diff --git a/Makefile.am b/src/Makefile.am similarity index 100% rename from Makefile.am rename to src/Makefile.am diff --git a/arduino.c b/src/arduino.c similarity index 100% rename from arduino.c rename to src/arduino.c diff --git a/arduino.h b/src/arduino.h similarity index 100% rename from arduino.h rename to src/arduino.h diff --git a/avr.c b/src/avr.c similarity index 100% rename from avr.c rename to src/avr.c diff --git a/avr910.c b/src/avr910.c similarity index 100% rename from avr910.c rename to src/avr910.c diff --git a/avr910.h b/src/avr910.h similarity index 100% rename from avr910.h rename to src/avr910.h diff --git a/avrdude.1 b/src/avrdude.1 similarity index 100% rename from avrdude.1 rename to src/avrdude.1 diff --git a/avrdude.conf.in b/src/avrdude.conf.in similarity index 100% rename from avrdude.conf.in rename to src/avrdude.conf.in diff --git a/avrdude.h b/src/avrdude.h similarity index 100% rename from avrdude.h rename to src/avrdude.h diff --git a/avrdude.spec.in b/src/avrdude.spec.in similarity index 100% rename from avrdude.spec.in rename to src/avrdude.spec.in diff --git a/avrftdi.c b/src/avrftdi.c similarity index 100% rename from avrftdi.c rename to src/avrftdi.c diff --git a/avrftdi.h b/src/avrftdi.h similarity index 100% rename from avrftdi.h rename to src/avrftdi.h diff --git a/avrftdi_private.h b/src/avrftdi_private.h similarity index 100% rename from avrftdi_private.h rename to src/avrftdi_private.h diff --git a/avrftdi_tpi.c b/src/avrftdi_tpi.c similarity index 100% rename from avrftdi_tpi.c rename to src/avrftdi_tpi.c diff --git a/avrftdi_tpi.h b/src/avrftdi_tpi.h similarity index 100% rename from avrftdi_tpi.h rename to src/avrftdi_tpi.h diff --git a/avrpart.c b/src/avrpart.c similarity index 100% rename from avrpart.c rename to src/avrpart.c diff --git a/bitbang.c b/src/bitbang.c similarity index 100% rename from bitbang.c rename to src/bitbang.c diff --git a/bitbang.h b/src/bitbang.h similarity index 100% rename from bitbang.h rename to src/bitbang.h diff --git a/bootstrap b/src/bootstrap old mode 100755 new mode 100644 similarity index 100% rename from bootstrap rename to src/bootstrap diff --git a/buspirate.c b/src/buspirate.c similarity index 100% rename from buspirate.c rename to src/buspirate.c diff --git a/buspirate.h b/src/buspirate.h similarity index 100% rename from buspirate.h rename to src/buspirate.h diff --git a/butterfly.c b/src/butterfly.c similarity index 100% rename from butterfly.c rename to src/butterfly.c diff --git a/butterfly.h b/src/butterfly.h similarity index 100% rename from butterfly.h rename to src/butterfly.h diff --git a/config.c b/src/config.c similarity index 100% rename from config.c rename to src/config.c diff --git a/config.h b/src/config.h similarity index 100% rename from config.h rename to src/config.h diff --git a/config_gram.y b/src/config_gram.y similarity index 100% rename from config_gram.y rename to src/config_gram.y diff --git a/configure.ac b/src/configure.ac similarity index 100% rename from configure.ac rename to src/configure.ac diff --git a/confwin.c b/src/confwin.c similarity index 100% rename from confwin.c rename to src/confwin.c diff --git a/crc16.c b/src/crc16.c similarity index 100% rename from crc16.c rename to src/crc16.c diff --git a/crc16.h b/src/crc16.h similarity index 100% rename from crc16.h rename to src/crc16.h diff --git a/dfu.c b/src/dfu.c similarity index 100% rename from dfu.c rename to src/dfu.c diff --git a/dfu.h b/src/dfu.h similarity index 100% rename from dfu.h rename to src/dfu.h diff --git a/doc/.gitignore b/src/doc/.gitignore similarity index 100% rename from doc/.gitignore rename to src/doc/.gitignore diff --git a/doc/Makefile.am b/src/doc/Makefile.am similarity index 100% rename from doc/Makefile.am rename to src/doc/Makefile.am diff --git a/doc/TODO b/src/doc/TODO similarity index 100% rename from doc/TODO rename to src/doc/TODO diff --git a/doc/avrdude.texi b/src/doc/avrdude.texi similarity index 100% rename from doc/avrdude.texi rename to src/doc/avrdude.texi diff --git a/doc/parts_comments.txt b/src/doc/parts_comments.txt similarity index 100% rename from doc/parts_comments.txt rename to src/doc/parts_comments.txt diff --git a/fileio.c b/src/fileio.c similarity index 100% rename from fileio.c rename to src/fileio.c diff --git a/flip1.c b/src/flip1.c similarity index 100% rename from flip1.c rename to src/flip1.c diff --git a/flip1.h b/src/flip1.h similarity index 100% rename from flip1.h rename to src/flip1.h diff --git a/flip2.c b/src/flip2.c similarity index 100% rename from flip2.c rename to src/flip2.c diff --git a/flip2.h b/src/flip2.h similarity index 100% rename from flip2.h rename to src/flip2.h diff --git a/freebsd_ppi.h b/src/freebsd_ppi.h similarity index 100% rename from freebsd_ppi.h rename to src/freebsd_ppi.h diff --git a/ft245r.c b/src/ft245r.c similarity index 100% rename from ft245r.c rename to src/ft245r.c diff --git a/ft245r.h b/src/ft245r.h similarity index 100% rename from ft245r.h rename to src/ft245r.h diff --git a/jtag3.c b/src/jtag3.c similarity index 100% rename from jtag3.c rename to src/jtag3.c diff --git a/jtag3.h b/src/jtag3.h similarity index 100% rename from jtag3.h rename to src/jtag3.h diff --git a/jtag3_private.h b/src/jtag3_private.h similarity index 100% rename from jtag3_private.h rename to src/jtag3_private.h diff --git a/jtagmkI.c b/src/jtagmkI.c similarity index 100% rename from jtagmkI.c rename to src/jtagmkI.c diff --git a/jtagmkI.h b/src/jtagmkI.h similarity index 100% rename from jtagmkI.h rename to src/jtagmkI.h diff --git a/jtagmkII.c b/src/jtagmkII.c similarity index 100% rename from jtagmkII.c rename to src/jtagmkII.c diff --git a/jtagmkII.h b/src/jtagmkII.h similarity index 100% rename from jtagmkII.h rename to src/jtagmkII.h diff --git a/jtagmkII_private.h b/src/jtagmkII_private.h similarity index 100% rename from jtagmkII_private.h rename to src/jtagmkII_private.h diff --git a/jtagmkI_private.h b/src/jtagmkI_private.h similarity index 100% rename from jtagmkI_private.h rename to src/jtagmkI_private.h diff --git a/lexer.l b/src/lexer.l similarity index 100% rename from lexer.l rename to src/lexer.l diff --git a/libavrdude.h b/src/libavrdude.h similarity index 100% rename from libavrdude.h rename to src/libavrdude.h diff --git a/linux_ppdev.h b/src/linux_ppdev.h similarity index 100% rename from linux_ppdev.h rename to src/linux_ppdev.h diff --git a/linuxgpio.c b/src/linuxgpio.c similarity index 100% rename from linuxgpio.c rename to src/linuxgpio.c diff --git a/linuxgpio.h b/src/linuxgpio.h similarity index 100% rename from linuxgpio.h rename to src/linuxgpio.h diff --git a/linuxspi.c b/src/linuxspi.c similarity index 100% rename from linuxspi.c rename to src/linuxspi.c diff --git a/linuxspi.h b/src/linuxspi.h similarity index 100% rename from linuxspi.h rename to src/linuxspi.h diff --git a/lists.c b/src/lists.c similarity index 100% rename from lists.c rename to src/lists.c diff --git a/main.c b/src/main.c similarity index 100% rename from main.c rename to src/main.c diff --git a/my_ddk_hidsdi.h b/src/my_ddk_hidsdi.h similarity index 100% rename from my_ddk_hidsdi.h rename to src/my_ddk_hidsdi.h diff --git a/par.c b/src/par.c similarity index 100% rename from par.c rename to src/par.c diff --git a/par.h b/src/par.h similarity index 100% rename from par.h rename to src/par.h diff --git a/pgm.c b/src/pgm.c similarity index 100% rename from pgm.c rename to src/pgm.c diff --git a/pgm_type.c b/src/pgm_type.c similarity index 100% rename from pgm_type.c rename to src/pgm_type.c diff --git a/pickit2.c b/src/pickit2.c similarity index 100% rename from pickit2.c rename to src/pickit2.c diff --git a/pickit2.h b/src/pickit2.h similarity index 100% rename from pickit2.h rename to src/pickit2.h diff --git a/pindefs.c b/src/pindefs.c similarity index 100% rename from pindefs.c rename to src/pindefs.c diff --git a/ppi.c b/src/ppi.c similarity index 100% rename from ppi.c rename to src/ppi.c diff --git a/ppi.h b/src/ppi.h similarity index 100% rename from ppi.h rename to src/ppi.h diff --git a/ppiwin.c b/src/ppiwin.c similarity index 100% rename from ppiwin.c rename to src/ppiwin.c diff --git a/safemode.c b/src/safemode.c similarity index 100% rename from safemode.c rename to src/safemode.c diff --git a/ser_avrdoper.c b/src/ser_avrdoper.c similarity index 100% rename from ser_avrdoper.c rename to src/ser_avrdoper.c diff --git a/ser_posix.c b/src/ser_posix.c similarity index 100% rename from ser_posix.c rename to src/ser_posix.c diff --git a/ser_win32.c b/src/ser_win32.c similarity index 100% rename from ser_win32.c rename to src/ser_win32.c diff --git a/serbb.h b/src/serbb.h similarity index 100% rename from serbb.h rename to src/serbb.h diff --git a/serbb_posix.c b/src/serbb_posix.c similarity index 100% rename from serbb_posix.c rename to src/serbb_posix.c diff --git a/serbb_win32.c b/src/serbb_win32.c similarity index 100% rename from serbb_win32.c rename to src/serbb_win32.c diff --git a/solaris_ecpp.h b/src/solaris_ecpp.h similarity index 100% rename from solaris_ecpp.h rename to src/solaris_ecpp.h diff --git a/stk500.c b/src/stk500.c similarity index 100% rename from stk500.c rename to src/stk500.c diff --git a/stk500.h b/src/stk500.h similarity index 100% rename from stk500.h rename to src/stk500.h diff --git a/stk500_private.h b/src/stk500_private.h similarity index 100% rename from stk500_private.h rename to src/stk500_private.h diff --git a/stk500generic.c b/src/stk500generic.c similarity index 100% rename from stk500generic.c rename to src/stk500generic.c diff --git a/stk500generic.h b/src/stk500generic.h similarity index 100% rename from stk500generic.h rename to src/stk500generic.h diff --git a/stk500v2.c b/src/stk500v2.c similarity index 100% rename from stk500v2.c rename to src/stk500v2.c diff --git a/stk500v2.h b/src/stk500v2.h similarity index 100% rename from stk500v2.h rename to src/stk500v2.h diff --git a/stk500v2_private.h b/src/stk500v2_private.h similarity index 100% rename from stk500v2_private.h rename to src/stk500v2_private.h diff --git a/term.c b/src/term.c similarity index 100% rename from term.c rename to src/term.c diff --git a/term.h b/src/term.h similarity index 100% rename from term.h rename to src/term.h diff --git a/tpi.h b/src/tpi.h similarity index 100% rename from tpi.h rename to src/tpi.h diff --git a/update.c b/src/update.c similarity index 100% rename from update.c rename to src/update.c diff --git a/usb_hidapi.c b/src/usb_hidapi.c similarity index 100% rename from usb_hidapi.c rename to src/usb_hidapi.c diff --git a/usb_libusb.c b/src/usb_libusb.c similarity index 100% rename from usb_libusb.c rename to src/usb_libusb.c diff --git a/usbasp.c b/src/usbasp.c similarity index 100% rename from usbasp.c rename to src/usbasp.c diff --git a/usbasp.h b/src/usbasp.h similarity index 100% rename from usbasp.h rename to src/usbasp.h diff --git a/usbdevs.h b/src/usbdevs.h similarity index 100% rename from usbdevs.h rename to src/usbdevs.h diff --git a/usbtiny.c b/src/usbtiny.c similarity index 100% rename from usbtiny.c rename to src/usbtiny.c diff --git a/usbtiny.h b/src/usbtiny.h similarity index 100% rename from usbtiny.h rename to src/usbtiny.h diff --git a/windows/.gitignore b/src/windows/.gitignore similarity index 100% rename from windows/.gitignore rename to src/windows/.gitignore diff --git a/windows/Makefile.am b/src/windows/Makefile.am similarity index 100% rename from windows/Makefile.am rename to src/windows/Makefile.am diff --git a/windows/giveio.c b/src/windows/giveio.c similarity index 100% rename from windows/giveio.c rename to src/windows/giveio.c diff --git a/windows/giveio.sys b/src/windows/giveio.sys similarity index 100% rename from windows/giveio.sys rename to src/windows/giveio.sys diff --git a/windows/install_giveio.bat b/src/windows/install_giveio.bat old mode 100755 new mode 100644 similarity index 100% rename from windows/install_giveio.bat rename to src/windows/install_giveio.bat diff --git a/windows/loaddrv.c b/src/windows/loaddrv.c similarity index 100% rename from windows/loaddrv.c rename to src/windows/loaddrv.c diff --git a/windows/loaddrv.h b/src/windows/loaddrv.h similarity index 100% rename from windows/loaddrv.h rename to src/windows/loaddrv.h diff --git a/windows/remove_giveio.bat b/src/windows/remove_giveio.bat old mode 100755 new mode 100644 similarity index 100% rename from windows/remove_giveio.bat rename to src/windows/remove_giveio.bat diff --git a/windows/status_giveio.bat b/src/windows/status_giveio.bat old mode 100755 new mode 100644 similarity index 100% rename from windows/status_giveio.bat rename to src/windows/status_giveio.bat diff --git a/wiring.c b/src/wiring.c similarity index 100% rename from wiring.c rename to src/wiring.c diff --git a/wiring.h b/src/wiring.h similarity index 100% rename from wiring.h rename to src/wiring.h diff --git a/xbee.c b/src/xbee.c similarity index 100% rename from xbee.c rename to src/xbee.c diff --git a/xbee.h b/src/xbee.h similarity index 100% rename from xbee.h rename to src/xbee.h