Finally a Makefile that seems to work.

st/Makefile

@@ -1,3 +1,8 @@
+#
+# This Makefile takes .st files in the jtalk/st directory and produces compiled
+# javascript files from them. It also produces one or more concatenated jtalk.js files
+# for development and deployment.
+#
 # Where we find the current runnable code and where we put our js files when we are done
 JS	:= ../js/
 
@@ -7,46 +12,49 @@ JTALKC	:= ../bin/jtalkc
 # Generic flags to JTALKC
 FLAGS   := -g
 
-# The js files that are hand written and we use "as is"
-CORE    := boot.js init.js
-
 # All corresponding js filenames for every st file available
 # In other words, if we have Kernel.st and Parser.st, then OBJECTS will be "Kernel.js Parser.js"
 OBJECTS := $(patsubst %.st,%.js,$(wildcard *.st))
 
-# Default make targets
+# Default make target since it is the first target in this Makefile
 all: jtalk.deploy.js jtalk.js
 
 # Step by step
 #
 # First we copy the core javascript files from current working files
-# into this directory. These files are hand written.
-boot.js:
-	cp ../js/boot.js ../js/init.js .
-
+# into this directory. These files are hand written. $@ is the target name.
+boot.js init.js:
+	cp ../js/$@ .
 
 # Then we compile Kernel.st using boot.js, Kernel.js, init.js
 # $< means the first dependency - in other words Kernel.st
-Kernel.js: Kernel.st $(CORE)
+Kernel.js: Kernel.st boot.js init.js
 	$(JTALKC) $(FLAGS) $<
 
+# And one for deployment, no flags.
+deploy-Kernel.js: Kernel.st boot.js init.js
+	$(JTALKC) -p deploy- $<
+
 # ...then Parser, but using the new Kernel from step above.
-# We only need to depend on Kernel.js since it in turn depends on CORE.
+# We only need to depend on Kernel.js since it in turn depends on boot.js and init.js.
 Parser.js: Parser.st Kernel.js
 	$(JTALKC) $(FLAGS) $<
 
 # ...and Compiler, but using the new Parser and Kernel from above.
-# We only need to depend on Parser.js since it in turn depends on Kernel.js, CORE etc
+# We only need to depend on Parser.js since it in turn depends on Kernel.js, boot.js etc
 Compiler.js: Compiler.st Parser.js
 	$(JTALKC) $(FLAGS) $<
 
 # ...now that we have a new Kernel/Parser/Compiler we use them
 # to compile the rest of st files that only depend on Compiler, like
-# for example Canvas.js and Benchfib.js
+# for example Canvas.js, Benchfib.js etc
 %.js: %.st Compiler.js 
 	$(JTALKC) $(FLAGS) $<
 
-# But there are some dependencies to care for:
+# But for some libraries there are dependencies to care for. Then
+# we need to use -l so that the compiler first loads that library
+# before compiling the .st file. Otherwise bindings will fail.
+#
 # JQuery uses Canvas
 JQuery.js: JQuery.st Canvas.js
 	$(JTALKC) $(FLAGS) -l Canvas.js $<
@@ -61,34 +69,27 @@ SUnit.js: SUnit.st IDE.js
 
 # Some Examples use SUnit
 Examples.js: Examples.st SUnit.js
-	$(JTALKC) $(FLAGS) -l Canvas.js,JQuery.js,IDE.js,SUnit.js $<
-
-# Complete Jtalk, here we give -J (will include all  libs for Jtalk IDE),
-# push it all through Closure (-O) and add init.js at end (-I).
-jtalk.js: $(OBJECTS)
-	$(JTALKC) -J -O -I jtalk
+	$(JTALKC) $(FLAGS) -l Canvas.js,JQuery.js,IDE.js,SUnit.js $<;
 
+# This is the deployment target with only the Jtalk Kernel compiled without -g.
+# Then we push it all through Closure (-O) and add init.js at end (-I).
+jtalk.deploy.js: boot.js init.js deploy-Kernel.js
+	$(JTALKC) -O -I boot.js deploy-Kernel.js jtalk.deploy;
 
-# Only Jtalk Kernel and compiled without -g. Thus we need to clean first to remake
-# all dependencies with new FLAGS.
-# Then we give -K (will include up to Compiler), push it all through Closure (-O)
-# and add init.js at end (-I).
-jtalk.deploy.js: FLAGS =
-jtalk.deploy.js: cleanobjects $(OBJECTS)
-	$(JTALKC) -K -O -I jtalk.deploy.js
+# Full IDE compiled with -g. We do not clean away objects at end.
+# Here we give -J (will include all  libs for Jtalk IDE),
+# push it all through Closure (-O) and add init.js at end (-I).
+jtalk.js: boot.js init.js $(OBJECTS)
+	$(JTALKC) -J -O -I jtalk;
 
 
 # Installing is simply copying all js files to js directory.
 install: all
 	cp *.js $(JS)
 
-# And cleaning
-clean: cleanobjects cleanjtalk
-
-.PHONY: cleanobjects
-cleanobjects:
-	rm -f $(OBJECTS)
+# And cleaning is trivial
+clean:
+	rm -f *.js; 
 
-.PHONY: cleanjtalk
-cleanjtalk:
-	rm -f jtalk.js jtalk.deploy.js
+# These three are phony
+.PHONY: all install clean