Fix pin_new already-initialized errors

.. by indexing with num_joints instead of num_axes as needed
Add a script to convert configurations to the joints_axes format.
The script brings back the [EMC]VERSION flag, and this particular iteration
is allocated the tag VERSION = 1.0.
Some limited thought has been given to future extensibility.
usage update_ini myconfig.ini
It shuffles the INI file sections to suit the new format, and also changes
the HAL pin names where necessary.

Signed-off-by: Andy Pugh <andy@bodgesoc.org>
puma560: make the config load under ja
Add dialog and force options to the update_ini script to make it more suited
to scripted use.
force (-f) means that it performs the best-guess behaviur with no prompting
dialog (-d) gives a user some information about what is going to happen, and
the option to opt out.
The script also now makes a complete backup of the config.
in -f mode this is deleted after successful completion
Arrange for the linuxcnc launch script to prompt to auto-convert non JA configs
Also includes a number of bug fixes:
Ignores missing values rather than putting "None" in the INI
Works from anywhere in the tree, not just the config directory
Fixes a {} [] confusion.

Signed-off-by: andypugh <andy@bodgesoc.org>