diff --git a/Makefile.am b/Makefile.am
index 65c31bdd..84a03325 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -23,29 +23,14 @@ missing
 
 EXTRA_DIST = \
 CMake/CheckHaveGetopt.cmake \
-CMake/CTestCustom.cmake.in \
 CMake/OpenJPEGConfig.cmake.in \
+testing/CTestCustom.cmake.in \
+testing/CTestConfig.cmake \
 CMakeLists.txt \
-CTestConfig.cmake \
-CTestCustom.cmake.in \
-CMakeLists.txt \
-JavaOpenJPEG/java-jni/include/jawt.h \
-JavaOpenJPEG/java-jni/include/jdwpTransport.h \
-JavaOpenJPEG/java-jni/include/jni.h \
-JavaOpenJPEG/java-jni/include/jvmdi.h \
-JavaOpenJPEG/java-jni/include/jvmpi.h \
-JavaOpenJPEG/java-jni/include/jvmti.h \
-JavaOpenJPEG/java-jni/include/win32/jawt_md.h \
-JavaOpenJPEG/java-jni/include/win32/jni_md.h \
-JavaOpenJPEG/java-jni/lib/jvm.lib \
-JavaOpenJPEG/JavaOpenJPEG.c \
-JavaOpenJPEG/JavaOpenJPEGDecoder.c \
-JavaOpenJPEG/java-sources/org/openJpeg/OpenJPEGJavaDecoder.java \
-JavaOpenJPEG/java-sources/org/openJpeg/OpenJPEGJavaEncoder.java \
-JavaOpenJPEG/org_openJpeg_OpenJPEGJavaDecoder.h \
-JavaOpenJPEG/org_openJpeg_OpenJPEGJavaEncoder.h \
 LICENSE \
 CHANGES \
+README \
+INSTALL \
 bootstrap.sh \
 libopenjpeg1.pc.cmake \
 libopenjpeg1.pc.in \
diff --git a/applications/Makefile.am b/applications/Makefile.am
index b5cecaa4..e7d11e52 100644
--- a/applications/Makefile.am
+++ b/applications/Makefile.am
@@ -12,8 +12,8 @@ endif
 
 EXTRA_DIST = \
 CMakeLists.txt \
-color.c \
-color.h \
-format_defs.h \
-getopt.c \
-getopt.h
+common/color.c \
+common/color.h \
+common/format_defs.h \
+common/getopt.c \
+common/getopt.h