Fix non-standard NXpositioner groups

[noemifrisina]

The writer for NXsample is writing transformations groups as NXpositioner, eg.

h5ls -vd file.nxs/entry/sample/
sample_phi               Group
    Attribute: NX_class scalar
        Type:      12-byte null-padded ASCII string
        Data:
               "NXpositioner"
    Location:  1:39098
    Links:     1

which contains

h5ls -v file.nxs/entry/sample/sample_phi
phi                      Dataset {75}
phi_end                  Dataset {75}
phi_increment_set        Dataset {SCALAR}

While NXsample might accept an NXpositioner group, these do not follow the standard, see here, and are actually NXtransformations groups.

Options to fix:

1. Make NXpositioner groups indicating axes into NXtransformations group.
2. Keep the NXpositioner group but move the axis_name fields into a further NXtransformations, making the tree look like /entry/sample/sample_phi/transformations/phi
3. Remove the NXpositioner groups altogether and have all the relevant information only in /entry/sample/transformations

[graeme-winter]

I vote for option 3

[noemifrisina]

A quick additional note: will need to do the same for the axes in /entry/instrument/detector/transformations/

[noemifrisina]

Tested nexus file generated with the changes in #205 which remove the non standard fields. DIALS still seems okay with them. AutoPROC fails because unable to find oscillation/scan axis.

[noemifrisina]

autoPROC seems fine with the changes made in #205 ie. add increment_set and end to /entry/sample/transformations and change the NXclass of the additional groups to a slightly more correct NXtransformation instead of NXpositioner.
The PR also makes these groups optional so that we can choose when to write them (always for eg. UDC).
This first fix will be in the next release of nexgen, complete removal may have to wait a bit.