Minor update to take advantage of msprime 0.6.0's Population and Individual
objects and fix various bugs.
**Breaking changes**:
- Bumped SampleData file format version to 1.0 because of the addition
of individuals and populations. Older SampleData files will not be
readable and must be regenerated.
- Changed the order of the `alleles` and `genotypes` arguments to
SampleData.add_site.
**New features**:
- Sample and individual metadata now handled correctly.
- Added --no-simplify option to CLI and simplify=True option to infer function.
- Better handling of missing files (raises correct exceptions).
- tsinfer list now presents basic information for .trees files.
**Bug fixes**:
- Degenerate examples with zero inference sites are now rooted (44)
- Simplify=False results in tree sequence with correct sample nodes.