Xia2run class: 1. Added substantial amount of inline documentation. 2. Removed redundant "get_crystal" method, and renamed get_dataset to    make it private. 3. Renamed "programs" method to "programs_used" to clarify function.
Xia2run class:
1. Added substantial amount of inline documentation.
2. Removed redundant "get_crystal" method, and renamed get_dataset to
   make it private.
3. Renamed "programs" method to "programs_used" to clarify function.

xia2/xia2,xia2/xia2