Whats your best practice method for backing up, documenting and adding Contributions?

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Anyone have recommendations on trying to keep track of the various changes being made to files as you add Contributions. The obvious 'backup' is a good start, but other than that is there other hints people can recommend to keep track of change?

 

I'm new to this and beginning to see a potential problem down the road as we work on building our site. The obvious problem I see is that certain files can get changed more than once as you add contributions and/or if you want to exclude certain features or functions. I have made changes to the original files to omit the Manufacturers and a few others, and I have also added 3 contributions. I figured I would just print the instructions and highlight the respective changes. However I also added another Contribution but the install asked for the script to be run from the PHP admin, so I am not really sure what changes it has made to the respective files. Add this to the growing pile of printouts and this does not seem to be a smart way to do it?

 

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