various cleanup in doc folder

docs/doxygen/Doxyfile

@@ -772,7 +772,6 @@ INPUT                  = ../../moose-core/basecode 	  \
                          ../../moose-core/msg                \
                          ../../moose-core/randnum            \
                          ../../moose-core/pymoose            \
-                         ../../moose-core/sbml               \
                          ../../moose-core/scheduling         \
                          ../../moose-core/shell              \
                          ../../moose-core/signeur            \

docs/user/markdown/Kkit12Documentation.markdown

@@ -242,6 +242,7 @@ but they make the assumption that the **E.S** is in a quasi-steady-state with **
 Summation object can be used to add specified variable values. The variables can be input from pool object.
 
 *   **Icon**: This is **Σ** in the example image below. The input pools **'A'** and **'B'** connect to the **Σ** with blue arrows. The function ouput's to BuffPool
+![](../../images/func.png)
 
 ### [Model operations](#TOC)
 

docs/user/markdown/markdown2rst.py

 import os
 import subprocess
 
-file_list = ["MooseGuiDocs","Kkit12Documentation","RdesigneurDocumentation"]
+file_list = ["MooseGuiDocs","Kkit12Documentation"]
 
 DOCUMENTATION_DESTINATION_DIR = '../GUI/'
 SOURCE_EXTENSION = '.markdown'
@@ -12,3 +12,15 @@ for filename in file_list:
     command = 'pandoc -s {0} -o {1}'.format(source_file, output_file)
     print(command)
     subprocess.call(command.split(' '))
+
+file_list = ["RdesigneurDocumentation"]
+DOCUMENTATION_DESTINATION_DIR = '../Rdesigneur/'
+SOURCE_EXTENSION = '.markdown'
+OUTPUT_EXTENSION = '.rst'
+for filename in file_list:
+    source_file = filename + SOURCE_EXTENSION
+    output_file = DOCUMENTATION_DESTINATION_DIR + filename + OUTPUT_EXTENSION
+    command = 'pandoc -s {0} -o {1}'.format(source_file, output_file)
+    print(command)
+    subprocess.call(command.split(' '))
+