added note about emperor transition
updated workflows to use make_emperor.py rather than make_3d_plots.py
updated to work with emperor plots instead of king plots
updating to use emperor plots
updated to emperor pcoa plots
modified script interface for king to emperor transition
added comment on script interface changes
updating for king to emperor transition
updated for king to emperor transition
updating for king to emperor transition
updated for king to emperor transition
improved the message on the king to emperor transition
Initial commit of changes
Merge branch 'emperor-transition' of github.com:gregcaporaso/qiime into emperor_transition
added emperor to the install document
added deprecation warnings
updated deprecation warning text
Fix #976

make_otu_heatmap.py would fail if a filepath was passed with the -s
option because the file was never opened.

Fixes #976
Remove pool_by_metadata.rst from the docs

This file kept showing in the documenatation and confused some users as
they would not be able to call this script from the CLI.

Fixes #966.
Fixing tutorial and tutorial images, and sh files