I’m trying to create a /etc/skel folder in desktop-overlay, but it gives me an error which says this file is already exists in file system. I can do it by editing build images but I don’t want to repeat it everytime I build an iso. Is there a way to force buildiso tool to overwrite the current filesystem? Thanks 
desktop-overlay is meant to be used exactly for that purpose. Maybe post the errors during your build so we may help. Also link to your code or at least share a tree list of the file structure you want to add. You can use the tool tree for that to list the current folder: tree .
If I try to overwrite calamares configs, I get this;
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/branding.desc exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/languages.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/logo.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/show.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/slide1.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/slide2.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/slide3.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/slide4.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/slide5.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/branding/manjaro/squid.png exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/chrootcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/contextualprocess.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/finished.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/finishedq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/fsresizer.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/fstab.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/grubcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/interactiveterminal.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/keyboard.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/keyboardq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/license.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/locale.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/localeq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/luksopenswaphookcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/machineid.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/mhwdcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/mount.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/netinstall.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/notesqml.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/oemid.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/openrcdmcryptcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/owncloud.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/packagechooser.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/packagechooserq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/packages.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/partition.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/plasmalnf.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/plymouthcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/postcfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/preservefiles.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/rawfs.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/removeuser.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/services.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/servicescfg.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/shellprocess.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/tracking.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/umount.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/users.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/usersq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/webview.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/welcome.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/welcomeq.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/modules/zfs.conf exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/BackButton.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/ForwardButton.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/NavButton.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/Presentation.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/Slide.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/SlideCounter.qml exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/qmldir exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/qml/calamares/slideshow/qmldir.license exists in filesystem
calamares: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/usr/share/calamares/settings.conf exists in filesystem
manjaro-live-skel: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/etc/skel/.config/autostart/disable-dpms.desktop exists in filesystem
manjaro-live-skel: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/etc/skel/.config/autostart/live-session.desktop exists in filesystem
manjaro-live-skel: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/etc/skel/.config/autostart/pulseaudio-ctl.desktop exists in filesystem
screen: /var/lib/manjaro-tools/buildiso/kde/x86_64/livefs/etc/skel/.screenrc exists in filesystem
Errors occurred, no packages were upgraded.
==> ERROR: Failed to install packages to new root
==> ERROR: Failed to install all packages
==> ERROR: A failure occurred in make_image_live().
Aborting...
--> overlayfs umount: [/var/lib/manjaro-tools/buildiso/kde/x86_64/livefs]
--> umount overlayfs: [/var/lib/manjaro-tools/buildiso/kde/x86_64/livefs]
tree;
.
├── etc
│ ├── locale.conf
│ ├── locale.gen
│ ├── localtime
│ ├── lsb-release
│ ├── pam.d
│ │ └── sddm
│ ├── sddm.conf
│ ├── skel
│ └── X11
│ └── xorg.conf.d
│ └── 30-touchpad.conf
└── usr
└── share
├── calamares
│ ├── branding
│ │ └── manjaro
│ │ ├── branding.desc
│ │ ├── languages.png
│ │ ├── logo.png
│ │ ├── show.qml
│ │ ├── slide1.png
│ │ ├── slide2.png
│ │ ├── slide3.png
│ │ ├── slide4.png
│ │ ├── slide5.png
│ │ └── squid.png
│ ├── modules
│ │ ├── bootloader.conf
│ │ ├── chrootcfg.conf
│ │ ├── contextualprocess.conf
│ │ ├── displaymanager.conf
│ │ ├── finished.conf
│ │ ├── finishedq.conf
│ │ ├── fsresizer.conf
│ │ ├── fstab.conf
│ │ ├── grubcfg.conf
│ │ ├── initcpio.conf
│ │ ├── interactiveterminal.conf
│ │ ├── keyboard.conf
│ │ ├── keyboardq.conf
│ │ ├── license.conf
│ │ ├── locale.conf
│ │ ├── localeq.conf
│ │ ├── luksopenswaphookcfg.conf
│ │ ├── machineid.conf
│ │ ├── mhwdcfg.conf
│ │ ├── mount.conf
│ │ ├── netinstall.conf
│ │ ├── notesqml.conf
│ │ ├── oemid.conf
│ │ ├── openrcdmcryptcfg.conf
│ │ ├── owncloud.conf
│ │ ├── packagechooser.conf
│ │ ├── packagechooserq.conf
│ │ ├── packages.conf
│ │ ├── partition.conf
│ │ ├── plasmalnf.conf
│ │ ├── plymouthcfg.conf
│ │ ├── postcfg.conf
│ │ ├── preservefiles.conf
│ │ ├── rawfs.conf
│ │ ├── removeuser.conf
│ │ ├── servicescfg.conf
│ │ ├── services.conf
│ │ ├── shellprocess.conf
│ │ ├── tracking.conf
│ │ ├── umount.conf
│ │ ├── unpackfs.conf
│ │ ├── users.conf
│ │ ├── usersq.conf
│ │ ├── webview.conf
│ │ ├── welcome.conf
│ │ ├── welcomeq.conf
│ │ └── zfs.conf
│ ├── qml
│ │ └── calamares
│ │ └── slideshow
│ │ ├── BackButton.qml
│ │ ├── ForwardButton.qml
│ │ ├── NavButton.qml
│ │ ├── Presentation.qml
│ │ ├── qmldir
│ │ ├── qmldir.license
│ │ ├── SlideCounter.qml
│ │ └── Slide.qml
│ └── settings.conf
├── icons
│ └── default
│ └── index.theme
├── mergen-logo.svg
└── wallpapers
└── mergen_wallpaper_tomris.jpg
17 directories, 76 files```