I've uploaded a new version that fixes this and #812658.
debdiff attached.

Ben.

-- 
Ben Hutchings
Tomorrow will be cancelled due to lack of interest.
diff -Nru astyle-2.04/debian/changelog astyle-2.04/debian/changelog
--- astyle-2.04/debian/changelog	2014-09-08 16:14:49.000000000 +0100
+++ astyle-2.04/debian/changelog	2016-02-20 22:07:29.000000000 +0000
@@ -1,3 +1,11 @@
+astyle (2.04-1.1) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * Fix FTBFS with DEB_BUILD_OPTIONS=nostrip (Closes: #812658)
+  * Fix JNI include path (Closes: #814580)
+
+ -- Ben Hutchings <b...@decadent.org.uk>  Sat, 20 Feb 2016 22:07:28 +0000
+
 astyle (2.04-1) unstable; urgency=medium
 
   * Acknowledging NMU.
diff -Nru astyle-2.04/debian/patches/fix-jni-include-path.patch astyle-2.04/debian/patches/fix-jni-include-path.patch
--- astyle-2.04/debian/patches/fix-jni-include-path.patch	1970-01-01 01:00:00.000000000 +0100
+++ astyle-2.04/debian/patches/fix-jni-include-path.patch	2016-02-20 21:59:41.000000000 +0000
@@ -0,0 +1,38 @@
+From: Ben Hutchings <b...@decadent.org.uk>
+Date: Sat, 20 Feb 2016 21:59:08 +0000
+Subject: Fix JNI include path
+Bug-Debian: https://bugs.debian.org/814580
+
+--- a/build/clang/Makefile
++++ b/build/clang/Makefile
+@@ -33,7 +33,7 @@ bindir = bin
+ objdir = obj
+ ipath=$(prefix)/bin
+ CBASEFLAGS = -W -Wall -fno-rtti -fno-exceptions
+-JAVAINCS   = -I$(JAVA_HOME)/include
++JAVAINCS   = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
+ CXX = clang++
+ INSTALL=install -o $(USER) -g $(USER)
+ 
+--- a/build/gcc/Makefile
++++ b/build/gcc/Makefile
+@@ -33,7 +33,7 @@ bindir = bin
+ objdir = obj
+ ipath=$(prefix)/bin
+ CBASEFLAGS = -W -Wall -fno-rtti -fno-exceptions
+-JAVAINCS   = -I$(JAVA_HOME)/include
++JAVAINCS   = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
+ CXX = g++
+ INSTALL=install -o $(USER) -g $(USER)
+ 
+--- a/build/intel/Makefile
++++ b/build/intel/Makefile
+@@ -47,7 +47,7 @@ ipath=$(prefix)/bin
+ #     -vec-report0 turns off BLOCK WAS VECTORIZED warnings. To disable vectorization use -mia32 instead.
+ #     -no-multibyte-chars is a temporary compiler bug work-around, http://software.intel.com/en-us/forums/intel-c-compiler/topic/56258
+ CBASEFLAGS = -w2 -Wall -fno-rtti -fno-exceptions
+-JAVAINCS   = -I$(JAVA_HOME)/include
++JAVAINCS   = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
+ CXX = icpc
+ INSTALL=install -o $(USER) -g $(USER)
+ 
diff -Nru astyle-2.04/debian/patches/series astyle-2.04/debian/patches/series
--- astyle-2.04/debian/patches/series	2014-09-08 16:14:49.000000000 +0100
+++ astyle-2.04/debian/patches/series	2016-02-20 22:05:03.000000000 +0000
@@ -1,3 +1,4 @@
 set_soname.patch
 privacy.patch
 FTBFS_PIC.patch
+fix-jni-include-path.patch
diff -Nru astyle-2.04/debian/rules astyle-2.04/debian/rules
--- astyle-2.04/debian/rules	2014-09-08 16:14:49.000000000 +0100
+++ astyle-2.04/debian/rules	2016-02-20 22:06:49.000000000 +0000
@@ -25,7 +25,7 @@
 
 override_dh_auto_build:
 	dh_auto_build -Smakefile -- -C build/gcc $(BUILD_TARGET) shared java
-	[ "$(BUILD_TARGET)" = "astyle" ] || mv bin/$(BUILD_TARGET) bin/astyle
+	[ "$(BUILD_TARGET)" = "astyle" ] || mv build/gcc/bin/$(BUILD_TARGET) build/gcc/bin/astyle
 
 override_dh_auto_clean:
 	dh_auto_clean

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