I have joined a new team, with that they have asked me to break down the differences of our RHEL environment settings compared to RHEL 6.x out of the box.  I have both images on one machine (one being the operating OS and one being the OS directory structure to compare.)  I know I can use diff or rsync but are those the best tools to use to see every single difference between folders/files in two OS's that should be identical?  Would some type of script work better?  
comparing two deployed Linux images
linux;shell script;filesystems