Howard,
I think 25GB of hidden files is a lot.
Have you tried figuring out which folder or file is taking up the most space?
I would try the following: LM has ncdu. If you donât have it installed, I would install it:
sudo apt install ncdu
Then, in the terminal, just type ncdu and a list will appear in descending order (with the folders that take up the most space at the top).
Use the UP and DOWN arrow keys to scroll through the list, and when you want to open a folder, press ENTER. It always works this way (if you want to go back to the previous folder, which is the first line of the listâit shows /.. - select that line and press ENTER).
Press âqâ to exit.
Try to find out which folder(s) take up the most space, and then which files.
Hereâs my example:
I selected /AppImages:
I selected /FreeCAD:
I think these examples make it clear how the program works.
I might be wrong, but I think youâre using Flatpak apps.
If you do, try checking the space used by Flatpak:
du -sh {/var/lib/flatpak,~/.local/share/flatpak,~/.var/app,~/.cache/flatpak}
Lists:
- If you want to list all the apps you have installed:
flatpak list --columns=name,size,application
- List of apps only
flatpak list --app --columns=name,size,application
- List of runtimes only (sets of libraries and core components that apps need to run)
flatpak list --runtime --columns=name,size,application
Note: runtimes are installed and shared by all programs that require those libraries - This is one of the core principles of Flatpak - but with updated runtimes, you may not want to delete the old runtime and installed programs that require a specific runtime; if you later uninstall those programs, the runtimes may remain, and if they are unique to those programs, they become âunusedâ
How to repair the cache:
flatpak repair
Clear data from removed applications:
flatpak uninstall --delete-data
How to clean up:
The two commands to clean up unused files and data from uninstalled programs:
flatpak uninstall --unused
flatpak uninstall --delete-data
Always make a backup before running these programsâyou know the routine 
In practice, Iâll demonstrate this with my examples:
Space used by Flatpak:

List:
List only runtimes:
Clean up:
Here you can see two things that happened: I have two files that are pinned and wonât be removed, and the one from org.rncbc.qpwgraph was deleted because I no longer have the program installed
About the 2 pinned files: these are files that have been marked so they wonât be automatically deleted.
These pinned files are themes that Flatpak may have installed so that Flatpak programs look the same as other programs, so I wonât delete them
I hope this helps with your research and understanding of the space occupied in your /home directory
Jorge