diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..388a02e
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,13 @@
+Makefile
+config.log
+config.status
+configure
+
+obj
+autom4te.cache
+
+debian/xilprg
+debian/*.substvars
+debian/files
+
+*-stamp
diff --git a/Makefile.in b/Makefile.in
new file mode 100755
index 0000000..3a7512c
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,112 @@
+PROJ = xilprg
+
+prefix = @prefix@
+CONFDIR = @datadir@/misc/
+
+########################################
+# 
+VER_MJ := $(shell gawk '/VERSION_MAJOR/ {print $$3}' src/xilprg.h)
+VER_MN := $(shell gawk '/VERSION_MINOR/ {print $$3}' src/xilprg.h)
+
+########################################
+# 
+IS_CYGWIN=$(shell uname | grep -i cygwin > /dev/null 2>&1 && echo yes || echo no)
+
+########################################
+# Directories
+
+SRC_DIR = src
+ifeq ($(IS_CYGWIN),yes)
+OBJ_DIR = obj/cygwin
+else
+OBJ_DIR = obj/linux
+endif 
+
+ifeq ($(IS_CYGWIN),yes)
+BIN_EXT = .exe
+else
+BIN_EXT =
+endif
+
+XILPRG_DIR = xilprg-$(VER_MJ).$(VER_MN)
+
+########################################
+# Compiler options
+
+SRCS = \
+	$(SRC_DIR)/xilprg.cpp \
+	$(SRC_DIR)/cmdline.cpp \
+	$(SRC_DIR)/cmds.cpp \
+	$(SRC_DIR)/utils.cpp \
+	$(SRC_DIR)/vartable.cpp \
+	$(SRC_DIR)/strtable.cpp \
+	$(SRC_DIR)/prgfile.cpp \
+	$(SRC_DIR)/chip.cpp \
+	$(SRC_DIR)/parport.cpp \
+	$(SRC_DIR)/cable.cpp \
+	$(SRC_DIR)/digilent.cpp \
+	$(SRC_DIR)/xilinx.cpp
+
+OBJS = $(addsuffix .o, \
+		$(addprefix $(OBJ_DIR)/, \
+		$(basename $(notdir $(SRCS)))))
+TARG = $(OBJ_DIR)/$(PROJ)$(BIN_EXT)
+
+CC    = g++
+LD    = g++
+
+CPFLAGS = -O3 -Wall -DCONFDIR=\"$(CONFDIR)\"
+LDFLAGS =
+
+ifeq ($(IS_CYGWIN),yes)
+LIBS = -lioperm -lreadline
+else
+LIBS = -lusb -lreadline
+endif
+
+########################################
+# Rules
+
+all: mkdirs $(TARG)
+
+clean:
+	-rm -rf obj
+
+$(TARG) : $(OBJS)
+	$(LD) $(LDFLAGS) $(OBJS) $(LIBS) -o $@
+
+mkdirs:
+	-mkdir -p $(OBJ_DIR)
+
+srctar:
+	tar -cjvf $(XILPRG_DIR)-src.tar.bz2 -C .. \
+		$(XILPRG_DIR)/src \
+		$(XILPRG_DIR)/makefile \
+		$(XILPRG_DIR)/xilprg.dsp \
+		$(XILPRG_DIR)/xilprg.dsw \
+		$(XILPRG_DIR)/xilprg.conf \
+		$(XILPRG_DIR)/readme.txt \
+		$(XILPRG_DIR)/license.txt
+
+winbintar:
+	tar -cjvf $(XILPRG_DIR)-win32.tar.bz2 \
+		xilprg.conf readme.txt license.txt \
+		-C obj/win32/Release xilprg.exe
+
+linuxbintar:
+	tar -cjvf $(XILPRG_DIR)-linux.tar.bz2 \
+		xilprg.conf readme.txt license.txt \
+		-C obj/linux xilprg
+
+tar: srctar winbintar linuxbintar
+
+install: obj/linux/xilprg xilprg.conf
+	@mkdir -p $(DESTDIR)@bindir@ $(DESTDIR)$(CONFDIR) $(DESTDIR)@mandir@/man1
+	install -m 4550 -g lpadmin -o root obj/linux/xilprg $(DESTDIR)@bindir@
+	install -m 444 xilprg.conf $(DESTDIR)$(CONFDIR)
+	install -m 444 xilprg.1 $(DESTDIR)@mandir@/man1
+
+#
+
+$(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp
+	$(CC) -c $(CPFLAGS) $< -o $@
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..458c157
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,6 @@
+AC_INIT(xilprg, 0.5, jepler@unpy.net)
+
+AC_PROG_MAKE_SET
+
+AC_CONFIG_FILES(Makefile)
+AC_OUTPUT
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..cc2e31d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+xilprg (0.5-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Jeff Epler <jepler@unpythonic.net>  Mon, 01 Sep 2008 21:33:01 -0500
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..b8626c4
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+4
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..d2bcf16
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,12 @@
+Source: xilprg
+Section: misc
+Priority: extra
+Maintainer: Jeff Epler <jepler@unpythonic.net>
+Build-Depends: libusb-dev
+
+Package: xilprg
+Architecture: any
+Depends: ${shlibs:Depends}
+Section: misc
+Description: Programmer for certain Xilinx devices using a JTAG interface
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e452b74
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,31 @@
+#!/usr/bin/make -f
+
+build: build-stamp
+build-stamp:
+	./configure --prefix=/usr
+	$(MAKE)
+	touch build-stamp
+
+install: install-stamp
+install-stamp: build
+	dh_testroot
+	$(MAKE) install DESTDIR=debian/xilprg
+	touch install-stamp
+
+clean:
+	if [ -f Makefile ]; then $(MAKE) clean; fi
+	rm -f Makefile config.log config.status *-stamp obj
+	dh_clean
+
+binary: install-stamp
+	dh_testroot
+	dh_shlibdeps
+	dh_installchangelogs
+	dh_installdocs xilinx.mk readme.txt
+	dh_installdeb
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+.PHONY:
+	build install clean
diff --git a/makefile b/makefile
deleted file mode 100755
index c381c55..0000000
--- a/makefile
+++ /dev/null
@@ -1,103 +0,0 @@
-PROJ = xilprg
-
-########################################
-# 
-VER_MJ := $(shell gawk '/VERSION_MAJOR/ {print $$3}' src/xilprg.h)
-VER_MN := $(shell gawk '/VERSION_MINOR/ {print $$3}' src/xilprg.h)
-
-########################################
-# 
-IS_CYGWIN=$(shell uname | grep -i cygwin > /dev/null 2>&1 && echo yes || echo no)
-
-########################################
-# Directories
-
-SRC_DIR = src
-ifeq ($(IS_CYGWIN),yes)
-OBJ_DIR = obj/cygwin
-else
-OBJ_DIR = obj/linux
-endif 
-
-ifeq ($(IS_CYGWIN),yes)
-BIN_EXT = .exe
-else
-BIN_EXT =
-endif
-
-XILPRG_DIR = xilprg-$(VER_MJ).$(VER_MN)
-
-########################################
-# Compiler options
-
-SRCS = \
-	$(SRC_DIR)/xilprg.cpp \
-	$(SRC_DIR)/cmdline.cpp \
-	$(SRC_DIR)/cmds.cpp \
-	$(SRC_DIR)/utils.cpp \
-	$(SRC_DIR)/vartable.cpp \
-	$(SRC_DIR)/strtable.cpp \
-	$(SRC_DIR)/prgfile.cpp \
-	$(SRC_DIR)/chip.cpp \
-	$(SRC_DIR)/parport.cpp \
-	$(SRC_DIR)/cable.cpp \
-	$(SRC_DIR)/digilent.cpp \
-	$(SRC_DIR)/xilinx.cpp
-
-OBJS = $(addsuffix .o, \
-		$(addprefix $(OBJ_DIR)/, \
-		$(basename $(notdir $(SRCS)))))
-TARG = $(OBJ_DIR)/$(PROJ)$(BIN_EXT)
-
-CC    = g++
-LD    = g++
-
-CPFLAGS = -O3 -Wall
-LDFLAGS =
-
-ifeq ($(IS_CYGWIN),yes)
-LIBS = -lioperm -lreadline
-else
-LIBS = -lusb -lreadline -lncurses
-endif
-
-########################################
-# Rules
-
-all: mkdirs $(TARG)
-
-clean:
-	-rm -rf $(OBJ_DIR)
-
-$(TARG) : $(OBJS)
-	$(LD) $(LDFLAGS) $(OBJS) $(LIBS) -o $@
-
-mkdirs:
-	-mkdir -p $(OBJ_DIR)
-
-srctar:
-	tar -cjvf $(XILPRG_DIR)-src.tar.bz2 -C .. \
-		$(XILPRG_DIR)/src \
-		$(XILPRG_DIR)/makefile \
-		$(XILPRG_DIR)/xilprg.dsp \
-		$(XILPRG_DIR)/xilprg.dsw \
-		$(XILPRG_DIR)/xilprg.conf \
-		$(XILPRG_DIR)/readme.txt \
-		$(XILPRG_DIR)/license.txt
-
-winbintar:
-	tar -cjvf $(XILPRG_DIR)-win32.tar.bz2 \
-		xilprg.conf readme.txt license.txt \
-		-C obj/win32/Release xilprg.exe
-
-linuxbintar:
-	tar -cjvf $(XILPRG_DIR)-linux.tar.bz2 \
-		xilprg.conf readme.txt license.txt \
-		-C obj/linux xilprg
-
-tar: srctar winbintar linuxbintar
-
-#
-
-$(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp
-	$(CC) -c $(CPFLAGS) $< -o $@
diff --git a/readme.txt b/readme.txt
index e954163..0b787cf 100755
--- a/readme.txt
+++ b/readme.txt
@@ -31,6 +31,8 @@ Program device:
     E.g.: program 1 c:\untitled.mcs
           program 2 download.bit
 
+    Common error: forgetting to erase a flash device before programming it
+
 Read device:
  
     read [-bin|-mcs] pos file
@@ -50,6 +52,7 @@ Supported cables:
 
 Xilinx Parallel III
     Win32: giveio.sys must be installed to enable user-mode I/O access!
+    Linux: program must be run as root
 
 Digilent USB
     Win32: Digilent driver must be installed!
diff --git a/src/xilprg.cpp b/src/xilprg.cpp
index efc6b10..bb8e623 100755
--- a/src/xilprg.cpp
+++ b/src/xilprg.cpp
@@ -135,6 +135,10 @@ chip* select_device_in_chain(int index)
 	return  g.dev_chain[index].dev;
 }
 
+#ifndef CONFDIR
+#define CONFDIR
+#endif
+
 int load_config_file()
 {
 	int rc = -1, line_index = 0;
@@ -148,7 +152,7 @@ int load_config_file()
     int id, mask;
     int ir_length;
 
-	f = fopen("xilprg.conf", "rt");
+	f = fopen(CONFDIR "xilprg.conf", "rt");
 	if (f == NULL)
 	{
         msgf(STR_FAILED_TO_OPEN_CONFIG_FILE);
@@ -256,10 +260,10 @@ cleanup:
 	return rc;
 }
 
-int main()
+int main(int argc, char **argv)
 {
     char line[1024];
-    int rc = -1;
+    int rc = EXIT_FAILURE;
 
     process_command_line("version");
     printf("\n");
@@ -270,14 +274,34 @@ int main()
 	if (load_config_file())
 		goto cleanup;
 
-    do
-    {
-        if (prompt_read_line("xilprg> ", line, sizeof(line)) < 0)
-			break;
+    if(argc != 1) {
+	std::string line;
+	for(int i=1; i<argc; i++) {
+            if(argv[i] == std::string(";")) {
+                int result = process_command_line(line.c_str());
+                if(result == CMDLINE_INVALID_PARAMETER) break;
+                if(result == CMDLINE_EXIT_PROGRAM) { rc = EXIT_SUCCESS; break; }
+                line.clear();
+            } else {
+                if(!line.empty()) line += " ";
+                line = line + argv[i];
+            }
+	}
+	if(!line.empty()) {
+            int result = process_command_line(line.c_str());
+            if(result == CMDLINE_EXIT_PROGRAM || result == CMDLINE_OK) {
+                rc = EXIT_SUCCESS;
+            }
+        }
+    } else {
+        do
+        {
+            if (prompt_read_line("xilprg> ", line, sizeof(line)) < 0)
+                            break;
+        }
+        while (process_command_line(line) != CMDLINE_EXIT_PROGRAM);
+        rc = EXIT_SUCCESS;
     }
-    while (process_command_line(line) != CMDLINE_EXIT_PROGRAM);
-
-    rc = 0;
 
 cleanup:
 
diff --git a/xilinx.mk b/xilinx.mk
new file mode 100644
index 0000000..a29c4a0
--- /dev/null
+++ b/xilinx.mk
@@ -0,0 +1,186 @@
+ifeq ($(XILINX),)
+   $(error "source ~/xilinx/settings.sh" to set env vars)
+endif
+
+vpath %.o work_sim
+
+help :
+	@echo "This Makefile is NOT part of the EMC2 build system."
+	@echo "It uses the zero-cost (non-free) Xilinx Webpack tools"
+	@echo "to convert VHDL source into bitfiles for the FPGA."
+	@echo "The completed bitfiles are distributed with EMC2, and"
+	@echo "do not need to be recreated except to fix bugs or to"
+	@echo "make a custom FPGA configuration."
+	@echo "It also uses the Free Software programs GHDL and GtkWave"
+	@echo "to allow simulation of the FPGA logic."
+
+%.o : %.vhd
+	@echo "analysis: making $@"
+	@if [ ! -d ./work_sim ] ; then mkdir work_sim; fi
+	@rm -f $@
+	@ghdl -a --ieee=synopsys -fexplicit --workdir=./work_sim $<
+
+%.bin : %.v %.o
+	@echo "elaboration: making $@"
+	@if [ ! -d ./work_sim ] ; then mkdir work_sim; fi
+	@rm -f $@
+	@ghdl -e --ieee=synopsys -fexplicit --workdir=./work_sim -o $@\
+	    `grep -m 1 "entity .* is" $< | \
+	     sed -e 's/^.*entity  *//' -e 's/  *is.*$$//'`
+
+%.bin : %.vhd %.o
+	@echo "elaboration: making $@"
+	@if [ ! -d ./work_sim ] ; then mkdir work_sim; fi
+	@rm -f $@
+	@ghdl -e --ieee=synopsys -fexplicit --workdir=./work_sim -o $@\
+	    `grep -m 1 "entity .* is" $< | \
+	     sed -e 's/^.*entity  *//' -e 's/  *is.*$$//'`
+
+%.ghw : %.bin
+	@echo "simulating: running $<"
+	@if [ ! -d ./work_sim ] ; then mkdir work_sim; fi
+	@rm -f $@
+	./$< --wave=$@
+
+%.wave : %.ghw
+	@gtkwave $< $*.sav &>/dev/null
+
+%.vprj :
+	@echo "making $@"
+	@rm -f $@
+	@for i in $(SOURCES); do echo '`include "'$$i'"'; done > $@
+
+%.prj :
+	@echo "making $@"
+	@rm -f $@
+	@for i in $(SOURCES); do echo $$i; done > $@
+
+%.vscr : %.v
+	@echo "making $@"
+	@if [ ! -d ./tmp_syn ] ; then mkdir tmp_syn; fi
+	@echo "set -tmpdir ./tmp_syn" >$@
+	@if [ ! -d ./work_syn ] ; then mkdir work_syn; fi
+	@echo "set -xsthdpdir ./work_syn" >>$@
+	@echo "run" >>$@
+	@echo "-ifmt Verilog -ifn $*.vprj" >>$@
+	@echo "-vlgpath ." >> $@
+	@echo "-vlgincdir ." >> $@
+	@echo "-top $*" >>$@
+	@echo "-ofmt NGC -ofn $*.ngc" >>$@
+	@echo "-p $(DEVICE)" >>$@
+
+
+%.scr : %.vhd
+	@echo "making $@"
+	@if [ ! -d ./tmp_syn ] ; then mkdir tmp_syn; fi
+	@echo "set -tmpdir ./tmp_syn" >$@
+	@if [ ! -d ./work_syn ] ; then mkdir work_syn; fi
+	@echo "set -xsthdpdir ./work_syn" >>$@
+	@echo "run" >>$@
+	@echo "-ifmt VHDL -ifn $*.prj" >>$@
+	@echo "-top `grep -m 1 "entity .* is" $< | sed -e 's/^.*entity  *//' -e 's/  *is.*$$//'`" >>$@
+	@echo "-ofmt NGC -ofn $*.ngc" >>$@
+	@echo "-p $(DEVICE)" >>$@
+
+%.ngc %.log.syn : %.vprj %.vscr
+	@echo "Synthesis: making $@"
+	@xst -ifn $*.vscr -ofn $*.log.syn
+
+%.ngc %.log.syn : %.prj %.scr
+	@echo "Synthesis: making $@"
+	@xst -ifn $*.scr -ofn $*.log.syn
+
+# The .usage target is dependent on the output format of the Xilinx tools.
+# If they change the text of their report, it will be necessary to change the
+# search text, and possibly to use different strings for various versions.
+%.usage : %.log.syn
+	@echo "Usage report:"
+	@cat $< | awk '/Selected Device/,/TIMING REPORT/' | head -n-3 >$@
+	@cat $@
+
+%.ngd %.log.ngd : %.ngc
+	@echo "NGDbuild: making $@ from $< with constraints from $(CONSTRAINTS)"
+	@ngdbuild -uc $(CONSTRAINTS) $< $@
+	@mv $*.bld $*.log.ngd
+
+# The extensions .nad and .nbd are actually .ncd files - the toolchain
+# uses .ncd for unplaced, placed-but-not-routed, and placed-and-routed files
+# The makefile uses distinct extensions to keep the dependencies straight,
+# and to preserve the intermediate files.
+
+%.nad : %.ngd
+	@echo "Mapping: making $@ (unplaced) from $^"
+	@map $<
+	@mv $*.ncd $*.nad
+	@mv $*.mrp $*.log.map
+
+%.nbd : %.nad
+	@echo "Placing: making $@ (unrouted) from $^"
+	@cp $*.nad raw.ncd
+	@par -nopad -r raw.ncd -w placed.ncd $*.pcf
+	@rm raw.ncd
+	@mv placed.ncd $*.nbd
+	@rm placed.unroutes
+	@rm placed.par
+	@rm placed.xpi
+
+%.ncd : %.nbd
+	@rm -f $@
+	@cp $*.nbd placed.ncd
+	@echo "Routing: making $@ (finished) from $^"
+	@par -p placed.ncd -w $*.ncd $*.pcf
+	@rm placed.ncd
+
+%.bit : %.ncd
+	@echo "Bitgen: making $@ from $^"
+	@bitgen -w $*.ncd $*.bit $*.pcf
+
+%.mcs: %.bit
+	echo "setmode -promfile" > $@.impact
+	echo "setsubmode -pffserial" >> $@.impact
+	echo "addPromDevice -p 1 -name xcf02s" >> $@.impact
+	echo "addDesign -version 0 -name 0" >> $@.impact
+	echo "addDeviceChain -index 0" >> $@.impact
+	echo "addDevice -position 1 -file $<" >> $@.impact
+	echo "generate -format mcs -fillvalue FF -output $@" >> $@.impact
+	echo quit >> $@.impact
+	impact -batch $@.impact
+	rm -f $@.impact
+
+%.svf: %.bit
+	echo "setmode -bs" > $@.impact
+	echo "setCable -port svf -file $@" >> $@.impact
+	echo "addDevice -position 1 -file $<" >> $@.impact
+	echo quit >> $@.impact
+	impact -batch $@.impact
+	rm -f $*.impact
+
+test: $(TARGET).bit
+	xilprg program 1 $(TARGET).bit
+
+flash: $(TARGET).mcs
+	xilprg erase 2 ";" program -mcs 2 $(TARGET).mcs
+
+# a .fpga file is a bitfile with config ram info added
+
+.PRECIOUS : %.v %.vhd %.rspec %.vprj %.prj %.vscr %.scr %.ngc %.ngd %.nad %.nbd %.ncd %.bit %.o %.bin %.ghw %.log.syn %.log.ngd %.log.map
+
+.PHONY : clean clean_all test flash
+
+# because placed and routed .fpga files might represent many hours
+# of work, 'make clean' doesn't remove them or their precursers,
+# it only removes incidental files that are generated along the way
+# if you truly want to remove everything, use 'make clean_all'
+# if you want to redo only a single FPGA file, touch the
+# corresponding .spec file
+clean :
+	@rm -f *.scr *.o *.bin
+	@rm -f *.pad *_pad.csv *_pad.txt *.par *.unroutes
+	@rm -f *.ghw *.log.syn *.log.ngd *.log.map *.bgn *.drc *.ngm *.usage
+	@rm -f *_usage.xml *~
+
+clean_all :
+	@rm -f *.prj *.scr *.ngc *.ngd *.nad *.nbd *.ncd *.o *.bin *.bit
+	@rm -f *.pad *_pad.csv *_pad.txt *.par *.unroutes *.xpi *.rspec *.fpga
+	@rm -f *.ghw *.log.syn *.log.ngd *.log.map *.bgn *.drc *.ngm *.usage
+	@rm -f *.pcf *.t *_usage.xml *~ *.vprj *.vscr
diff --git a/xilprg.1 b/xilprg.1
new file mode 100644
index 0000000..8abf3ca
--- /dev/null
+++ b/xilprg.1
@@ -0,0 +1,63 @@
+.TH XILPRG "1"
+
+.SH NAME 
+xilprg \- Program xilinx FPGAs and Flash using JTAG interfaces
+
+.SH SYNOPSIS
+.B xilprg [command] [; command ...]
+If no commands are on the commandline, an interactive mode is entered.
+
+.SH COMMANDS
+.SS help [command]
+Shows help
+.SS detect
+Detects JTAG device chain
+.SS cable {xil3 [ioaddr]|dusb}
+Sets programmer cable
+.SS chips
+Prints supported devices
+.SS program [-e] [-bit|-mcs|-bin] position file
+Programs device, with optional erase (-e) before programming
+.SS erase position
+Erases device
+.SS read position file
+Read device content and saves in a file
+.SS verify [-bit|-mcs|-bin] position file
+Verifies device
+.SS idcode position
+Shows device IDCODE
+.SS cd [dir]
+Shows/changes current directory
+.SS version
+Shows version information
+.SS exit
+Exits program
+	
+.SH FILES
+.TP
+\fBxilprg.conf\fR
+Lists devices known to xilprg
+
+.SH Examples
+To test a .bit file in the xc3s200 FPGA on the digilentinc "s3board",
+.RS 4
+xilprg program 1 example.bit
+.RE
+
+To replace the program in the xcf02s Platform Flash on the digilentinc
+"s3board",
+"s3board"
+.RS 4
+xilprg program -e 2 example.bit
+.RE
+Without "-e" to erase, this command will leave the flash in a non-working
+state.
+
+.SH COPYRIGHT
+Copyright (c) 2006 Zoltan Csizmadia <zoltan_csizmadia@yahoo.com>
+All rights reserved.
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2 of the License, or (at your option) any later version.