v2.0.0-pre15

A couple of changes:

1. The manual is now completely up to date
2. PF2 now includes a dependency checker. This will hopefully catch the common error where people download PF2 and just try to run it like PF1 without reading the manual. It checks for necessary dependencies, and if they don't have them it points them in the right direction (either get Anacondo distro, or RTFM).
3. ML starting trees are now the default for all analyses. This is much better than using other trees, and the additional analysis time is minimal. Issues with PhyML are now sorted out.
4. Confusing options w.r.t. TIGER rates are now sorted. Entropy is now the only option for DNA and protein datasets. Morphology datasets can use TIGER or Entropy. The default is the latter, and to use TIGER you specify --kmeans tiger at the command line.
5. Morphology models have been checked and are all correct.