Change all executables to use default output name 'unnamed.nc'.

The User Manual does not need to be cluttered with the strange
historical naming scheme.
Remove option -pismversion.  As far as I can tell, no script or documented run even uses it.  Option -version remains.
Edits to Practical Usage section of User Manual, including move of flow-line example script into util/
Fix minor manual build error caused by imperfect rebase.