add auto-finishing for nexus files

[roblanf]

I have some output files from *BEAST which are not properly finished and so don't load with read.nexus().

The issue is simple, the file are supposed to end with these two lines:

			;
End;

but they don't.

The fix is also simple - we just ask what the last two lines are, and if they're not as above (we can strip whitespace and convert to all caps for simple comparisons), we should make sure the last two lines are like that. This will mean people can load chains that are not finished yet too.

My suggestion is that we do this by doing find-replace on read.nexus and replace it with replace.nexus.rwty, then write an additional function which this would call before calling read.nexus, something like check.nexus.ending().