db: always create directories during install

We dont care if a directory have references or not, we care if directory
is relly there.

Only the creator of the direcotry will set the permissions.

This fixes the situation where you install a package owning a dir then
you remove this dir manually and try install a second package also owning
the dir.

For example:

  apk add e2fsprogs-dev
  rm -rf /usr/lib/pkgconfig
  apk add zlib-dev