Deprecate Tree.newick and replace with Tree.as_newick (or similar) #1671
Description
The default behaviour of Tree.newick of making node labels the sample ID + 1 is horrible, and makes it very hard to integrate well with other libraries. This was done originally for compatibility with ms, but that's not a good reason to keep it.
We should make a new function which does the right thing. It cant use the same infrastructure (we don't need to fiddle with the C code, for now). We can keep Tree.newick indefinitely, but it should be marked as deprecated.
@hyanwong - are there other phylo-type functions we need to consider deprecating which inherited this behaviour?