[doc] changelog fix formatting and added note about #788.

doc/Makefile

@@ -46,6 +46,7 @@ ipython-rst: source/generated
 	@$(eval nb_names:= $$(shell grep generated source/ipython.rst | sed -re 's/\s+generated\/(.+)/\/\1.ipynb|/g'))
 	@$(eval notebooks:= $$(shell find ../pyemma-ipython -name *.ipynb | grep -E "$(nb_names)" ))
 	cd source/generated
+	pwd
 	set -x; for nb in $(notebooks); do $(NBCONVERT_CMD) $$nb || true; done
 	@echo "Conversion finished."
 

doc/source/CHANGELOG.rst

@@ -5,17 +5,20 @@ Changelog
 ----------------
 
 **New features**:
+
 - thermo: added TRAM estimation.
 - thermo: show convergence progress during estimation.
 
 **Fixes**:
+
 - clustering: fix parallel cluster assignment with minRMSD metric.
 - base: during estimation the model was accessed in an inappropriate way,
   which led to the crash "AttributeError: object has no attribute '_model'" #764.
 - coordinates.io: fixed a bug when trying to pyemma.coordinates.load certain MD formats.
   The iterator could have returned None in some cases #790.
 - coordiantes.save_traj(s): use new backend introduced in 2.1, speed up for non random
-  accessible trajectory formats like XTC.
+  accessible trajectory formats like XTC. Avoids reading trajectory info for files not
+  being indexed by the input mapping. Fixes #788.
 
 
 2.1.1 (4-18-2016)