Not so long ago integrating software meant doing configuration management at the virtual machine level as integration took place. Taking snapshots and reverting if there was trouble. What you're left with a ~4Gb clunky file that you have to push around and convert to your eventual deployment environment. This is inefficient and risky. There's all the cruft that tags along as the builds take place. There's the complexities of image conversion. Some painful workarounds sometimes need to take place to move it between environments (VmWare, deleting network interfaces). Hostname problems (Oracle, thanks for that). Security implementation guidelines also change at a moments notice or in different environments. And what if you want to deploy it to bare metal after all?
Thankfully, some better tools are available. If you haven't figured out how to use Vagrant yet, go learn it right now. If you know what a vm is and can use the linux command line, it will probably take you all of 15 minutes to master it.
Here's the website: http://www.vagrantup.com/
Basically vagrant has one configuration file where you specify a baseline OS image (a .box file), some other parameters about how you want it to behave. I say basically because this file does kick off and point to other config files that deploy your software. To kick all of this off you type 'vagrant up'.
Log in to the resultant system ('vagrant ssh') then test, develop, capture the changes you care about in the deployment files. When you mess it up, instead of reverting, wipe the whole thing out of existence with another command: 'vagrant destroy'. Lather, rinse, repeat. Within a short amount of time, what you're left with are some finely tuned deployment scripts that can take any baseline OS image and get it to where you want with one command. Vagrant allows you to spin up multiple vms at the same time so you can emulate and test more complex environments in this manner.
Although vagrant supports chef and puppet, my preference has been to use bash scripts to deploy software. Bash scripting is accessible to most people. When collaborating with groups of people from different organizations, it serves as common language. Recently, I've taken my boilerplate vagrant configurations and put them online.
It's best to separate parts of the deployment process. Don't write the commands that secure the system in the same file as the commands that deploy software components or data. Abstract it all. Then, when your deployment environment changes you only have to modify or switch out that one file. You can capture the security requirements for Site A and keep them separate from Site B. Want to deploy to a Site C? Build it out and you're only one command away from testing if everything works. If a security auditor asks how you configured your system, then send them the deployment file. If they have a critique (and they're good) they can make the recommended changes and send them back to you where you can just test them by running 'vagrant up' again.
My boilerplate includes simple snippets for how to create users, push around files, append to files, wget things to where you want them, and other useful things that people forget when doing things from scratch (like writing the .gitignore). It should be easy to go through and modify it to do what you want it to do.
Here's a link:
It has Ubuntu as the base OS, here's a list of a bunch of other base OS's you can use without having to roll your own. Just modify the vagrant file.