`Adjacency` fixes & enhancements

[ejolly]

We had talked about sublcassing at some point #254 which might be worth re-discussing

Relevant issues:

• Potential Bug with Adjacency reading files containing multiple directed_flat #371
• Adjacency.plot_mds errors with n_components = 3 #381
• Fix bug where Adjacency can't load .h5 file using a Path object #383
• Add support for optionally including main diagonal in Adjacency.distance #384
• Figure out adjacency append error #390
• Add network-based statistics to Adjacency Class #394
• Adjacency.similarity() can't handle NaNs #432
• add 2d_permutation for Adjacency ttest methods.  #244
• add cluster method to adjacency class #233