Check for links in update

h5py complained when updating an unlocked file with links, since we
weren’t checking if the links already existed before trying to write
them again.
Added confirm_action to BaseDialog

A useful utility for dialogs.
Added new script menu

Now, scripts can be created, edited (with syntax coloring), saved to a
file, run in the console, using the console namespace, and deleted if
not needed. There is a new scripts subdirectory in ~/.nexpy.