Some files exist in the root directory (installer/data/mysql) and some other in the mandatory/ one. All should be put in the mandatory one. The current 'layout' becomes particularly troublesome on this commit: https://gitlab.com/koha-community/koha-misc4dev/commit/7ecb9de5b6c7ef660ff63254e802a8ec42199a13 After that commit, the tools won't work for earlier versions that don't have that .sql files. If they were put in the mandatory directory there would be no need to explicitly list them or branching in the code depending on the version (possible workaround in koha-misc4dev).
See bug 23895 which I think it's a duplicate of this. Actually, just moving them doesn't mean they don't have to be explicitly listed, right now the code in C4/Installer lists all mandatory files to nature correct load order.. silly huh. What 'tools' are you talking about? I've already updated misc4dev.
*** This bug has been marked as a duplicate of bug 23895 ***