Is this for a generic installer iso that can be installed on any hardware or just an existing system system clone.
Both can be done, but one is a little more difficult than the other.
Some people simply use "dd" ( disk duplicator ), but the problem is the back-up disk has to be the same size as the original disk, even if it's just empty file system space.
Some people create VMs with small "sparse" disks, ( that automatically grow as you add more stuff to them ).
Some simply create small VMs, with a 4 or 5GB disk, install what they want on there, and use "dd" to burn it
to an iso file.
Clonezilla also has an option to create a backup iso image with all the unused disk space removed.
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If you're making an installer disk, the first problem is getting the installer to know about the additional packages.
It's different for different distro's. For redhat and fedora you copy the rpms to the correct directories. But then
you run a command called "createrepo" in the directories. For debian/ubuntu I believe it's called dpkg-scanpackages.
Then there is sometimes a second problem, some installers, specifically use a checksum to see if the installer
image has been modified. Fedora for example will block the installer if the checksum doesn't match. here are ways around this
if you know how make a checksum file and where the file is located in the squashfs file system.
You can mount an iso image with this command.
mount -o loop /path/to/iso/image.iso /mnt
You can then copy this image to your local filesystem.
cp -rvf /mnt/* /my/iso/filesystem
change the permissions
chmod -R 755 /my/iso/filesystem
Once everything is copied over, add your rpms or debs to the correct directories, run either createrepo or dpkg-scan-packages.
(If you'r not running a deb or rpm based distro, I don't know if other distro's have a similar tool).
Once you've done all of that, burn the filesystem back to an iso. I use dd.
cd /my/iso
dd if=filesystem of=/dev/sdb/mycustom.iso
Change /dev/sdb to whatever path your usb thumb drive is.