The .project file has be exported, too. Because the StandaloneSetup of the MWE2 only register a bundle to it's PlatformResourceMap if the Bundle is a .jar or contains a .project file.

plugins/org.yakindu.sct.model.sexec/build.properties

@@ -7,7 +7,8 @@
 bin.includes = .,\
                model/,\
                META-INF/,\
-               plugin.xml
+               plugin.xml,\
+               .project
 jars.compile.order = .
 source.. = src/,\
            xtend-gen/,\

plugins/org.yakindu.sct.model.sgraph/build.properties

@@ -10,7 +10,8 @@
 bin.includes = .,\
                model/,\
                META-INF/,\
-               plugin.xml
+               plugin.xml,\
+               .project
 jars.compile.order = .
 source.. = src/
 output.. = bin/

plugins/org.yakindu.sct.model.stext/build.properties

@@ -5,4 +5,5 @@ bin.includes = META-INF/,\
                .,\
                plugin.xml,\
                libraries/,\
-               model/
+               model/,\
+               .project