I am contemplating a fresh install of my os, should I clone it or will just backing up the contents of my home directory allow me to transplant things across after the reinstall. This will not be a dual boot.

I found after installing a particular program things went awry, and is the sole motivation for reinstall.

Also is Gparted enough to get cloning done? Thanks in adavnce

If you have the opportunity to do a back up, do it; you only need your personal files, then re install, & copy back your data.

Some distros will re install just the system, allowing you to reuse your original /home; but it is still good practice to have a back up of your personal data.

Do the programs that I installed get transferred over with /home back up?

It depends on your setup. Usually /home does not hold installed programs, but again, it depends on you.
If you have a single program which "went awry" you need to fix that, and do not reinstall the whole system.

You could try using Before resorting to re installing.

Is there a way to tell whether my setup does or doesn't contain programs I installed within home or not?

Is there a way to tell if home does or doesn't hold my installed programs?

Yes, ask if someone installed something in your home. Usually it is intentional, so the one who installed it should know it. Do you run anything from your home dir?
But anyway, without knowing any details hard to say more.

No need to clone. Just rsync all your data folders (if outside of /home) and /home to one or more external backup drives. Verify that backup(s) did occur. Then, just install the new version of the distro (clean install). Add your users as usual in order that you did them before so the user ids are same. Once the new OS is installed and updated, then restore the data folders and /home folders back. Should be good to go. Anyway, that is the way I handle it as I use Thunderbird Email and Firefox and all my setting are stored in the /home/<user> folder. I Don't want to lose any of that! After that occurs, I am back to the way I was except on a 'new' system. Obviously any applications that you had originally installed from repository (like with: sudo apt install <application>) will have to be 're-installed'. Hope that helps.

I only back up my home folder. That said, I have a script in my home folder that builds a file documenting certain settings, and another file with a list of all installed packages. That way after I reinstall I can examine that backup, restore missing settings, add any special packages for the functions and features I treasure.

BTW: making a clone of your OS would clone the problem, so you would ahve to have done that before the problem started.
Do you have images or backups form before the problem was caused?

I am the sole user.

I don't know, is there a way I can check to see if something is running from home dir?

You did mention in post #4 I most likely would have stuck to default settings during install procedure and I assume that programs are not installed on my /home directory, not sure though.

What other details do you need?

If there's no need to clone why is it always advocated? I've never cloned before but it comes across as an arduous process over what you are suggesting.

Is the data folder labelled literally 'data folder', so I start searching for it in /home and if it's not there then search where? What's beyond /home? Root?

Even your programs?

What's preventing these from being from being rsync too?

What language did you use to script it?
Why didn't you script it in a way that would accommodate a few of your treasured features/special packages?

Not that I am aware of, I am inspired by contingency.

Theoretically it is quite simple. By default nothing is installed in your home.
The only exception is if you have installed something as user, not as root (like python packages).

I use cloning when moving from current Disk A to another newer disk B... Example, from a old SATA HDD drive to a brand new NVMe SSD drive I want to run current system off of. Once cloned, remove old disk, install new disk and off an running. Same OS just a different disk. This is different than just backing up data you want to keep. Rsync is a program that backs up just the folders/files you want to keep. Note: The cloning process can save you, if you just want to get back to where you were at time the clone was built. However you'd lose any changes made since the time you 'cloned' it.

What I mean by <data> folder/file is any folder that you might have data you want to keep. For example, I might create a folder called development under root folder. Ie. /development/ This is not under the /home folder so it would a 'data' folder I want to backup. Remember, when you do a clean install, the disk will be wiped clean. So you need to save the files you want (pictures, databases, documents, etc.) . I suspect from your response you store everything under your /home/<user> folder, so backing up /home is all you need to do.

Most program settings are setup per user. So 'your' settings (like for libreOffice, screen saver, background color, task bar color, Email, browser bookmarks, etc) are in your /home/<user> folder. On the other hand Ethernet settings, samba, nfs, etc. are 'global' settings which are usually found under /etc/. Most times the global settings are easy to re-create. If not, you go find them and store in your /home/<user> directory so you can copy back. Like samba.conf as an example. From the sounds of it, you probably don't have any custom setups here (inferred from info you have relayed), so don't need to worry about them.

As for programs. They are normally stored in other system folders /usr/bin or some such. There is no need to back them up as there will be new 'versions' in the newer OS you are going to install. You don't want to mix old and new (you'll get library mis-matches, etc. Big problems) . Ie. Bottom line, after clean install, re-install the apps you are missing. That said, most distros have an 'upgrade' process that upgrades the system in place. This is the only way you 'may' get away with not having to re-install used apps. This is completely different from a clean install.

Hope that helps.