What is the difference between Linux distributions? E.g. Fedora and Ubuntu
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Some are stable. They have tested software, and therefore, are dependable with few or no bugs. They will work every time the computer is turned on. Others are less dependable, with newer software that occassionally has bugs.
Some are built around a specific GUI, while others are GUI independent.
Some have a committment to free software, where others could not care less about the goals and values of free software and include all manner of proprietary software.
Distribution: Debian Sid AMD64, Raspbian Wheezy, various VMs
As I understand it Fedora and Ubuntu use different flags when compiling the kernel and I dare say this will be the same with other software. Without looking through the source and make files for everything nobody's going to be able to give a quick answer beyond the lists you, yourself, have given.
I mean in terms of code what is the difference between Fedora and Ubuntu.
Well, the large part of that answer was posted above by Randicus Draco Albus in the post above yours. Every time that you take a decision, you decide for something and against other things. When you take decisions, time after time, that builds up and it all then depends on the basis on which you were taking those decisions (prioritising stability above 'latest, greatest', for example).
So, what sets distros apart:
'one GUI' vs 'multi GUI' (which is sort of package availability, but the most important, in many cases)
support arrangements (paid, fora, tech docs, bug reporting, community, etc)
The stuff that a lot of people get hung up about (wallpapers and appearance) isn't really that important, as that's more a matter of defaults, because, if you really wanted to, you could use wallpapers from another distro...a slight pain, but not much more than that, if you are determined.
Another factor would be the extent to which the distro chooses sensible defaults when it installs apps, or the extent to which it thinks that it should be left you or gives you tools to manage that - particularly, if you think about networking apps, you can probably install a similar collection of apps on almost any distro, but do you have to do all of the footling around with config files yourself, or is there some help? And if you set an ip, does it go everywhere that needs it, or do you have to set it in a lot of bits separately (and will always miss one or more, first time out the box).
BTW, you have probably earned the ire of St Gnucius (sp?); you haven't given any credit to the GNU utils, and particularly the choice of something like busybox, or not. (And, embedded, if you were targeting a deeply embedded application, there would probably be a completely different set of apps that you would want...or a network appliance, such as a firewall box, it would be undesirable to have extra apps installed, because they could represent an extra security risk...so you would want an installer that didn't default you into, eg, Libre Office, or something, so you would need that granularity of control, in the way that would probably just be a pain if you wanted to install 100 desktop systems).
Well, as said before. Many valid points. The main difference is what you want to achieve.
I personally like stable and don't care aboit gui's so i like things to just work for what i need. So i never have extravagent hardware or the latest this and that. So i choose RHEL, Centos or debian. He first and 3rd being pretty much dinosaurs and and not too pretty to work with but they get the job done first time round.
Fedora ubuntu et al. If you have more modern hardware or looking for an easy transition from windows or want to run the greatest and latest.
One big thing is the kernel parameters they use for tuning to specific needs. I personally like all the policies that RHEL and centos has with selinux whee almost nothing works until you permit the required MAC booleans.
I can't speak "in terms of code," but reputation is something to be considered. Fedora is thought to be somewhat cutting edge, staying close to new versions of software. Ubuntu is the distribution that made Linux "user friendly" for "the masses." It has an easy installer and makes installing new software very simple, either from the command line or from the Software Centre. When I was learning Linux on Ubuntu or its derivatives, I really appreciated that I'd get a response like "<command> is not found. To install it, type 'sudo apt-get install <command>' ". I think Fedora assumes its users know that.
Otherwise, it's a matter of the default Desktop Environments and program managers. I didn't care for either Fedora's default Gnome or Ubuntu's default Unity, which is one reason I no longer use either distribution.
Another element is the amount of control the user is given in configuring the system, or how easy it is to configure. In Ubuntu, Ubuntu is the root user. The best you can do is use sudo. People who like more control over their systems tend to gravitate toward other distributions. The ultimate control freaks choose Arch, Slackware, or Gentoo. Others find a middle ground between Ubuntu and those, ones with "sensible defaults," as a lot of materials phrase it, but sensible is very much in the eyes of the user.
Fedora will use more up-to-date software. So will Arch and possibly Gentoo. Other distributions, like Ubuntu, will use older versions of software, upgrading only when they think enough of the bugs have been worked out and they know the software provides a good-enough experience for the user. The same is true of kernels.