storing configuration management files in Git works. Puppet and Chef are the most popular configuration management systems, they work just fine.

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Chef for configuration files. Customisations for Chef Attributes are in a json.php file on the chef host that merges various things like specific settings for a datacenter, host role, etc.

Google Docs for certain information as well as a wiki. There are Standard Operating Proceedures (SOP's) for numerous tasks also in the wiki which explains things in detail.

Munin for graphing along with some metrics being polulated into Zabbix.

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