This issue normally happens because you've manually added, copied, or created a file. It can also happen when you install software using a downloaded executable, run a make install, or use a third-party package system such as conda. It also occurs when you install an AUR package which installs files that conflict with a repo package.
For more details and possible solution please refer to
https://forum.manjaro.org/t/update-or-package-installation-returns-failed-to-commit-transaction-conflicting-files-filename-exists-in-filesystem/3598Also please be advised that we provide support of AmiKit - that is the Amiga side of the thing, not the underlying Linux. By default, the Linux part is optimally configured for AmiKit and it works fine out of the box. Any additional changes you make to the Linux part, including updates, are on your own responsibility.