Mike3 wrote: ↑Thu May 12, 2022 9:15 pm
So I deleted a buncha apps like libreoffice and palemoon from all the sfs's (the main puppy.sfs, the adrv.sfs, fdrv.sfs & zdrv.sfs) using unsquashfs and mksquashfs....
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The way you're going about it is almost certain to create problems. As williams2 indicated your Puppy has a layered file-system.
Read How Puppy Works, viewtopic.php?p=55827#p55827
Layman's understanding, short-version: The file-systems Puppys will use are on storage. On boot-up Puppys copy some file-systems into RAM and cache/compress them; other file-system on storage are just mounted. When boot-up has completed, Puppys will have indexed files currently, potentially available. Those indexes are later used to call files into 'Available-for-work' RAM where they can actively perform their function, or be modified.
Know which of the files in storage provides each application[/b]: it could be the puppy.sfs, your SaveFile/Folder, an adrv.sfs, a yrdv.sfs or an application (extra) sfs.
Puppy has tools for removing applications. If the application is provided by the puppy.sfs, Menu>Setup>Remove Builtin will place a '.w=white-out' file next to files not to be used by your system. When you remaster, those files will not be included.
If you installed an application, it is only in your SaveFile or SaveFolder. Menu>Setup>Puppy Package Manger, Click the Uninstall button to select applications to be uninstalled.
If the application is in the form of an extra SFS, you load and unload it by Right-Clicking the SFS and selecting Sfs-load, it's a toggle; or by Menu>Setup>SFS load on the fly. Your SaveFile/Folder holds instructions as to what application.sfses on boot-up are to be part of your 'current-operating-system-in-RAM'. If an application is loaded when your execute a Save, it will continue to be loaded on boot-up until you unload it and again execute a Save. That's likely why libreoffice reappeared.
On boot-up Puppys will automatically copy into RAM the files of applications contained in an adrv.sfs or ydrv.sfs. Removing applications from them isn't straight forward. The easiest way is boot pfix=RAM so as not to have the applications in your SaveFile/Folder as part of your current system. After boot-up install nicOS-Utility-Suite, viewtopic.php?p=12983#p12983: extract the 'gz', run the pet, then run Menu>Exit>Restart-X (AKA Graphic Server) to have Puppy re-catalog what makes up its system.
If you're lucky, the primary folder containing the application files will be in /opt with just a couple of files elsewhere: a desktop file in /usr/share/applications, an icon maybe in /usr/share/pixmaps and maybe a script or symbolic link in /usr/bin. If you delete those files and run the Save2SFS module of nicOS-Suite, a new adrv.sfs or ydrv.sfs will be created without those files and, thus, that application. pfind can be used search for other files. But, before deleting anything, be certain its not required by some other application. Having a few 'orphaned' files is better than a broken application.
If you weren't lucky, if the bulk of the application wasn't in /opt, then you'll have to use pfind to locate where each of an applications files are. There might-or-might-not be a file in a hidden folder named packages in /root or /var which may tell you what files an application uses --but doesn't tell you that that file is used by some other application.
My recommendation in that case is to make a note of what applications you want which are provided by an adrv.sfs or ydrv.sfs. The move the adrv/ydrv.sfs away from your puppy.sfs and boot pfix=ram. Install those applications. Then run the Save2SFS module to create your own adrv/ydrv.sfs.