diff --git a/flaim/Makefile.am b/flaim/Makefile.am
index f19c68b..4db5a52 100644
--- a/flaim/Makefile.am
+++ b/flaim/Makefile.am
@@ -13,9 +13,9 @@ rpms srcrpm: dist
 	$(MAKE) -C obs $(AM_MAKEFLAGS) $@
 	rpmarch=`rpm --showrc | grep ^build\ arch | sed 's/\(.*: \)\(.*\)/\2/'`; \
 	test -z $$rpmarch || ( mv $$rpmarch/* .; rm -rf $$rpmarch )
-	-rm -rf $(distdir)
+	rm -rf $(distdir)
 
 dist-hook:
-	-rm -rf `find $(distdir) -name .svn`
+	rm -rf `find $(distdir) -name .svn`
 
 .PHONY: srcrpm rpms
diff --git a/flaim/configure.ac b/flaim/configure.ac
index 6126ab8..a5c86a7 100644
--- a/flaim/configure.ac
+++ b/flaim/configure.ac
@@ -31,7 +31,11 @@ AC_ARG_ENABLE([debug],
   [debug="$withval"], [debug=no])
 
 # Automake conditionals
-AM_CONDITIONAL([HAVE_DOXYGEN], [test "x$DOXYGEN" != x])
+AM_CONDITIONAL([HAVE_DOXYGEN], [test -n "$DOXYGEN"])
+if test -n "$DOXYGEN"; then
+  AC_CONFIG_FILES([docs/doxygen/Makefile
+                   docs/doxygen/doxyfile])
+fi
 
 # Check for pthreads
 ACX_PTHREAD(
@@ -115,8 +119,6 @@ esac
 
 AC_CONFIG_FILES([Makefile
                  docs/Makefile
-                 docs/doxygen/Makefile
-                 docs/doxygen/doxyfile
                  obs/flaim.spec
                  obs/Makefile
                  sample/Makefile
diff --git a/flaim/docs/doxygen/Makefile.am b/flaim/docs/doxygen/Makefile.am
index 580edb1..5d89df0 100644
--- a/flaim/docs/doxygen/Makefile.am
+++ b/flaim/docs/doxygen/Makefile.am
@@ -12,4 +12,4 @@ doxygen.stamp: doxyfile
 CLEANFILES = doxywarn.txt doxygen.stamp $(docpkg)
 
 clean-local:
-	-rm -rf html
+	rm -rf html
diff --git a/flaim/util/Makefile.am b/flaim/util/Makefile.am
index 97204aa..278b9e1 100644
--- a/flaim/util/Makefile.am
+++ b/flaim/util/Makefile.am
@@ -66,4 +66,4 @@ ut_basictest_LDADD = libutil.la ../src/libflaim.la
 TESTS = ut_basictest
 
 clean-local:
-	-rm -rf samplebackup samplerestore.*
+	rm -rf samplebackup samplerestore.*
diff --git a/ftk/Makefile.am b/ftk/Makefile.am
index 5b76892..100ddce 100644
--- a/ftk/Makefile.am
+++ b/ftk/Makefile.am
@@ -14,9 +14,9 @@ rpms srcrpm: dist
 	$(MAKE) -C obs $(AM_MAKEFLAGS) $@
 	rpmarch=`rpm --showrc | grep ^build\ arch | sed 's/\(.*: \)\(.*\)/\2/'`; \
 	test -z $$rpmarch || ( mv $$rpmarch/* .; rm -rf $$rpmarch )
-	-rm -rf $(distdir)
+	rm -rf $(distdir)
 
 dist-hook:
-	-rm -rf `find $(distdir) -name .svn`
+	rm -rf `find $(distdir) -name .svn`
 
 .PHONY: srcrpm rpms
diff --git a/ftk/configure.ac b/ftk/configure.ac
index c3f23d9..52aa79f 100644
--- a/ftk/configure.ac
+++ b/ftk/configure.ac
@@ -34,6 +34,10 @@ AC_ARG_ENABLE([openssl],
 
 # Create Automake conditional based on the DOXYGEN variable
 AM_CONDITIONAL([HAVE_DOXYGEN], [test -n "$DOXYGEN"])
+if test -n "$DOXYGEN"; then
+  AC_CONFIG_FILES([docs/Makefile
+                   docs/doxyfile])
+fi
 
 # Check for pthreads
 ACX_PTHREAD(
@@ -137,8 +141,6 @@ case $host in
 esac
 
 AC_CONFIG_FILES([Makefile
-                 docs/Makefile
-                 docs/doxyfile
                  obs/Makefile
                  obs/ftk.spec
                  src/Makefile
diff --git a/ftk/docs/Makefile.am b/ftk/docs/Makefile.am
index 580edb1..5d89df0 100644
--- a/ftk/docs/Makefile.am
+++ b/ftk/docs/Makefile.am
@@ -12,4 +12,4 @@ doxygen.stamp: doxyfile
 CLEANFILES = doxywarn.txt doxygen.stamp $(docpkg)
 
 clean-local:
-	-rm -rf html
+	rm -rf html
diff --git a/sql/Makefile.am b/sql/Makefile.am
index b4abc83..a79c250 100644
--- a/sql/Makefile.am
+++ b/sql/Makefile.am
@@ -13,9 +13,9 @@ rpms srcrpm: dist
 	$(MAKE) -C obs $(AM_MAKEFLAGS) $@
 	rpmarch=`rpm --showrc | grep ^build\ arch | sed 's/\(.*: \)\(.*\)/\2/'`; \
 	test -z $$rpmarch || ( mv $$rpmarch/* .; rm -rf $$rpmarch )
-	-rm -rf $(distdir)
+	rm -rf $(distdir)
 
 dist-hook:
-	-rm -rf `find $(distdir) -name .svn`
+	rm -rf `find $(distdir) -name .svn`
 
 .PHONY: srcrpm rpms
diff --git a/xflaim/Makefile.am b/xflaim/Makefile.am
index 37f7510..d6a294c 100644
--- a/xflaim/Makefile.am
+++ b/xflaim/Makefile.am
@@ -13,9 +13,9 @@ rpms srcrpm: dist
 	$(MAKE) -C obs $(AM_MAKEFLAGS) $@
 	rpmarch=`rpm --showrc | grep ^build\ arch | sed 's/\(.*: \)\(.*\)/\2/'`; \
 	test -z $$rpmarch || ( mv $$rpmarch/* .; rm -rf $$rpmarch )
-	-rm -rf $(distdir)
+	rm -rf $(distdir)
 
 dist-hook:
-	-rm -rf `find $(distdir) -name .svn`
+	rm -rf `find $(distdir) -name .svn`
 
 .PHONY: srcrpm rpms
diff --git a/xflaim/configure.ac b/xflaim/configure.ac
index a127374..ccc10df 100644
--- a/xflaim/configure.ac
+++ b/xflaim/configure.ac
@@ -37,8 +37,22 @@ AC_ARG_ENABLE([debug],
 
 # Automake conditionals
 AM_CONDITIONAL([HAVE_JAVA], [test "x$ac_prog_have_jni" = xyes])
+if test "x$ac_prog_have_jni" = xyes; then
+  AC_CONFIG_FILES([src/java/Makefile
+                   src/java/wrapper/Makefile])
+fi
+
 AM_CONDITIONAL([HAVE_CSHARP], [test -n "$CSC"])
+if test -n "$CSC"; then
+  AC_CONFIG_FILES([src/cs/Makefile
+                   src/cs/wrapper/Makefile])
+fi
+
 AM_CONDITIONAL([HAVE_DOXYGEN], [test -n "$DOXYGEN"])
+if test -n "$DOXYGEN"; then
+  AC_CONFIG_FILES([docs/doxygen/Makefile
+                   docs/doxygen/doxyfile])
+fi
 
 # Check for pthreads
 ACX_PTHREAD(
@@ -123,16 +137,10 @@ esac
 
 AC_CONFIG_FILES([Makefile
                  docs/Makefile
-                 docs/doxygen/Makefile
-                 docs/doxygen/doxyfile
                  obs/Makefile
                  obs/xflaim.spec
                  sample/Makefile
                  src/Makefile
-                 src/cs/Makefile
-                 src/cs/wrapper/Makefile
-                 src/java/Makefile
-                 src/java/wrapper/Makefile
                  util/Makefile
                  libxflaim.pc])
 AC_OUTPUT
diff --git a/xflaim/docs/doxygen/Makefile.am b/xflaim/docs/doxygen/Makefile.am
index 580edb1..5d89df0 100644
--- a/xflaim/docs/doxygen/Makefile.am
+++ b/xflaim/docs/doxygen/Makefile.am
@@ -12,4 +12,4 @@ doxygen.stamp: doxyfile
 CLEANFILES = doxywarn.txt doxygen.stamp $(docpkg)
 
 clean-local:
-	-rm -rf html
+	rm -rf html
diff --git a/xflaim/src/cs/wrapper/Makefile.am b/xflaim/src/cs/wrapper/Makefile.am
index d27fef8..528b997 100644
--- a/xflaim/src/cs/wrapper/Makefile.am
+++ b/xflaim/src/cs/wrapper/Makefile.am
@@ -50,9 +50,9 @@ AM_CSCFLAGS = -d:mono -nologo -warn:4 -warnaserror+ -optimize+
 all-local: xflaim_csharp.dll
 
 clean-local:
-	-rm xflaim_csharp.dll xflaim_csharp.xml cstest_script cstest.exe libxflaim.so
-	-rm Output_Stream 
-	-rm -rf abc backup test.*
+	rm -f xflaim_csharp.dll xflaim_csharp.xml cstest_script cstest.exe libxflaim.so
+	rm -f Output_Stream 
+	rm -rf abc backup test.*
 
 check-local: cstest.exe cstest_script
 	
diff --git a/xflaim/util/Makefile.am b/xflaim/util/Makefile.am
index fdbff5f..b2384d0 100644
--- a/xflaim/util/Makefile.am
+++ b/xflaim/util/Makefile.am
@@ -200,8 +200,8 @@ copy-xml-files.stamp:
 	echo Timestamp > $@
 
 clean-local: 
-	-rm -rf ix2.*
-	-rm -rf bld.*
-	-rm -rf tst.bak
-	-rm -f *.xml
-	-rm -f copy-xml-files.stamp
+	rm -rf ix2.*
+	rm -rf bld.*
+	rm -rf tst.bak
+	rm -f *.xml
+	rm -f copy-xml-files.stamp