Move include statements to end of file. Add section for overriding recipes
Fix ifdef statments
Cleanup makefiles

1. Makefile.angsd

  - add utility variables
  - add .ln rule
  - add ngstk

2. Makefile.halo
   Move two recipies after include statement. May not be necessary

3. Makefile.analysis.angsd
   Add docstrings and examples
Merge branch 'feature/angsd-improvements' into develop