diff --git a/doxy/Doxyfile.java.in b/doxy/Doxyfile.java.in
index 0a31ff97..bc873d18 100644
--- a/doxy/Doxyfile.java.in
+++ b/doxy/Doxyfile.java.in
@@ -765,8 +765,8 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/src/upm.h \
-                         @CMAKE_BUILD_DIR@/src/ \
-                         @CMAKE_CURRENT_SOURCE_DIR@/docs/ \
+                         @CMAKE_BINARY_DIR@/src \
+                         @CMAKE_CURRENT_SOURCE_DIR@/docs \
                          @CMAKE_CURRENT_SOURCE_DIR@/doxy/README.java.md
 
 # This tag can be used to specify the character encoding of the source files
@@ -787,48 +787,8 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = *.c \
-                         *.cc \
-                         *.cxx \
-                         *.cpp \
-                         *.c++ \
-                         *.java \
-                         *.ii \
-                         *.ixx \
-                         *.ipp \
-                         *.i++ \
-                         *.inl \
-                         *.idl \
-                         *.ddl \
-                         *.odl \
-                         *.h \
-                         *.hh \
-                         *.hxx \
-                         *.hpp \
-                         *.h++ \
-                         *.cs \
-                         *.d \
-                         *.php \
-                         *.php4 \
-                         *.php5 \
-                         *.phtml \
-                         *.inc \
-                         *.m \
-                         *.markdown \
-                         *.md \
-                         *.mm \
-                         *.dox \
-                         *.py \
-                         *.f90 \
-                         *.f \
-                         *.for \
-                         *.tcl \
-                         *.vhd \
-                         *.vhdl \
-                         *.ucf \
-                         *.qsf \
-                         *.as \
-                         *.js
+FILE_PATTERNS          = *.java \
+                         *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -885,7 +845,9 @@ EXAMPLE_PATH           = @CMAKE_CURRENT_SOURCE_DIR@/examples/java/ \
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       = *.java *.cxx
+EXAMPLE_PATTERNS       = *.cxx \
+                         *.java \
+                         *.md
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands