The source layout of jdk.vm.ci doesn't work with the modular build. We currently workaround it in jake (see the patch below).

It has one subdirectory for almost each package and it also contains the source files of build tool (annotation processor) to generate source (that are explicitly excluded when building jdk.vm.ci module). In addition, looks like share/classes contains platform-specific code that I'm not sure if it's intentional to have jdk.vm.ci module to contain classes for all platforms.

Here is the list of directories of source files to compile for jdk.vm.ci module:

jdk.vm.ci/share/classes//jdk.vm.ci.amd64/src/jdk/vm/ci/amd64
jdk.vm.ci/share/classes//jdk.vm.ci.code/src/jdk/vm/ci/code/stack
jdk.vm.ci/share/classes//jdk.vm.ci.common/src/jdk/vm/ci/common
jdk.vm.ci/share/classes//jdk.vm.ci.compiler/src/jdk/vm/ci/compiler
jdk.vm.ci/share/classes//jdk.vm.ci.hotspot/src/jdk/vm/ci/hotspot
jdk.vm.ci/share/classes//jdk.vm.ci.hotspot/src/jdk/vm/ci/hotspot/events
jdk.vm.ci/share/classes//jdk.vm.ci.hotspot/src/jdk/vm/ci/hotspot/logging
jdk.vm.ci/share/classes//jdk.vm.ci.hotspot.amd64/src/jdk/vm/ci/hotspot/amd64
jdk.vm.ci/share/classes//jdk.vm.ci.hotspot.sparc/src/jdk/vm/ci/hotspot/sparc
jdk.vm.ci/share/classes//jdk.vm.ci.hotspotvmconfig/src/jdk/vm/ci/hotspotvmconfig
jdk.vm.ci/share/classes//jdk.vm.ci.inittimer/src/jdk/vm/ci/inittimer
jdk.vm.ci/share/classes//jdk.vm.ci.meta/src/jdk/vm/ci/meta
jdk.vm.ci/share/classes//jdk.vm.ci.options/src/jdk/vm/ci/options
jdk.vm.ci/share/classes//jdk.vm.ci.service.processor/src/jdk/vm/ci/service
jdk.vm.ci/share/classes//jdk.vm.ci.sparc/src/jdk/vm/ci/sparc

The source layout should be re-examined and remove the "<PACKAGE-NAME>/src" from the file hierarchy.

The build tool should be moved to the proper home.
jdk.vm.ci/share/classes//jdk.vm.ci.service.processor/src/jdk/vm/ci/service/processor
jdk.vm.ci/share/classes//jdk.vm.ci.options.processor/src/jdk/vm/ci/options/processor

--- old/make/CompileJavaModules.gmk 2015-11-12 20:32:54.000000000 -0800
+++ new/make/CompileJavaModules.gmk 2015-11-12 20:32:54.000000000 -0800
@@ -523,6 +523,28 @@
 # Add imported modules to the moduleclasspath
 MODULECLASSPATH := $(subst $(SPACE),$(PATH_SEP), $(IMPORT_MODULES_CLASSES))
 
+ifneq ($(findstring $(MODULE), jdk.vm.ci jdk.jfr), )
+ ## WORKAROUND jdk.vm.ci source structure issue
+ HOTSPOT_JVMCI_SRC := $(subst $(MODULE),*,$(HOTSPOT_TOPDIR)/src/jdk.vm.ci/share/classes)
+ JVMCI_SUBDIRS := \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.amd64/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.code/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.common/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.compiler/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.hotspot/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.hotspot.amd64/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.hotspot.sparc/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.hotspotvmconfig/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.inittimer/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.meta/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.options/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.runtime/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.service/src \
+ $(HOTSPOT_JVMCI_SRC)/jdk.vm.ci.sparc/src
+
+ MODULESOURCEPATH += $(subst $(SPACE),$(PATH_SEP), $(JVMCI_SUBDIRS))
+endif
+
 # Make sure the generated source base dirs exist. Not all modules have generated
 # source in all of these directories and because of timing, all of them might not
 # exist at the time this makefile gets called. Javac will complain if there are