Add a 'nx-copy' application

TODO

• Add application to copy an NXtomo from one file to another (or to a folder)
  • add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is required will be done in another PR
• Add test
• Add doc
• Update tomwer doc once done (user corner / python script - how to copy an NXtomo)

API

copy a single file (with potentially several NXtomo):

nxtomomill nx-copy /path/to/nxomofile.nx .
nxtomomill nx-copy /path/to/nxomofile.nx new.nx

copy a single NXtomo (potentially contained in a file with several NXtomo):

nxtomomill nx-copy /path/to/nxomofile.nx --entry entry0000  .
nxtomomill nx-copy /path/to/nxomofile.nx --entries entry0000,entry0001  .

copy a set of file:

for file in *.nx
do
    nxtomomill nx-copy "$file" /new/path/"$file"
done

To replace HDF5 virtual datasets by a standard dataset you can also use the --remove-vds option. In this case the full dataset will be load in memory before dumping it.

related to nxtomo!8 (merged)