diff --git a/Makefile b/Makefile
index 02b5bec4c..db440fa4f 100644
--- a/Makefile
+++ b/Makefile
@@ -8,7 +8,8 @@ default all: build
 
 .PHONY: build
 build:
-	${MAKE} -C src
+	dune build -p ocsigenserver
+	${MAKE} -C src/server build
 doc:
 	$(MAKE) -C doc
 
@@ -28,13 +29,14 @@ top:
 ### Cleaning ###
 
 clean: clean.local
-	${MAKE} -C src clean
+	${MAKE} -C src/server clean
 
 clean.local:
+	dune clean
 	-rm -f ocsigenserver-*.tar.gz
 
 distclean: clean.local
-	${MAKE} -C src distclean
+	${MAKE} -C src/server distclean
 	-make -C doc clean
 	-rm Makefile.config
 	-rm -f *~ \#* .\#*
@@ -76,9 +78,9 @@ install.files:
 	@echo INSTALL_CAN_PUT_PERMISSIONS: ${INSTALL_CAN_PUT_PERMISSIONS}
 	 ## Configuration files
 	$(INSTALL) -m ${INSTALL_MOD_755} -d $(TEMPROOT)$(CONFIGDIR)/conf.d
-	${INSTALL} -m ${INSTALL_MOD_644} ocsigenserver.conf.sample $(TEMPROOT)$(CONFIGDIR)/
+	${INSTALL} -m ${INSTALL_MOD_644} _build/install/default/etc/ocsigenserver/ocsigenserver.conf.sample $(TEMPROOT)$(CONFIGDIR)/
 	[ -f $(TEMPROOT)$(CONFIGDIR)/ocsigenserver.conf ] || \
-	  { $(INSTALL) -m ${INSTALL_MOD_644} ocsigenserver.conf.sample \
+	  { $(INSTALL) -m ${INSTALL_MOD_644} _build/install/default/etc/ocsigenserver/ocsigenserver.conf.sample \
 		$(TEMPROOT)$(CONFIGDIR)/ocsigenserver.conf;  }
 	-mv $(TEMPROOT)$(CONFIGDIR)/mime.types $(TEMPROOT)$(CONFIGDIR)/mime.types.old
 	 ## Log directory
diff --git a/Makefile.options b/Makefile.options
index a89718d54..698ab4b11 100644
--- a/Makefile.options
+++ b/Makefile.options
@@ -26,12 +26,3 @@ INCS=   -I ${BLD}/server/.ocsigenserver.objs/byte \
 SERVER_PACKAGE := lwt_ssl,bytes,lwt.unix,lwt_log,ipaddr,findlib,cryptokit,re,str,xml-light,dynlink,cohttp-lwt-unix
 
 LIBS := -package ${SERVER_PACKAGE} ${INCS}
-
-INITPACKAGE := \"$(shell ${OCAMLFIND} query -p-format -recursive        \
-				    -separator '\";\"' ${SERVER_PACKAGE})\"; \
-	       \"ocsigenserver.polytables\";   \
-	       \"ocsigenserver.cookies\";      \
-	       \"ocsigenserver.baselib.base\"; \
-	       \"ocsigenserver.baselib\";      \
-	       \"ocsigenserver.http\";         \
-	       \"ocsigenserver\";              \
diff --git a/configure b/configure
index 5cedef2fd..9545297aa 100755
--- a/configure
+++ b/configure
@@ -80,6 +80,7 @@ set_defaults () {
     bindir=""
     logdir=""
     libdir=""
+    libdir_set=0
     mandir=""
     docdir=""
     sysconfdir="/etc/ocsigenserver"
@@ -282,6 +283,7 @@ while [ "$#" -gt 0 ]; do
                         ;;
                 --libdir)
                         libdir="$2"
+                        libdir_set=1
                         shift
                         shift
                         ;;
@@ -485,32 +487,14 @@ CC        := gcc
 # optional
 RLWRAP    := $rlwrap
 
-
-### Options ###
-
-# User who will run Ocsigen server (not root) (eg, for debian, www-data)
-# (This user must exist on your system)
-OCSIGENUSER := $ocsigen_user
-
-# group who will run Ocsigen server (not root) (eg, for debian, www-data)
-# (This group must exist)
-OCSIGENGROUP := $ocsigen_group
-
-
 ### Paths ###
 
 # Temporary root directory to install the package (usually always "" but for package makers)
 TEMPROOT := $temproot
 
-# The directory for ocsigen server (binary):
-BINDIR := $root$bindir
-
 # The directory for ocsigen manpage:
 MANDIR := $root$mandir
 
-# Where to install the libraries
-LIBDIR := $libdir
-
 # ocsigen's logs:
 LOGDIR := $root$logdir
 
@@ -538,6 +522,23 @@ SRC := $full_pwd
 include \$(SRC)/Makefile.options
 _EOF_
 
+echo "Writing config options"
+cat <<_EOF_ > $my_pwd/src/files/ocsigenserver.conf/options.ml
+let version = "$version"
+let src = "$full_pwd"
+let port = 80
+let bindir = "$root$bindir"
+let libdir = "$libdir"
+let libdir_set = $libdir_set
+let logdir = "$root$logdir"
+let configdir = "$root$sysconfdir"
+let staticpagesdir = "$root$staticpagesdir"
+let datadir = "$root$datadir"
+let uploaddir = "$root$uploaddir"
+let commandpipe = "$root$commandpipe"
+let mimefile = "$root$sysconfdir/mime.types"
+_EOF_
+
 ######################################################################
 # Finish
 
diff --git a/dune b/dune
index f749468dd..791d2fe2b 100644
--- a/dune
+++ b/dune
@@ -2,3 +2,26 @@
  (_
   (flags
    (:standard -w -69))))
+
+(rule
+ (target ocsigenserver.conf.sample)
+ (action
+  (with-stdout-to
+   %{target}
+   (run src/files/ocsigenserver.conf/gen.exe sample))))
+
+(install
+ (files ocsigenserver.conf.sample)
+ (section etc)
+ (package ocsigenserver))
+
+(subdir
+ local/etc
+ (rule
+  (mode
+   (promote (until-clean)))
+  (target ocsigenserver.conf)
+  (action
+   (with-stdout-to
+    %{target}
+    (run ../../src/files/ocsigenserver.conf/gen.exe local)))))
diff --git a/ocsigenserver.opam b/ocsigenserver.opam
index 14db6226f..7bf573af9 100644
--- a/ocsigenserver.opam
+++ b/ocsigenserver.opam
@@ -61,7 +61,6 @@ build: [
     "--sysconfdir"
     "%{lib}%/ocsigenserver/etc/ocsigenserver"
   ]
-  [make "-C" "src" "confs"]
   ["dune" "build" "-p" name "-j" jobs]
 ]
 install:[make "install.files"]
diff --git a/ocsigenserver.opam.template b/ocsigenserver.opam.template
index 09d8559d2..85f63d47b 100644
--- a/ocsigenserver.opam.template
+++ b/ocsigenserver.opam.template
@@ -27,7 +27,6 @@ build: [
     "--sysconfdir"
     "%{lib}%/ocsigenserver/etc/ocsigenserver"
   ]
-  [make "-C" "src" "confs"]
   ["dune" "build" "-p" name "-j" jobs]
 ]
 install:[make "install.files"]
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index f28b91bd9..000000000
--- a/src/Makefile
+++ /dev/null
@@ -1,65 +0,0 @@
-include ../Makefile.config
-
-all: confs
-	dune build @all
-
-### CONF ####
-
-confs: ../ocsigenserver.conf.sample ../local/etc/ocsigenserver.conf
-	${MAKE} -C baselib confs
-
-../ocsigenserver.conf.sample: files/ocsigenserver.conf.in ../Makefile.config Makefile
-	cat $< \
-	  | sed s%_LOGDIR_%$(LOGDIR)%g \
-	  | sed s%_DATADIR_%$(DATADIR)%g \
-	  | sed s%_COMMANDPIPE_%$(COMMANDPIPE)%g \
-	  | sed s%_MIMEFILE_%$(CONFIGDIR)/mime.types%g \
-	  | sed s%_METADIR_%$(LIBDIR)%g \
-	  | sed s%_LIBDIR_%$(LIBDIR)%g \
-	  | sed s%_EXTDIR_%$(LIBDIR)/ocsigenserver/extensions%g \
-	  | sed s%_CONFIGDIR_%$(CONFIGDIR)%g \
-	  | sed s%_STATICPAGESDIR_%$(STATICPAGESDIR)%g \
-	  | sed s%_EXTPACKAGENAME_%ocsigenserver.ext%g \
-	  > $@
-
-../local/etc/ocsigenserver.conf: files/ocsigenserver.conf.in ../Makefile.config Makefile
-	mkdir -p ../local/etc ../local/var/log ../local/var/run
-	cat $< \
-	  | sed s%80\</port\>%8080\</port\>%g \
-	  | sed s%_LOGDIR_%$(SRC)/local/var/log%g \
-	  | sed s%_DATADIR_%$(SRC)/local/var/lib%g \
-	  | sed s%_COMMANDPIPE_%$(SRC)/local/var/run/ocsigenserver_command%g \
-	  | sed s%_MIMEFILE_%$(SRC)/src/files/mime.types%g \
-	  | sed s%_METADIR_%${LIBDIR}\"/\>\<findlib\ path=\"$(SRC)/src/files/\"/\>\<findlib\ path=\"$(SRC)/src/extensions/files/%g \
-	  | sed s%_CONFIGDIR_%$(SRC)/local/etc/ocsigenserver%g \
-	  | sed s%_STATICPAGESDIR_%$(SRC)/local/var/www%g \
-	  | sed s%_EXTPACKAGENAME_%ocsigenserver.ext%g \
-	  | sed s%\<\!--\ \<commandpipe%\<commandpipe%g \
-	  | sed s%\</commandpipe\>\ --\>%\</commandpipe\>%g \
-	  | sed s%\<\!--\ \<mimefile%\<mimefile%g \
-	  | sed s%\</mimefile\>\ --\>%\</mimefile\>%g \
-	  > $@
-
-###
-
-clean: clean.local
-	${MAKE} -C baselib clean
-	dune clean
-
-clean.local:
-	-rm -f ../ocsigenserver.conf.sample
-	-rm -f ../ocsigenserver.conf.opt.sample
-	-rm -f ../ocsigenserver.conf.local
-	-rm -f ../ocsigenserver.conf.opt.local
-
-distclean: clean.local
-	${MAKE} -C baselib distclean
-	${MAKE} -C http distclean
-	${MAKE} -C server distclean
-	${MAKE} -C extensions distclean
-	-rm -f *~ \#* .\#*
-	-cd files; rm -f *~ \#* .\#*
-	-rm -fr ../local/var/log/*.log
-	-rm -fr ../local/var/lib/ocsidb
-	-rm -fr ../local/etc/ocsigenserver.conf
-	-rm -fr ../local/etc/ocsigenserver.conf.opt
diff --git a/src/baselib/Makefile b/src/baselib/Makefile
deleted file mode 100644
index 0165bb25b..000000000
--- a/src/baselib/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-include ../../Makefile.config
-
-.PHONY: default
-default: build
-
-.PHONY: build
-build: confs
-	dune build
-
-.PHONY: confs
-confs: ocsigen_config_static.ml
-
-## Ocsigen_config ##
-
-VERSION := $(shell head -n 1 ../../VERSION)
-
-ocsigen_config_static.ml: ocsigen_config_static.ml.in ../../Makefile.config ../../Makefile.options ../../VERSION
-	cat ocsigen_config_static.ml.in \
-	| sed s%_VERSION_%${VERSION}% \
-	| sed s%_WARNING_%"Warning: this file has been generated from ocsigen_config_static.ml.in - DO NOT MODIFY MANUALLY!"% \
-	| sed s%_LOGDIR_%$(LOGDIR)% \
-	| sed s%_DATADIR_%$(DATADIR)%g \
-	| sed s%_BINDIR_%$(BINDIR)%g \
-	| sed s%_EXTDIR_%$(LIBDIR)/ocsigenserver/extensions%g \
-	| sed s%_STATICPAGESDIR_%$(STATICPAGESDIR)% \
-	| sed s%_UP_%$(UPLOADDIR)%g \
-	| sed s%_COMMANDPIPE_%$(COMMANDPIPE)%g \
-	| sed s%_CONFIGDIR_%$(CONFIGDIR)% \
-	| sed s%_ISNATIVE_%$(NATIVECODE_RUNTIME_DETECT)%g \
-	| sed "s%_DEPS_%$(INITPACKAGE)%g" \
-	> ocsigen_config_static.ml
-
-## Clean up
-
-clean:
-	-rm -f ocsigen_config_static.ml
-
-distclean: clean
-	-rm -f *~ \#* .\#*
diff --git a/src/baselib/dune b/src/baselib/dune
index 37d2e2281..c9f64d100 100644
--- a/src/baselib/dune
+++ b/src/baselib/dune
@@ -32,3 +32,8 @@
    from
    (dynlink -> dynlink_wrapper.natdynlink.ml)
    (_ -> dynlink_wrapper.nonatdynlink.ml))))
+
+(rule
+ (with-stdout-to
+  ocsigen_config_static.ml
+  (run ../files/ocsigenserver.conf/gen.exe static.ml)))
diff --git a/src/extensions/Makefile b/src/extensions/Makefile
deleted file mode 100644
index 28dbae0ff..000000000
--- a/src/extensions/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-include ../../Makefile.config
-
-.PHONY: default
-default: build
-
-.PHONY: build
-build::
-	dune build
-
-## Clean up
-
-distclean: clean
-	-rm -f *~ \#* .\#*
-	${MAKE} -C deflatemod distclean
diff --git a/src/files/ocsigenserver.conf.in b/src/files/ocsigenserver.conf.in
deleted file mode 100644
index 8a5b50a61..000000000
--- a/src/files/ocsigenserver.conf.in
+++ /dev/null
@@ -1,40 +0,0 @@
-<!-- -*- Mode: Xml -*- -->
-<!-- This file is intentionnaly very basic. See http://ocsigen.org/ocsigenserver/manual/config
-     a more elaborate one, as well as for comments on the various options -->
-<!-- DO NOT MODIFY. This a generated file.
-     Additional configurations sit in conf.d/ -->
-<ocsigen>
-
-
-  <server>
-
-    <port>80</port>
-
-    <logdir>_LOGDIR_</logdir>
-    <datadir>_DATADIR_</datadir>
-    <!-- <commandpipe>_COMMANDPIPE_</commandpipe> -->
-    <!-- <mimefile>_MIMEFILE_</mimefile> -->
-
-    <charset>utf-8</charset>
-
-    <findlib path="_METADIR_"/>
-
-    <extension findlib-package="_EXTPACKAGENAME_.staticmod"/>
-
-    <!-- Inclusion of all external configuration files matching *.conf
-         from the directory 'dir' (in alphabetical order): -->
-    <extconf dir="_CONFIGDIR_/conf.d" />
-
-    <host charset="utf-8" hostfilter="*">
-
-      <site path="ocsigenstuff" charset="utf-8">
-        <static dir="_STATICPAGESDIR_/ocsigenstuff" />
-      </site>
-
-      <static dir="_STATICPAGESDIR_" />
-
-    </host>
-
-  </server>
-
-</ocsigen>
diff --git a/src/files/ocsigenserver.conf/dune b/src/files/ocsigenserver.conf/dune
new file mode 100644
index 000000000..c33a6c361
--- /dev/null
+++ b/src/files/ocsigenserver.conf/dune
@@ -0,0 +1,3 @@
+(executable
+ (name gen)
+ (libraries str unix))
diff --git a/src/files/ocsigenserver.conf/gen.ml b/src/files/ocsigenserver.conf/gen.ml
new file mode 100644
index 000000000..8976b2fb4
--- /dev/null
+++ b/src/files/ocsigenserver.conf/gen.ml
@@ -0,0 +1,158 @@
+let conf_in =
+  {|<!-- -*- Mode: Xml -*- -->
+<!-- This file is intentionnaly very basic. See http://ocsigen.org/ocsigenserver/manual/config
+     a more elaborate one, as well as for comments on the various options -->
+<!-- DO NOT MODIFY. This a generated file.
+     Additional configurations sit in conf.d/ -->
+<ocsigen>
+
+
+  <server>
+
+    <port>_PORT_</port>
+
+    <logdir>_LOGDIR_</logdir>
+    <datadir>_DATADIR_</datadir>
+    _COMMANDPIPE_
+    _MIMEFILE_
+
+    <charset>utf-8</charset>
+
+    <findlib path="_METADIR_"/>_FINDLIBEXTRA_
+
+    <extension findlib-package="_EXTPACKAGENAME_.staticmod"/>
+
+    <!-- Inclusion of all external configuration files matching *.conf
+         from the directory 'dir' (in alphabetical order): -->
+    <extconf dir="_CONFIGDIR_/conf.d" />
+
+    <host charset="utf-8" hostfilter="*">
+
+      <site path="ocsigenstuff" charset="utf-8">
+        <static dir="_STATICPAGESDIR_/ocsigenstuff" />
+      </site>
+
+      <static dir="_STATICPAGESDIR_" />
+
+    </host>
+
+  </server>
+
+</ocsigen>|}
+
+let conf_ml =
+  {|(* Warning: this file has been generated - DO NOT MODIFY! *)
+
+let version_number = _VERSION_
+let config_file = ref _CONFIGFILE_
+let is_native = Sys.backend_type = Sys.Native
+let logdir = ref (Some _LOGDIR_)
+let mimefile = ref _MIMEFILE_
+let datadir = ref _DATADIR_
+let bindir = ref _BINDIR_
+let extdir = ref _EXTDIR_
+let command_pipe = ref _COMMANDPIPE_
+let builtin_packages =
+  List.fold_left
+    (fun a s -> Ocsigen_lib.String.Set.add s a)
+    Ocsigen_lib.String.Set.empty
+    [_DEPS_]|}
+
+let interpolate f s =
+  let regexp = Str.regexp "_\\([A-Z]+\\)_" in
+  let f s = f (Str.matched_group 1 s) in
+  Str.global_substitute regexp f s
+
+open Options
+
+let libdir () =
+  if libdir_set = 0
+  then (
+    let inp = Unix.open_process_in "ocamlfind printconf destdir" in
+    let libdir = input_line inp in
+    ignore (Unix.close_process_in inp);
+    libdir)
+  else libdir
+
+let deps () =
+  let extra_deps =
+    [ "ocsigenserver.polytables"
+    ; "ocsigenserver.cookies"
+    ; "ocsigenserver.baselib.base"
+    ; "ocsigenserver.baselib"
+    ; "ocsigenserver.http"
+    ; "ocsigenserver" ]
+  in
+  let packages =
+    "lwt_ssl,bytes,lwt.unix,lwt_log,ipaddr,findlib,cryptokit,re,str,xml-light,dynlink,cohttp-lwt-unix,hmap"
+  in
+  let inp =
+    Unix.open_process_in ("ocamlfind query -p-format -recursive " ^ packages)
+  in
+  let deps = ref [] in
+  (try
+     while true do
+       deps := input_line inp :: !deps
+     done
+   with End_of_file -> ());
+  ignore (Unix.close_process_in inp);
+  !deps @ extra_deps
+
+(* Encode a string as a string literal that can be included in an ocaml file. *)
+let str = Printf.sprintf "%S"
+let ( // ) = Filename.concat
+
+let static_options = function
+  | "VERSION" -> str version
+  | "LOGDIR" -> str logdir
+  | "DATADIR" -> str datadir
+  | "BINDIR" -> str bindir
+  | "EXTDIR" -> str (libdir () // "ocsigenserver" // "extensions")
+  | "STATICPAGESDIR" -> str staticpagesdir
+  | "UP" -> str uploaddir
+  | "COMMANDPIPE" -> str commandpipe
+  | "CONFIGDIR" -> str configdir
+  | "CONFIGFILE" -> str (configdir // "ocsigenserver.conf")
+  | "MIMEFILE" -> str (configdir // "mime.types")
+  | "DEPS" -> String.concat ";" (List.map (Format.asprintf "%S") (deps ()))
+  | _ as s -> failwith s
+
+let sample_options = function
+  | "PORT" -> string_of_int port
+  | "LOGDIR" -> logdir
+  | "DATADIR" -> datadir
+  | "COMMANDPIPE" -> "<!-- <commandpipe>" ^ commandpipe ^ "</commandpipe> -->"
+  | "MIMEFILE" -> "<!-- <mimefile>" ^ mimefile ^ "</mimefile> -->"
+  | "LIBDIR" | "METADIR" -> libdir ()
+  | "EXTPACKAGENAME" -> "ocsigenserver.ext"
+  | "CONFIGDIR" -> configdir
+  | "STATICPAGESDIR" -> staticpagesdir
+  | "FINDLIBEXTRA" -> ""
+  | _ as s -> failwith s
+
+let local_options = function
+  | "PORT" -> "8080"
+  | "LOGDIR" -> src ^ "/local/var/log"
+  | "DATADIR" -> src ^ "/local/var/lib"
+  | "COMMANDPIPE" ->
+      "<commandpipe>" ^ src
+      ^ "/local/var/run/ocsigenserver_command</commandpipe>"
+  | "MIMEFILE" -> "<mimefile>" ^ src ^ "/src/files/mime.types</mimefile>"
+  | "LIBDIR" | "METADIR" -> libdir ()
+  | "EXTPACKAGENAME" -> "ocsigenserver.ext"
+  | "CONFIGDIR" -> src ^ "/local/etc/ocsigenserver"
+  | "STATICPAGESDIR" -> src ^ "/local/var/www"
+  | "FINDLIBEXTRA" ->
+      "<findlib path=\"" ^ src ^ "/src/files/\"/><findlib path=\"" ^ src
+      ^ "/src/extensions/files/\"/>"
+  | _ as s -> failwith s
+
+let () =
+  let arg = if Array.length Sys.argv > 1 then Sys.argv.(1) else "" in
+  print_endline
+  @@
+  match arg with
+  | "static.ml" -> interpolate static_options conf_ml
+  | "local" -> interpolate local_options conf_in
+  | "sample" -> interpolate sample_options conf_in
+  | _ -> failwith arg
diff --git a/src/files/ocsigenserver.conf/options.ml b/src/files/ocsigenserver.conf/options.ml
new file mode 100644
index 000000000..263688f24
--- /dev/null
+++ b/src/files/ocsigenserver.conf/options.ml
@@ -0,0 +1,13 @@
+let version = "dev"
+let src = ""
+let port = 80
+let bindir = ""
+let libdir = ""
+let libdir_set = 0
+let logdir = ""
+let configdir = ""
+let staticpagesdir = ""
+let datadir = ""
+let uploaddir = ""
+let commandpipe = ""
+let mimefile = ""
diff --git a/src/http/Makefile b/src/http/Makefile
deleted file mode 100644
index 4520a8aef..000000000
--- a/src/http/Makefile
+++ /dev/null
@@ -1,11 +0,0 @@
-.PHONY: default
-default: build
-
-.PHONY: build
-build:
-	dune build
-
-## Clean up
-
-distclean: clean
-	-rm -f *~ \#* .\#*