Even if you don't feel confident enough to modify the program, you can often get an idea of how it works on the inside, and this can be very helpful in using it. But more important, it allows you to apply patches to the code.
Many special customizations for Linux are distributed as patches to the source code. You take a patch file, apply it to the source code with the 'patch' utility, and recompile. You then have an application customized in a way that's nearly unheard of outside the world of Linux.
For example, I increased the size of my SCSI data buffer using a patch, so that my scanner could transfer data faster and my scans would finish quickly.
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