Mdthbs

so when I google all kinds of variations on this, all I see are results on how to update the GitHub app itself or to update the version of the OS, and I can't find instructions on how to update individual apps that I have installed using git clone.

so if I downloaded an app like bettercap or hcxtools and I get a response that I should update from the master to fix an error how is that done?

if I just go and overwrite the original folder like for example my oh my zsh or my powerlevel9k won't it wipe out all my settings and customizations that I like???

You shouldn't have to wipe out/overwrite the folder, as that would indeed wipe out any customizations you've made.

The command you're looking for is git pull, which will pull any changes from the repository and merge them into your current directory. If you have committed changes to the repository, using git pull --rebase will keep your history cleaner, since it avoids a merge commit with the update. Depending on how you checked out the code, you may need to specify a remote (default is origin) and branch (master, based on your question), so your full command may be git pull origin master --rebase

There is a possibility that you could have made changes that will conflict with updates, in which case you'll have to resolve conflicts - the Git manual provides more details on that should you need it.

If you want to be careful, first make a copy of the folder that you want to update, then update the original folder. If something goes wrong, delete the original folder and move your copy back into place and start over.

Now you know why packaging systems like dpkg and rpm were invented - managing the install, upgrade, downgrade or removal of software is harder than it seems.

If at all possible, you should install packaged versions of software for your distribution of choice. This might limit you to an older version of particular packages, depending on how "bleeding edge" your distro is. This is not generally a problem - in most cases, you don't actually need the latest version, and in most of the remaining cases having the latest version isn't worth the price of breaking out of your distro's packaging system.

However, if there's no packaged version or if you really do need the latest version:

1. your best bet is to package the program yourself. This takes some effort and some time to learn how to do it, but has the best result - software that can be easily installed, upgraded, removed, etc using your distro's package tools.



2. 
   

   Use GNU Stow or CheckInstall when you build and install the software.

   
   
   

   Either of these will give you many of the features of a real package (like being able to easily uninstall or upgrade your installed software), and keep your self-installed software nicely separated (e.g. in subdirs of /usr/local or /opt) from packaged software.

   
   
   

   Note: both of these (and similar programs like xstow) are probably available as packages for your distro. That's certainly true for Debian.

   
   



3. For software meant to run directly out of a cloned git repository (e.g. scripts, or omzsh), just use git pull to update it as described in @Steven's answer. Note, however, that if there's a packaged version available for your distro then you should probably use that.