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I was recently attempting to update some files using apt-get and was given an out space error. I then realized everything was being installed to the boot partition which is only 40mb (on a 32gb card). I am using the Raspbian Stretch Desktop image from https://www.raspberrypi.org/downloads/raspbian/. I simply flashed my card with that image.
How I do install stuff from apt to the other partition and rely on them always being in the system path?
Windows does not acknowledge the existence of Linux partitions. Your card will look like it has been shrunk down to 40 - 60 MB. This is obviously not the whole picture and Linux laptops and PCs will be able to access and show everything (including the correct amount of free space which will be in the gigabyte range !)
Please note that few packages touch /boot. APT honors such conventions and therefore /boot getting filled up is not default behaviour. It can only be achieved through severe misconfiguration.
In addition to the answer from @flakeshake there is no way to tell apt and apt-get where to install packets. This is coded in the packets itself. They all will install into directories from the root file system following the Linux Standard Base (LSB). On your SD Card you have two partitions: one 40mb boot partition with a fat file system and a root partition with the rest of the SD Card (nearly 32gb) with an ext4 file system, called the root file system. On this root file system there is an empty directory called /boot/. The 40mb boot partition is mounted to this directory so packets that install into the /boot/ directory will fill this limited partition. Seems there are some big unneeded files in the /boot/ directory (boot partition). Clean it up so packets needed very small space on the boot partition can be installed (firmware and hardware drivers).
