Fixing formatting issues revealed by the nxdl to rst conversion and a…

…dded NXms application definition

contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml

@@ -891,7 +891,7 @@
                                         <doc>
                                              Triangle normals are oriented in the direction of the
                                              gradient vector of the local delocalized scalar field.
-                                             :mathref:`$\sum_{x, y, z} {\nabla{c}_i}^2$`.
+                                             :math:`$\sum_{x, y, z} {\nabla{c}_i}^2$`.
                                         </doc>
                                         <dimensions rank="1">
                                             <dim index="1" value="k"/>
@@ -1023,7 +1023,7 @@
                                         <dim index="1" value="j"/>
                                     </dimensions>
                                 </field>
-                                <group name="objects" type="NXms_three_d_feature_set" optional="true">
+                                <group name="objects" type="NXprocess" optional="true">
                                     <doc>
                                          Details for features which are (closed) objects.
                                          Identifier have to exist in feature_identifier
@@ -1097,7 +1097,7 @@
                                             </field>
                                         </group>
                                     </group>
-                                    <group name="objects_close_to_edge" type="NXms_three_d_feature_set" optional="true">
+                                    <group name="objects_close_to_edge" type="NXprocess" optional="true">
                                         <doc>
                                              Details for all those objects close to edge, i.e. those which
                                              have at least one ion which lays closer to a modelled edge
@@ -1180,7 +1180,7 @@
                                             </group>
                                         </group>
                                     </group>
-                                    <group name="objects_far_from_edge" type="NXms_three_d_feature_set" optional="true">
+                                    <group name="objects_far_from_edge" type="NXprocess" optional="true">
                                         <doc>
                                              Details for all those objects far from edge, i.e. those
                                              whose ions lay all at least threshold distant from a
@@ -1264,7 +1264,7 @@
                                         </group>
                                     </group>
                                 </group>
-                                <group name="proxies" type="NXms_three_d_feature_set" optional="true">
+                                <group name="proxies" type="NXprocess" optional="true">
                                     <doc>
                                          Details for features which are so-called proxies, i.e. objects
                                          which have been reconstructed and combinatorially closed with
@@ -1283,7 +1283,7 @@
                                             <dim index="1" value="i"/>
                                         </dimensions>
                                     </field>
-                                    <group name="proxies_close_to_edge" type="NXms_three_d_feature_set" optional="true">
+                                    <group name="proxies_close_to_edge" type="NXprocess" optional="true">
                                         <doc>
                                              Details for those proxies close to edge, i.e. those which
                                              have at least one ion which lays closer to a modelled edge
@@ -1365,7 +1365,7 @@
                                             </group>
                                         </group>
                                     </group>
-                                    <group name="proxies_far_from_edge" type="NXms_three_d_feature_set" optional="true">
+                                    <group name="proxies_far_from_edge" type="NXprocess" optional="true">
                                         <doc>
                                              Details for those proxies far from edge, i.e. those whose
                                              ions lay all at least threshold distant from a