Linux From Scratch 7 Released

Personally, I tracked file/package relationships with a simple script. Easy to do.

Tracking package dependencies is more difficult, and I usually did this manually with some help with some specialized scripts.

Plus side is you can avoid dependencies you don't like and add functionality where you need it. You can make a developers heaven this way. Usually the only way I do serious Linux development is with an LFS-based system. When I use distros I usually spend a lot of time creating a specialized environment and the time saving in using a distro is sort of nullified.

Bad side is obviously if you want to upgrade a vital dependency you'd have to upgrade all forward dependencies also. Not so difficult if you have it scripted, but errors are hard to handle. Of course, an LFSer would usually know how to install different versions of packages and have them co-exist. However, mostly you just want to keep top-level packages updated, which is easy to do (e.g. Firefox, developer tools).

http://www.linuxfromscratch.org/alfs/

Although there's little documentation to speak of, so I can't tell whether it helps with upgrades.

If you want to build from source and tinker with compile flags but also be able to upgrade seamlessly, Gentoo or Arch Linux is probably more appropriate.

Some time ago when I started to learn Linux I have tried a lot of different distributions. All of them had their quirks. Some were buggy. Some were slow. Some had extremely weird and bloated configuration systems. Imagine several layers of abstraction above plain standard configuration files when you have to learn everything basically from the beginning with a different distribution. For example on top of standard config files they may have some configuration system (like YaST in SUSE) on top of which the GUI sits (so 3 layers just to change the screen resolution). Many distros have their own "unique" way of configuring the system. And when something will brake you will have no idea where the problem might be. Is it a bug in the package or in some layer of configuration system or somewhere else? I understand that they try to make the system more user friendly. Well, every one has its own niche.

With LFS you just learn the configuration of basic packages once. The way that package creator intended. Plain text files and nothing more. As an additional bonus you have great performance and security because you only have the packages you need. Plus everything is optimized for your architecture. If you have ever used some distribution in a virtual machine on a slow notebook you know what I am talking about.

When I built LFS for the first time I did everything by hand. It was a very useful experience and a nice way to learn. Of course now I don't do it manually. You can use automated tools (jhalfs for example) which extract instructions from the book and do everything for you. I don't use any graphical environment so no need to build a lot of stuff beyond the base system.

Of course LSF has its own issues. Lack of package management is one of them. But if you like minimalistic and fast systems you should give LFS a try.

I'm not sure it's worth the hassle for an ongoing installation, unless you have specific requirements around a minimal tuned distro. But it's excellent for learning.

Nowadays distributions like Ubuntu allow you to install a full system with just a few mouse clicks, which is great for usability but not much use if you want to learn how everything works.