pmb.config.init: fix init when work path is an empty directory

In case a user removes all contents of the work path then pmbootstrap
init will fail and show

  WARNING: Your work folder version needs to be migrated (from version 0 to 6)!

Later the migration would fail with the error

  ERROR: We have split the aports repository from the pmbootstrap repository (#383). Please run 'pmbootstrap init' again to clone it.

This is due to the existing check not accounting for e.g. log.txt being
written in the work path before we get to this check. Now change it so
we always create the version file if it doesn't exist yet.

Test plan:
$ grep work ~/.config/pmbootstrap.cfg
work = /tmp/pmbootstrap-work
$ rm -rf /tmp/pmbootstrap-work
$ mkdir /tmp/pmbootstrap-work
$ pmbootstrap init

This was previously attempted to be fixed in !1975

!1975 (merged)