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I was facing a lot of grub problems which couldn't be solved otherwise, and hence reinstalled. But to keep my old software, I did not format the usr n opt for which I've separate directories. Afterwards, I mounted them in their positions and edited/etc/fstab to get back my previous state .. of course I had to install mono again, since I guess it's stored in bin, lib, et al, rather than usr/bin, usr/lib, et al .. every software is working perfectly as expected. However, I had no idea that the dpkg stuff aren't stored in usr. (/var, /etc was & is in the same partition as / ) Hence, I can't upgrade my kernel or other stuff .. is there any way to make apt-get check all the software in usr and update it's lists, and maybe correct the dependencies of they are available under the repos in /etc/.../sources.list? Of course, I must add the required ppas, and reinstall stuff outside usr, such as some compilers. Furthermore, just a suggestion in the wrong place I believe, can't there be 2 or more extra lists, in usr & under /, which store the names of the packages installed under it, and cross location (in or out of usr) dependencies, so that apt-get accesses them such that in case someone does something like what I did, apt searches the list and updates it's main list?

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seems like you messed up your installation with the reinstall, there are complicated methods to fix this, and yet you might end up with a broken installation, which would be very susceptible to future version upgrades, i won't advice that, given that i tried them a while back and its kind of more work than output, hence keeping usr or other dirs from old installations in not very "cool" so as to say, for reinstalation i now maintain a script of all the stuff(pkgs and repos) i need in a script file and run that after a reinstall, i only catch being you need to have an unlimited(so as to say) data connection.

the simple redundant process would be a complete re-installation, for the grub related problems i'd advice you to get to know grub installations or in case of a dual booting sytem use grub4dos which is much simpler, from a usb live system or checkout the gui distro http://sourceforge.net/p/boot-repair-cd/home/Home/ or boot-repair in general,

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