Apparently make 3.81 treats the following
```
define foo =
bar
baz
endef
```
differently than make 4.2.1 (most notably, the equals sign).

The error messages

    error: could not lock config file .git/modules/foo/config: No such file or directory
    warning: Could not unset core.worktree setting in submodule \'foo\'

can be seen for all non-local mode wrappers (source code as git
submodule).

This happens if doing a `git submodule deinit` before a submodule has
been initialised. If a submodule has been initialised, but then is
deinitialised twice, the second error message shown above is still
displayed.

This fixes the above cases by instead doing a forced recursive deletion
of the submodule directory.

Synchronised all of the config files in configure/E3 and configure/modules in order to merge the two configuration directories.