To prevent the former causing future problems, use the setting in Synaptic Package Manager:
Settings -> Preferences
Files tab
Delete downloaded packages after installation
Or manually clear the packages each time with
sudo apt-get clean
sudo apt-get clean
You can repair the boot sector of Windows system partition via "fixboot" from a Windows XP CD, or "bootrect /fixboot" from a Windows Vista/7 CD. But in my experience testdisk works best in this situation. So boot into a Linux OS or Live CD. If your system uses "apt-get" and has "testdisk" in its repositories (in Ubuntu: the universe repository needs to be enabled), you can install and run testdisk via
sudo apt-get install testdisk
sudo testdisk
or you can download the tar.bz2 file of the newest version from testdisk to your desktop and install and run it via
cd ~/Desktop
tar -xvf testdisk-*linux*.tar.bz2
sudo testdisk-*/linux/testdisk_static
In either case:
First screen: Select "No Log" and press enter.
Second screen: Select the hard drive containing the Windows system partition and choose "proceed".
Third screen: "intel"
Fourth screen: "advanced",
Fifth screen: Select the Windows system partition and choose "boot"
Sixth screen: "BackupBS"
Seventh screen: type "Y" to confirm
then press "q" a few times to quit testdisk, reboot and see whether you can boot into Windows. If the sixth screen did not have a "BackupBS" tab, it usually means that the original and backup boot sector are identical, and you are probably suffering from a different problem. But it could also mean that your backup boot sector is corrupted, in which case you will of to use "fixboot" from a Windows CD to repair the boot sector.
After you fixed the Windows boot sector, you might have to update the Grub Menu. For Grub 2 just run
sudo update-grub
in your Linux OS. For Legacy grub you might have manually edit /boot/grub/menu.lst
Upgrade Packages: Over time, updated versions of packages currently installed on your computer may become available from the package repositories (for example security updated). To upgrade your system, first update your package with
sudo apt-get update
and then type:
sudo apt-get upgrade