diff --git a/CMakeLists.txt b/CMakeLists.txt
index c67f73aeea..6e5d9cc400 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,5 @@
 cmake_minimum_required( VERSION 2.4 )
+project(ZDoom)
 
 IF( NOT CMAKE_BUILD_TYPE )
 	SET( CMAKE_BUILD_TYPE Debug CACHE STRING
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 056b659377..67993f4e0e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -485,8 +485,10 @@ endif( BACKPATCH )
 
 # Update svnrevision.h
 
+get_target_property( UPDATEREVISION_EXE updaterevision LOCATION )
+
 add_custom_target( revision_check ALL
-	COMMAND ${CMAKE_BINARY_DIR}/tools/updaterevision/updaterevision . src/svnrevision.h
+	COMMAND ${UPDATEREVISION_EXE} . src/svnrevision.h
 	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
 	DEPENDS updaterevision )
 
@@ -568,14 +570,17 @@ else( NO_ASM )
 	endif( X64 )
 endif( NO_ASM )
 
+get_target_property( LEMON_EXE lemon LOCATION )
+get_target_property( RE2C_EXE re2c LOCATION )
+
 add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/xlat_parser.c ${CMAKE_CURRENT_BINARY_DIR}/xlat_parser.h
 	COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/xlat/xlat_parser.y .
-	COMMAND ${CMAKE_BINARY_DIR}/tools/lemon/lemon xlat_parser.y
+	COMMAND ${LEMON_EXE} xlat_parser.y
 	WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 	DEPENDS lemon ${CMAKE_CURRENT_SOURCE_DIR}/xlat/xlat_parser.y )
 
 add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/sc_man_scanner.h
-	COMMAND ${CMAKE_BINARY_DIR}/tools/re2c/re2c --no-generation-date -s -o ${CMAKE_CURRENT_BINARY_DIR}/sc_man_scanner.h ${CMAKE_CURRENT_SOURCE_DIR}/sc_man_scanner.re
+	COMMAND ${RE2C_EXE} --no-generation-date -s -o ${CMAKE_CURRENT_BINARY_DIR}/sc_man_scanner.h ${CMAKE_CURRENT_SOURCE_DIR}/sc_man_scanner.re
 	DEPENDS re2c ${CMAKE_CURRENT_SOURCE_DIR}/sc_man_scanner.re )
 
 include_directories( ${CMAKE_CURRENT_BINARY_DIR} )
@@ -598,7 +603,37 @@ elseif( FLUIDSYNTH_FOUND )
 	add_definitions( -DHAVE_FLUIDSYNTH )
 endif( DYN_FLUIDSYNTH )
 
+# Project files should be aware of the header files. We can GLOB these since
+# there's generally a new cpp for every header so this file will get changed
+if( WIN32 )
+	set( EXTRA_HEADER_DIRS win32/*.h )
+else( WIN32 )
+	set( EXTRA_HEADER_DIRS sdl/*.h )
+endif( WIN32 )
+file( GLOB HEADER_FILES
+	${EXTRA_HEADER_DIRS}
+	fragglescript/*.h
+	g_doom/*.h
+	g_heretic/*.h
+	g_hexen/*.h
+	g_raven/*.h
+	g_shared/*.h
+	g_strife/*.h
+	intermission/*.h
+	menu/*.h
+	oplsynth/*.h
+	r_data/*.h
+	resourcefiles/*.h
+	sfmt/*.h
+	sound/*.h
+	textures/*.h
+	thingdef/*.h
+	xlat/*.h
+	*.h
+)
+
 add_executable( zdoom WIN32
+	${HEADER_FILES}
 	autostart.cpp
 	${ASM_SOURCES}
 	${SYSTEM_SOURCES}
diff --git a/tools/lemon/CMakeLists.txt b/tools/lemon/CMakeLists.txt
index 0a6b2319cd..91b1445759 100644
--- a/tools/lemon/CMakeLists.txt
+++ b/tools/lemon/CMakeLists.txt
@@ -5,6 +5,13 @@ set( CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -D_DEBUG" )
 add_executable( lemon lemon.c )
 
 # Lemon wants lempar.c in its directory
+if( MSVC )
+add_custom_command( TARGET lemon
+	POST_BUILD
+	COMMAND echo $<TARGET_FILE_DIR:lemon>
+	COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/lempar.c $<TARGET_FILE_DIR:lemon> )	
+else( MSVC )
 add_custom_command( TARGET lemon
 	POST_BUILD
 	COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/lempar.c ${CMAKE_CURRENT_BINARY_DIR} )
+endif( MSVC )
\ No newline at end of file
diff --git a/wadsrc/CMakeLists.txt b/wadsrc/CMakeLists.txt
index 19a210abc6..a24d712e1b 100644
--- a/wadsrc/CMakeLists.txt
+++ b/wadsrc/CMakeLists.txt
@@ -1,9 +1,10 @@
 cmake_minimum_required( VERSION 2.4 )
 
-	
+get_target_property(ZIPDIR_EXE zipdir LOCATION)
+
 add_custom_command( OUTPUT ${ZDOOM_OUTPUT_DIR}/zdoom.pk3
-   COMMAND ${CMAKE_BINARY_DIR}/tools/zipdir/zipdir -udf ${ZDOOM_OUTPUT_DIR}/zdoom.pk3 ${CMAKE_CURRENT_SOURCE_DIR}/static 
-   DEPENDS zipdir ${CMAKE_CURRENT_SOURCE_DIR}/static )
-	
+	COMMAND ${ZIPDIR_EXE} -udf ${ZDOOM_OUTPUT_DIR}/zdoom.pk3 ${CMAKE_CURRENT_SOURCE_DIR}/static 
+	DEPENDS zipdir ${CMAKE_CURRENT_SOURCE_DIR}/static )
+
 add_custom_target( pk3 ALL
 	DEPENDS ${ZDOOM_OUTPUT_DIR}/zdoom.pk3 )