How to reinstall Jessie without loosing files?

How can I reinstall Jessie without loosing files and already configured
applications? I am a Linux beginner and have my Raspi running for a long
time but it seems that it gets more and more corrupted. It does not load
any updates anymore for weeks although I did not installed anything.
I use the Raspi for Resilio sync and Nextcloud. There are more than 26
GB data on the card for syncing. I won't setup the programs again
because I had to setup connected remote computers as well (security keys
for Resilio). This would cause endless resyncing even when I manually
copy the files to the Raspberry Pi. I would like to avoid this.
Therefore, is it possible to replace the running operating system for a
fresh one and keep the configurations and data of the programs?
Steffen
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Steffen Bendix
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Put them on a double leash?
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Truth welcomes investigation because truth knows investigation will lead  
to converts. It is deception that uses all the other techniques.
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The Natural Philosopher
The following link explains how I do clean restores for Redhat Fedora systems:
formatting link

The same approach should work for a standard Raspbian installation except that /home is just another top-level directory in the main ext3 partition. So, the clean install will overwrite /home with its default content and after its complete you'll have to put it back the way it used to be by overwriting it with the contents of your latest backup, which will be quite slow.
Your back up scheme should keep at least two copies of /home and its subdirectories, and you may also want to keep backup copies of /etc. so you can look at modified configuration files in the backups and/or compare them with the version set up by the clean install instead of scratching your head while trying remember what changes you've made to them.
I use two USB-attached external hard drives for backups and keep them in a fire safe, though there's no reason why you shouldn't use SD cards in place of hard drives for this. I use two hard drives so that there is ALWAYS a backup copy in the firesafe with the door closed. This is protection against the disk being used to make the most recent backup getting corrupted by a bad backup, fried by a mains spike or otherwise destroyed.
I use rsync to make the backups. There's no reason you shouldn't use tar or another program that can copy a complete directory tree, except that:
- rsync is much faster because it does the minimum work needed to make the backup copy identical to the directory tree its copying, i.e. it deletes copies of files that you got rid of, adds copies of new files and copies files that have been changed. It takes about the same time as tar to make each of the initial backup copies but after that its a lot quicker.
- don't use zip. Its fine for exchanging files with other operating systems, but as a backup its deficient because it can scramble permissions and may not deal correctly with symbolic and hard links.
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martin@   | Martin Gregorie 
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Martin Gregorie
Backup your home directory which contains all the user application configuration, and restore that on to a new card containing a fresh install of the OS. Reinstall applications, and for any system config files that you had to manually modify, such as those in /etc, take a copy, but manually reapply the changes to the new OS.
For that type of use don't rely on the SD card, they will die after a finite period of time. Get yourself a modestly sized (64GB or 120GB) SSD and keep the OS and data on that, it will be far more reliable. Just use a small SD card to hold the boot partition, you can find the instructions on how to do this on many websites.
---druck
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