diff --git a/tool/run/boot_dir/fiasco b/tool/run/boot_dir/fiasco
index 4e4fc60d3..74e28a07d 100644
--- a/tool/run/boot_dir/fiasco
+++ b/tool/run/boot_dir/fiasco
@@ -14,13 +14,34 @@ proc core_link_address     { } { return "0x01000000" }
 #
 proc run_boot_dir {binaries} {
 
-	build { lib/ld/fiasco kernel/fiasco }
+	#
+	# Build kernel and dynamic linker on demand, if not yet present in
+	# '[run_dir]/genode/'
+	#
+	set kernel_arg ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/fiasco]}    { set kernel_arg "kernel/fiasco" }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { set ld_arg     "lib/ld/fiasco" }
+	set targets "$kernel_arg $ld_arg"
+
+	if {[llength $targets]} { build $targets }
+
+	if {$kernel_arg != ""} {
+		file copy -force [pwd]/bin/fiasco           [run_dir]/genode/fiasco
+		file copy -force [pwd]/bin/sigma0-fiasco    [run_dir]/genode/sigma0-fiasco
+		file copy -force [pwd]/bin/bootstrap-fiasco [run_dir]/genode/bootstrap-fiasco
+	}
 
 	build_core_image $binaries
 
-	file copy -force kernel/fiasco/kernel    [run_dir]/kernel
-	file copy -force kernel/fiasco/sigma0    [run_dir]/sigma0
-	file copy -force kernel/fiasco/bootstrap [run_dir]/bootstrap
+	#
+	# Move kernel files to distinct location within the boot directory so that
+	# we can remove [run_dir]/genode after the core image has been built.
+	#
+	file copy -force [run_dir]/genode/fiasco           [run_dir]/kernel
+	file copy -force [run_dir]/genode/sigma0-fiasco    [run_dir]/sigma0
+	file copy -force [run_dir]/genode/bootstrap-fiasco [run_dir]/bootstrap
+	exec rm -r [run_dir]/genode
 
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
 
diff --git a/tool/run/boot_dir/foc b/tool/run/boot_dir/foc
index a93372f47..38be9ca4c 100644
--- a/tool/run/boot_dir/foc
+++ b/tool/run/boot_dir/foc
@@ -57,13 +57,34 @@ proc l4_bin_dir { } {
 
 proc run_boot_dir_x86 {binaries} {
 
-	build { lib/ld/foc kernel/foc }
+	#
+	# Build kernel and dynamic linker on demand, if not yet present in
+	# '[run_dir]/genode/'
+	#
+	set kernel_arg ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/foc]}       { set kernel_arg "kernel/foc" }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { set ld_arg     "lib/ld/foc" }
+	set targets "$kernel_arg $ld_arg"
+
+	if {[llength $targets]} { build $targets }
+
+	if {$kernel_arg != ""} {
+		file copy -force [pwd]/bin/foc           [run_dir]/genode/foc
+		file copy -force [pwd]/bin/sigma0-foc    [run_dir]/genode/sigma0-foc
+		file copy -force [pwd]/bin/bootstrap-foc [run_dir]/genode/bootstrap-foc
+	}
 
 	build_core_image $binaries
 
-	file copy -force [pwd]/bin/foc           [run_dir]/kernel
-	file copy -force [pwd]/bin/sigma0-foc    [run_dir]/sigma0
-	file copy -force [pwd]/bin/bootstrap-foc [run_dir]/bootstrap
+	#
+	# Move kernel files to distinct location within the boot directory so that
+	# we can remove [run_dir]/genode after the core image has been built.
+	#
+	file copy -force [run_dir]/genode/foc           [run_dir]/kernel
+	file copy -force [run_dir]/genode/sigma0-foc    [run_dir]/sigma0
+	file copy -force [run_dir]/genode/bootstrap-foc [run_dir]/bootstrap
+	exec rm -r [run_dir]/genode
 
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
 
diff --git a/tool/run/boot_dir/hw b/tool/run/boot_dir/hw
index 8c011845c..f17625332 100644
--- a/tool/run/boot_dir/hw
+++ b/tool/run/boot_dir/hw
@@ -41,30 +41,58 @@ proc run_boot_dir {binaries} {
 		close $fh
 	}
 
-	build { lib/ld/hw bootstrap }
+	#
+	# Build bootstrap, the core object, and the dynamic linker on demand
+	#
+	# If those parts were imported from the depot, the build step is skipped.
+	#
+	set bootstrap_arg ""
+	set core_arg      ""
+	set ld_arg        ""
 
-	# boot module list without core
+	if {![file exists [run_dir]/genode/ld.lib.so]}      { set ld_arg        lib/ld/hw    }
+	if {![file exists [run_dir]/genode/core-hw.o]}      { set core_arg      core/hw      }
+	if {![file exists [run_dir]/genode/bootstrap-hw.o]} { set bootstrap_arg bootstrap/hw }
+
+	set build_args "$bootstrap_arg $core_arg $ld_arg"
+	if {[llength $build_args]} { build $build_args }
+
+	if {$ld_arg        != ""} { file copy -force bin/ld-hw.lib.so   [run_dir]/genode/ld.lib.so }
+	if {$core_arg      != ""} { file copy -force bin/core-hw.o      [run_dir]/genode/core-hw.o }
+	if {$bootstrap_arg != ""} { file copy -force bin/bootstrap-hw.o [run_dir]/genode/bootstrap-hw.o }
+
+	#
+	# Copy specified modules to the run directory, excluding core.
+	#
 	set idx [lsearch $binaries "core"]
 	set modules [lreplace $binaries $idx $idx]
-
-	# strip binaries
-	copy_and_strip_genode_binaries_to_run_dir $modules
-	lappend modules "config"
+	copy_genode_binaries_to_run_dir $modules
 
 	puts "core link address is [core_link_address]"
 
-	set core_obj core/hw/core-hw.o
-	set bootstrap_obj bootstrap/hw/bootstrap.o
+	set core_obj      core-hw.o
+	set bootstrap_obj bootstrap-hw.o
 
 	# create core and bootstrap binary without modules for debugging
-	build_core $core_obj      {} [run_dir].core      [core_link_address]
-	build_core $bootstrap_obj {} [run_dir].bootstrap [bootstrap_link_address]
+	build_core [run_dir]/genode/$core_obj      {} [run_dir].core      [core_link_address]
+	build_core [run_dir]/genode/$bootstrap_obj {} [run_dir].bootstrap [bootstrap_link_address]
+
+	# determine modules to be incorporated into the core image
+	set modules [glob -tails -directory [run_dir]/genode/ *]
+	set excluded_modules {}
+	lappend excluded_modules $core_obj $bootstrap_obj
+	foreach excluded $excluded_modules {
+		set modules [lsearch -inline -not -all $modules $excluded] }
+
+	# check syntax of all boot modules named *.config
+	foreach file [glob -nocomplain [run_dir]/genode/*.config] {
+		check_xml_syntax $file }
 
 	# create core binary containing the boot modules
-	build_core $core_obj $modules [run_dir]/genode/core.elf [core_link_address]
+	build_core [run_dir]/genode/$core_obj $modules [run_dir]/genode/core.elf [core_link_address]
 	exec [cross_dev_prefix]strip [run_dir]/genode/core.elf
-	build_core $bootstrap_obj { core.elf } [run_dir]/image.elf [bootstrap_link_address]
-	exec rm -f [run_dir]/genode/core.elf
+	build_core [run_dir]/genode/$bootstrap_obj { core.elf } [run_dir]/image.elf [bootstrap_link_address]
+	exec rm -fr [run_dir]/genode
 	exec [cross_dev_prefix]strip [run_dir]/image.elf
 
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
diff --git a/tool/run/boot_dir/linux b/tool/run/boot_dir/linux
index e2da4430d..4bb6e0f57 100644
--- a/tool/run/boot_dir/linux
+++ b/tool/run/boot_dir/linux
@@ -8,11 +8,15 @@ proc binary_name_timer     { } { return "linux_timer_drv" }
 #
 proc run_boot_dir {binaries} {
 
-	build { lib/ld/linux }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { build { lib/ld/linux } }
 
 	foreach binary $binaries {
 		set src_binary_path "../../../../bin/[kernel_specific_binary $binary]"
 		exec ln -sf $src_binary_path [run_dir]/genode/$binary }
+
+	# check syntax of all boot modules named *.config
+	foreach file [glob -nocomplain [run_dir]/genode/*.config] {
+		check_xml_syntax $file }
 }
 
 
diff --git a/tool/run/boot_dir/nova b/tool/run/boot_dir/nova
index a55e090fd..32221cbfc 100644
--- a/tool/run/boot_dir/nova
+++ b/tool/run/boot_dir/nova
@@ -2,31 +2,7 @@ proc binary_name_ld_lib_so { } { return "ld-nova.lib.so" }
 proc binary_name_core_o    { } { return "core-nova.o" }
 proc binary_name_timer     { } { return "nova_timer_drv" }
 
-
-##
-# Read the location of the NOVA kernel directory from 'etc/nova.conf'
-#
-proc nova_kernel { } {
-	global _nova_kernel
-
-	if {![info exists _nova_kernel]} {
-		if {[file exists etc/nova.conf]} {
-			set _nova_kernel [exec sed -n "/^NOVA_KERNEL/s/^.*=\\s*//p" etc/nova.conf]
-		} else {
-		        set _nova_kernel "[pwd]/kernel/nova/hypervisor"
-		}
-	}
-	return $_nova_kernel
-}
-
-
-##
-# Return whether nova is provided from the outside
-#
-proc nova_external { } {
-	if {[nova_kernel] == "[pwd]/kernel/nova/hypervisor"} { return 0 }
-	return 1
-}
+proc kernel_files { } { return hypervisor }
 
 
 proc run_boot_string { } {
@@ -36,6 +12,7 @@ proc run_boot_string { } {
 
 proc core_link_address { } { return "0x100000" }
 
+
 proc core_ld_opts { } {
 	set ret { -Wl,-T }
 	lappend ret "-Wl,[genode_dir]/repos/base/src/ld/genode.ld"
@@ -48,21 +25,36 @@ proc core_ld_opts { } {
 #
 proc run_boot_dir {binaries} {
 
-	if {![nova_external]} {
-		build { lib/ld/nova kernel }
-	} else {
-		build { lib/ld/nova }
-	}
+	#
+	# Build kernel-specific targets if needed
+	#
+	# If the run scripts imports the base-nova binary archive, [run_dir] is
+	# already populated, so we can skip the build.
+	#
+	set kernel_arg ""
+	set core_arg   ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/hypervisor]}  { set kernel_arg kernel }
+	if {![file exists [run_dir]/genode/core-nova.o]} { set core_arg   core/nova }
+	if {![file exists [run_dir]/genode/ld.lib.so]}   { set ld_arg     lib/ld/nova }
+
+	set targets "$kernel_arg $core_arg $ld_arg"
+	if {[llength $targets]} { build $targets }
+
+	if {$kernel_arg != ""} { file copy -force bin/hypervisor     [run_dir]/genode/hypervisor }
+	if {$core_arg   != ""} { file copy -force bin/core-nova.o    [run_dir]/genode/core.o }
+	if {$ld_arg     != ""} { file copy -force bin/ld-nova.lib.so [run_dir]/genode/ld.lib.so }
 
 	#
 	# Collect contents of the ISO image
 	#
 	build_core_image $binaries
 
-	puts "using NOVA kernel at [nova_kernel]"
-	exec [cross_dev_prefix]objcopy -O elf32-i386 [nova_kernel] [run_dir]/hypervisor
+	exec [cross_dev_prefix]objcopy -O elf32-i386 [run_dir]/genode/hypervisor [run_dir]/hypervisor
 	exec [cross_dev_prefix]strip [run_dir]/hypervisor
 
+	exec rm -rf [run_dir]/genode
+
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
 		#
 		# Install isolinux/GRUB files and bender
diff --git a/tool/run/boot_dir/okl4 b/tool/run/boot_dir/okl4
index cb3adbc46..1c9c0c41a 100644
--- a/tool/run/boot_dir/okl4
+++ b/tool/run/boot_dir/okl4
@@ -2,6 +2,8 @@ proc binary_name_ld_lib_so { } { return "ld-okl4.lib.so" }
 proc binary_name_core_o    { } { return "core-okl4.o"    }
 proc binary_name_timer     { } { return "pit_timer_drv"  }
 
+proc kernel_files { } { return okl4 }
+
 
 ##
 # Get the base-okl4 repository
@@ -28,15 +30,6 @@ proc okl4_dir { } {
 }
 
 
-##
-# Return whether okl4 kernel is provided from the outside
-#
-proc okl4_external { } {
-	if {"[okl4_dir]" == "[base_okl4_dir]/contrib/okl4"} { return 0 }
-	return 1
-}
-
-
 set weaver_xml_template {
 	<machine>
 		<word_size size="0x20" />
@@ -113,25 +106,19 @@ proc run_boot_dir {binaries} {
 	global weaver_xml_template
 
 	#
-	# Build kernel if needed
+	# Build kernel and dynamic linker if needed
 	#
-	# Once the kernel is exists, it gets never revisited automatically.
-	# Consequently, when changing the kernel sources, the kernel build must be
-	# issued explicitly via 'make kernel'. This way, the rare case of changing
-	# the kernel does not stand in the way of the everyday's work flow of
-	# executing run scripts as quick as possible.
-	#
-	if {![okl4_external] && ![file exists bin/okl4]} {
-		build { lib/ld/okl4 kernel/okl4 }
-	} else {
-		build { lib/ld/okl4 }
-	}
+	set kernel_arg ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/okl4]}      { set kernel_arg kernel/okl4 }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { set ld_arg     lib/ld/okl4 }
+	set targets "$kernel_arg $ld_arg"
+	if {[llength $targets]} { build $targets }
+	if {$kernel_arg != ""} { file copy -force bin/okl4 [run_dir]/genode/okl4 }
 
 	build_core_image $binaries
 	exec mv [run_dir]/image.elf [run_dir].image
 
-	exec cp bin/okl4 [run_dir]/kernel
-
 	#
 	# Generate ELF weaver config
 	#
@@ -139,7 +126,7 @@ proc run_boot_dir {binaries} {
 	puts $fh {<?xml version="1.0"?>}
 	puts $fh {<!DOCTYPE image SYSTEM "weaver-1.1.dtd">}
 	puts $fh {<image>}
-	regsub okl4_kernel $weaver_xml_template "[run_dir]/kernel" weaver_xml_template
+	regsub okl4_kernel $weaver_xml_template "[run_dir]/genode/okl4" weaver_xml_template
 	regsub core $weaver_xml_template "[run_dir].image" weaver_xml_template
 	puts $fh $weaver_xml_template
 	puts $fh {</image>}
diff --git a/tool/run/boot_dir/pistachio b/tool/run/boot_dir/pistachio
index 7807dc8c8..d2fdbeb36 100644
--- a/tool/run/boot_dir/pistachio
+++ b/tool/run/boot_dir/pistachio
@@ -2,6 +2,7 @@ proc binary_name_ld_lib_so { } { return "ld-pistachio.lib.so" }
 proc binary_name_core_o    { } { return "core-pistachio.o"    }
 proc binary_name_timer     { } { return "pit_timer_drv" }
 
+proc kernel_files { } { return { pistachio sigma0-pistachio kickstart-pistachio } }
 
 proc run_boot_string   { } { return "\n\r\033\\\[1m\033\\\[33mL4Ka::Pistachio -" }
 proc core_link_address { } { return "0x02000000" }
@@ -12,13 +13,35 @@ proc core_link_address { } { return "0x02000000" }
 #
 proc run_boot_dir {binaries} {
 
-	build { lib/ld/pistachio kernel/pistachio }
+	#
+	# Build kernel and dynamic linker on demand, if not yet present in
+	# '[run_dir]/genode/'
+	#
+	set kernel_arg ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/pistachio]} { set kernel_arg "kernel/pistachio" }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { set ld_arg     "lib/ld/pistachio" }
+	set targets "$kernel_arg $ld_arg"
+
+	if {[llength $targets]} { build $targets }
+
+	if {$kernel_arg != ""} {
+		file copy -force bin/pistachio           [run_dir]/genode/pistachio
+		file copy -force bin/sigma0-pistachio    [run_dir]/genode/sigma0-pistachio
+		file copy -force bin/kickstart-pistachio [run_dir]/genode/kickstart-pistachio
+	}
 
 	build_core_image $binaries
 
-	exec cp bin/pistachio           [run_dir]/kernel
-	exec cp bin/sigma0-pistachio    [run_dir]/sigma0
-	exec cp bin/kickstart-pistachio [run_dir]/kickstart
+	#
+	# Move kernel files to distinct location within the boot directory so that
+	# we can remove [run_dir]/genode after the core image has been built.
+	#
+	exec mkdir -p [run_dir]/pistachio
+	file copy -force [run_dir]/genode/pistachio           [run_dir]/kernel
+	file copy -force [run_dir]/genode/sigma0-pistachio    [run_dir]/sigma0
+	file copy -force [run_dir]/genode/kickstart-pistachio [run_dir]/kickstart
+	exec rm -r [run_dir]/genode
 
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
 
diff --git a/tool/run/boot_dir/sel4 b/tool/run/boot_dir/sel4
index 3abcc0756..ff126fc38 100644
--- a/tool/run/boot_dir/sel4
+++ b/tool/run/boot_dir/sel4
@@ -12,12 +12,31 @@ proc core_link_address { } { return "0x02000000" }
 #
 proc run_boot_dir {binaries} {
 
-	# build sel4 kernel
-	build { lib/ld/sel4 kernel/sel4 }
-	exec cp bin/sel4 [run_dir]/sel4
+	#
+	# Build kernel and dynamic linker on demand, if not yet present in
+	# '[run_dir]/genode/'
+	#
+	set kernel_arg ""
+	set ld_arg     ""
+	if {![file exists [run_dir]/genode/sel4]}      { set kernel_arg "kernel/sel4" }
+	if {![file exists [run_dir]/genode/ld.lib.so]} { set ld_arg     "lib/ld/sel4" }
+	set targets "$kernel_arg $ld_arg"
+
+	if {[llength $targets]} { build $targets }
+
+	if {$kernel_arg != ""} {
+		file copy -force [pwd]/bin/sel4 [run_dir]/genode/sel4
+	}
 
 	build_core_image $binaries
 
+	#
+	# Move kernel files to distinct location within the boot directory so that
+	# we can remove [run_dir]/genode after the core image has been built.
+	#
+	file copy -force [run_dir]/genode/sel4 [run_dir]/sel4
+	exec rm -r [run_dir]/genode
+
 	if {[have_include "image/iso"] || [have_include "image/disk"]} {
 		#
 		# Install isolinux/GRUB files and bender
diff --git a/tool/run/run b/tool/run/run
index c43f09e54..b90989d93 100755
--- a/tool/run/run
+++ b/tool/run/run
@@ -466,16 +466,10 @@ proc kernel_specific_binary { binary } {
 }
 
 
-##
-# Copy the specified binaries from the 'bin/' directory to the run
-# directory and try to strip executables.
-#
-proc copy_and_strip_genode_binaries_to_run_dir { binaries } {
+proc copy_genode_binaries_to_run_dir { binaries } {
 
 	foreach binary $binaries {
-		exec cp bin/[kernel_specific_binary $binary] [run_dir]/genode/$binary
-		catch {
-			exec [cross_dev_prefix]strip [run_dir]/genode/$binary || true }
+		file copy -force bin/[kernel_specific_binary $binary] [run_dir]/genode/$binary
 	}
 }
 
@@ -520,13 +514,16 @@ proc wait_for_output { wait_for_re timeout_value running_spawn_id } {
 
 ##
 # Dummy boot_string procedure
+#
 proc run_boot_string { } { return ""; }
 
+
 ##
 # Fall-back boot_dir module
 #
 # If this function is called someone forgot to include an appropriate boot_dir
 # module. So, we exit with an error.
+#
 proc run_boot_dir { binaries } {
 	puts stderr "Error: boot_dir module missing, e.g., '--include boot_dir/hw'"
 	exit 1
@@ -764,33 +761,48 @@ proc build_core {lib modules target link_address} {
 }
 
 
+##
+# Return kernel-specific files to be excluded from the core image
+#
+proc kernel_files { } { return { } }
+
+
 ##
 # Generate bootable core image containing all boot-modules
 #
-proc build_core_image {binaries} {
+proc build_core_image { modules } {
 
-	# boot module list without core
-	set idx [lsearch $binaries "core"]
-	set modules [lreplace $binaries $idx $idx]
+	set core_obj [kernel_specific_binary core.o]
 
-	# strip binaries
-	copy_and_strip_genode_binaries_to_run_dir $modules
-	lappend modules "config"
+	# replace 'core' with actual core-object name in 'modules' list
+	if {[lsearch $modules "core"] != -1} {
+		set idx [lsearch $modules "core"]
+		set modules [lreplace $modules $idx $idx]
+		lappend modules $core_obj
+	}
 
-	set core_obj bin/[kernel_specific_binary core.o]
+	copy_genode_binaries_to_run_dir $modules
 
 	# create core binary without modules for debugging
-	build_core $core_obj {} [run_dir].core [core_link_address]
+	build_core [run_dir]/genode/$core_obj {} [run_dir].core [core_link_address]
+
+	# determine modules to be incorporated into the core image
+	set modules [glob -nocomplain -tails -directory [run_dir]/genode/ *]
+	set excluded_modules [kernel_files]
+	lappend excluded_modules $core_obj
+	foreach excluded $excluded_modules {
+		set modules [lsearch -inline -not -all $modules $excluded] }
+
+	# check syntax of all boot modules named *.config
+	foreach file [glob -nocomplain [run_dir]/genode/*.config] {
+		check_xml_syntax $file }
 
 	# create core binary containing the boot modules
-	build_core $core_obj $modules [run_dir]/image.elf [core_link_address]
+	build_core [run_dir]/genode/$core_obj $modules [run_dir]/image.elf [core_link_address]
 	exec [cross_dev_prefix]strip [run_dir]/image.elf
 
 	# Save config part of the image.elf for easy inspection
-	exec cp -f  [run_dir]/genode/config [run_dir].config
-
-	# remove individual binaries, which are now contained in 'image.elf'
-	exec rm -rf [run_dir]/genode
+	exec cp -f [run_dir]/genode/config [run_dir].config
 }
 
 source [genode_dir]/tool/run/depot.inc