diff --git a/build/linux/dist/tools/avrdude b/build/linux/dist/tools/avrdude
index 0fcb62294..96f489c15 100755
Binary files a/build/linux/dist/tools/avrdude and b/build/linux/dist/tools/avrdude differ
diff --git a/build/linux/dist/tools/avrdude.conf b/build/linux/dist/tools/avrdude.conf
index faf1ba331..6f078b167 100644
--- a/build/linux/dist/tools/avrdude.conf
+++ b/build/linux/dist/tools/avrdude.conf
@@ -377,6 +377,12 @@ programmer
   type  = usbasp;
 ;
 
+programmer
+  id    = "usbtiny";
+  desc  = "USBtiny simple USB programmer";
+  type  = usbtiny;
+;
+
 programmer
   id    = "butterfly";
   desc  = "Atmel Butterfly Development Board";
diff --git a/build/linux/dist/tools/uisp b/build/linux/dist/tools/uisp
deleted file mode 100755
index f25e5e709..000000000
Binary files a/build/linux/dist/tools/uisp and /dev/null differ
diff --git a/build/linux/make.sh b/build/linux/make.sh
index 51b8e15c9..24de33f43 100755
--- a/build/linux/make.sh
+++ b/build/linux/make.sh
@@ -49,8 +49,7 @@ fi
 echo Copying shared and core files...
 cp -r ../shared/* work
 rm -rf work/dist
-cp -r ../../targets work/lib
-cp -r ../../bootloader168 work
+cp -r ../../hardware work
 rm work/reference.zip
 
 echo Copying examples...
@@ -60,8 +59,7 @@ cp -r ../shared/dist/examples work/
 echo Copying dist files...
 cp -r dist/lib work/
 #cp -r dist/core work/
-cp -r dist/bootloader work/
-cp -r dist/tools work/
+cp -r dist/tools work/hardware/
 
 ### -- START BUILDING -------------------------------------------
 
@@ -71,14 +69,6 @@ cd ../..
 ### -- BUILD GCC ------------------------------------------------
 # in the future we will build avr-gcc and tools (if they don't exist)
 
-### -- COPY BOOTLOADER  -----------------------------------------
-cd bootloader
-# don't make the bootloader, since it rarely changes and requires
-# installation of make.
-# make
-cp ATmegaBOOT.hex ../build/linux/work/bootloader
-cd ..
-
 ### -- BUILD PARSER ---------------------------------------------
 
 cd app
@@ -105,7 +95,7 @@ echo Building the PDE...
 # show the user an error, rather than crapping out with some strange
 # "class not found" crap
 #jikes -classpath ../build/linux/work/classes:../build/linux/work/lib/antlr.jar:../build/linux/work/lib/oro.jar:../build/linux/work/lib/registry.jar:../build/linux/work/lib/RXTXcomm.jar:../build/linux/work/lib/mrj.jar:$CLASSPATH -d ../build/linux/work/classes tools/*.java preproc/*.java syntax/*.java *.java 
-javac -source 1.4 -target 1.4 -classpath ../build/linux/work/class:../build/linux/work/lib/antlr.jar:../build/linux/work/lib/oro.jar:../build/linux/work/lib/registry.jar:../build/linux/work/lib/RXTXcomm.jar:../build/linux/work/lib/mrj.jar:$CLASSPATH -d ../build/linux/work/classes tools/*.java preproc/*.java syntax/*java *.java
+javac -source 1.4 -target 1.4 -classpath ../build/linux/work/class:../build/linux/work/lib/antlr.jar:../build/linux/work/lib/oro.jar:../build/linux/work/lib/registry.jar:../build/linux/work/lib/RXTXcomm.jar:../build/linux/work/lib/mrj.jar:$CLASSPATH -d ../build/linux/work/classes ../core/*.java tools/*.java preproc/*.java syntax/*java *.java
 
 cd ../build/linux/work/classes
 rm -f ../lib/pde.jar