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I recently bought a 240GB SSD. Before that, the system (Elementary OS Loki) was installed on a 1TB HDD, consuming 512Gb. My idea would be to leave the user's folder on the HDD, which consumes lots of disk space, and clone only the system folders to the SSD. If this really is not possible, I'd like to know how I can back up and restore programs (.deb packages) from one system to another.

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Short answer (if this was your question): Yes it is possible to mount the user folder, system folders etc. on different disks.

First of all for a better understanding of the directory structure:

/bin : All the executable binary programs (file) required during booting, repairing, files required to run into single-user-mode, and other important, basic commands viz., cat, du, df, tar, rpm, wc, history, etc.
/boot : Holds important files during boot-up process, including Linux Kernel.
/dev : Contains device files for all the hardware devices on the machine e.g., cdrom, cpu, etc
/etc : Contains Application’s configuration files, startup, shutdown, start, stop script for every individual program.
/home : Home directory of the users. Every time a new user is created, a directory in the name of user is created within home directory which contains other directories like Desktop, Downloads, Documents, etc.
/lib : The Lib directory contains kernel modules and shared library images required to boot the system and run commands in root file system.
/lost+found : This Directory is installed during installation of Linux, useful for recovering files which may be broken due to unexpected shut-down.
/media : Temporary mount directory is created for removable devices viz., media/cdrom.
/mnt : Temporary mount directory for mounting file system.
/opt : Optional is abbreviated as opt. Contains third party application software. Viz., Java, etc.
/proc : A virtual and pseudo file-system which contains information about running process with a particular Process-id aka pid.
/root : This is the home directory of root user and should never be confused with ‘/‘
/run : This directory is the only clean solution for early-runtime-dir problem.
/sbin : Contains binary executable programs, required by System Administrator, for Maintenance. Viz., iptables, fdisk, ifconfig, swapon, reboot, etc.
/srv : Service is abbreviated as ‘srv‘. This directory contains server specific and service related files.
/sys : Modern Linux distributions include a /sys directory as a virtual filesystem, which stores and allows modification of the devices connected to the system.
/tmp :System’s Temporary Directory, Accessible by users and root. Stores temporary files for user and system, till next boot.
/usr : Contains executable binaries, documentation, source code, libraries for second level program.
/var : Stands for variable. The contents of this file is expected to grow. This directory contains log, lock, spool, mail and temp files.

During a new installation choose custom install and create a new partition with the mounting point /home on your hdd. For the ssd choose '/' as a mounting point.

To backup and restore your programs you can follow this guide

Hope that helps a bit...

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