fix some bugs, change default setting

• set temporal constraint and using variances by default (so now don't need to use -c and -v 1)
• fix bugs missing internal nodes label (or support) in output tree in some cases (rooting the tree)
• fix bugs setting minblen=-1 when estimating relative dates
• allow mix of date formats among year-month-day, year-month and year
• allow to not collapse any branch by setting a negative value for -l
• improve nexus format to be able to read in R