diff --git a/sw/apps/atax/Makefile b/sw/apps/atax/Makefile
deleted file mode 100644
index c926fdcc2..000000000
--- a/sw/apps/atax/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR   := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-DATA_DIR := $(realpath $(MK_DIR)/data)
-SRC_DIR  := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-APP     ?= atax
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(DATA_DIR) $(SRC_DIR)
-
-DATAGEN_PY = $(MK_DIR)/scripts/datagen.py
-DATA_H     = $(DATA_DIR)/data.h
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG)
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
diff --git a/sw/apps/common.mk b/sw/apps/common.mk
new file mode 100644
index 000000000..89f5da9f6
--- /dev/null
+++ b/sw/apps/common.mk
@@ -0,0 +1,23 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+DATA_DIR    := $(realpath $(SRC_DIR)/../data)
+SCRIPTS_DIR := $(realpath $(SRC_DIR)/../scripts)
+
+$(APP)_DATA_CFG ?= $(DATA_DIR)/params.json
+SECTION         ?=
+DATA_H          := $($(APP)_BUILD_DIR)/data.h
+DATAGEN_PY       = $(SCRIPTS_DIR)/datagen.py
+
+$(APP)_HEADERS := $(DATA_H)
+$(APP)_INCDIRS := $(dir $(DATA_H)) $(SRC_DIR)
+
+$(dir $(DATA_H)):
+	mkdir -p $@
+
+$(DATA_H): DATA_CFG := $($(APP)_DATA_CFG)
+$(DATA_H): $(DATAGEN_PY) $($(APP)_DATA_CFG) | $(dir $(DATA_H))
+	$< -c $(DATA_CFG) --section="$(SECTION)" $@
diff --git a/sw/apps/correlation/Makefile b/sw/apps/correlation/Makefile
deleted file mode 100644
index 0f6487830..000000000
--- a/sw/apps/correlation/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR   := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-DATA_DIR := $(realpath $(MK_DIR)/data)
-SRC_DIR  := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-APP     ?= correlation
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(DATA_DIR) $(SRC_DIR)
-
-DATAGEN_PY = $(MK_DIR)/scripts/datagen.py
-DATA_H     = $(DATA_DIR)/data.h
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG)
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
diff --git a/sw/apps/covariance/Makefile b/sw/apps/covariance/Makefile
deleted file mode 100644
index b24c2e872..000000000
--- a/sw/apps/covariance/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR   := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-DATA_DIR := $(realpath $(MK_DIR)/data)
-SRC_DIR  := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-APP     ?= covariance
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(DATA_DIR) $(SRC_DIR)
-
-DATAGEN_PY = $(MK_DIR)/scripts/datagen.py
-DATA_H     = $(DATA_DIR)/data.h
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG)
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
diff --git a/sw/apps/lto/Makefile b/sw/apps/lto/Makefile
deleted file mode 100644
index 83a6ea21f..000000000
--- a/sw/apps/lto/Makefile
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-
-APP  := lto
-SRCS := $(addprefix $(MK_DIR),lto.c lto_a.c)
diff --git a/sw/apps/lto/lto.c b/sw/apps/lto/lto.c
deleted file mode 100644
index 112ed6bab..000000000
--- a/sw/apps/lto/lto.c
+++ /dev/null
@@ -1,18 +0,0 @@
-// Copyright 2020 ETH Zurich and University of Bologna.
-// Licensed under the Apache License, Version 2.0, see LICENSE for details.
-// SPDX-License-Identifier: Apache-2.0
-
-#include "lto_a.h"
-#include "snrt.h"
-
-void foo4(void) { printf("Hi\n"); }
-
-int main() {
-    // The call to foo1() is optimized by the linker if LTO is enabled
-    // so the number of cycles t1-t0 should be 1
-    size_t t0 = read_csr(minstret);
-    int res = foo1();
-    size_t t1 = read_csr(minstret);
-
-    return (t1 - t0 - 1);
-}
diff --git a/sw/apps/lto/lto_a.c b/sw/apps/lto/lto_a.c
deleted file mode 100644
index 8726f2843..000000000
--- a/sw/apps/lto/lto_a.c
+++ /dev/null
@@ -1,23 +0,0 @@
-// Copyright 2020 ETH Zurich and University of Bologna.
-// Licensed under the Apache License, Version 2.0, see LICENSE for details.
-// SPDX-License-Identifier: Apache-2.0
-
-#include "lto_a.h"
-
-static signed int i = 0;
-
-void foo2(void) { i = -1; }
-
-static int foo3() {
-    foo4();
-    return 10;
-}
-
-int foo1(void) {
-    int data = 0;
-
-    if (i < 0) data = foo3();
-
-    data = data + 42;
-    return data;
-}
diff --git a/sw/apps/lto/lto_a.h b/sw/apps/lto/lto_a.h
deleted file mode 100644
index 3aae4d9d4..000000000
--- a/sw/apps/lto/lto_a.h
+++ /dev/null
@@ -1,7 +0,0 @@
-// Copyright 2020 ETH Zurich and University of Bologna.
-// Licensed under the Apache License, Version 2.0, see LICENSE for details.
-// SPDX-License-Identifier: Apache-2.0
-
-extern int foo1(void);
-extern void foo2(void);
-extern void foo4(void);
diff --git a/sw/blas/axpy/Makefile b/sw/blas/axpy/Makefile
deleted file mode 100644
index 2a755a640..000000000
--- a/sw/blas/axpy/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR   := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-DATA_DIR := $(realpath $(MK_DIR)/data)
-SRC_DIR  := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-APP     ?= axpy
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(dir $(DATA_H)) $(SRC_DIR)
-
-DATAGEN_PY = $(MK_DIR)/scripts/datagen.py
-DATA_H    ?= $(DATA_DIR)/data.h
-
-$(dir $(DATA_H)):
-	mkdir -p $@
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG) | $(dir $(DATA_H))
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
diff --git a/sw/blas/gemm/Makefile b/sw/blas/gemm/Makefile
deleted file mode 100644
index 889cb44f3..000000000
--- a/sw/blas/gemm/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Tim Fischer <fischeti@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR   := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-DATA_DIR := $(realpath $(MK_DIR)/data)
-SRC_DIR  := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-APP     ?= gemm
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(dir $(DATA_H)) $(SRC_DIR)
-
-DATAGEN_PY = $(MK_DIR)/scripts/datagen.py
-DATA_H    ?= $(DATA_DIR)/data.h
-
-$(dir $(DATA_H)):
-	mkdir -p $@
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG) | $(dir $(DATA_H))
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
diff --git a/sw/dnn/common.mk b/sw/dnn/common.mk
index 7bd84a3d7..2e3f45233 100644
--- a/sw/dnn/common.mk
+++ b/sw/dnn/common.mk
@@ -4,32 +4,6 @@
 #
 # Luca Colagrande <colluca@iis.ee.ethz.ch>
 
-# Usage of absolute paths is required to externally include this Makefile
-MK_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-
-DATA_DIR       := $(realpath $(MK_DIR)/$(APP)/data)
-SCRIPTS_DIR    := $(realpath $(MK_DIR)/$(APP)/scripts)
-SRC_DIR        := $(realpath $(MK_DIR)/$(APP)/src)
-COMMON_SRC_DIR := $(realpath $(MK_DIR)/src)
-
-DATA_CFG ?= $(DATA_DIR)/params.json
-SECTION  ?=
-
-SRCS    ?= $(realpath $(SRC_DIR)/main.c)
-INCDIRS ?= $(dir $(DATA_H)) $(SRC_DIR) $(COMMON_SRC_DIR)
-
-DATAGEN_PY = $(SCRIPTS_DIR)/datagen.py
-DATA_H    ?= $(DATA_DIR)/data.h
-
-$(dir $(DATA_H)):
-	mkdir -p $@
-
-$(DATA_H): $(DATAGEN_PY) $(DATA_CFG) | $(dir $(DATA_H))
-	$< -c $(DATA_CFG) --section="$(SECTION)" $@
-
-.PHONY: clean-data clean
-
-clean-data:
-	rm -f $(DATA_H)
-
-clean: clean-data
+include $(ROOT)/sw/apps/common.mk
+$(APP)_INCDIRS += $(ROOT)/sw/dnn/src
+$(APP)_INCDIRS += $(ROOT)/sw/blas
diff --git a/sw/examples/.gitignore b/sw/examples/.gitignore
deleted file mode 100644
index 796b96d1c..000000000
--- a/sw/examples/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/build
diff --git a/sw/examples/CMakeLists.txt b/sw/examples/CMakeLists.txt
deleted file mode 100644
index 2c83d4b58..000000000
--- a/sw/examples/CMakeLists.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2020 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-
-cmake_minimum_required(VERSION 3.13)
-
-# Read SnitchUtilities
-list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../cmake)
-include(SnitchUtilities)
-
-# Link simulator
-set(SNITCH_SIMULATOR ../../../hw/system/snitch_cluster/bin/snitch_cluster.vlt)
-
-# Create project
-project(Examples LANGUAGES C ASM)
-
-# Compile options
-add_compile_options(-O3 -g -ffunction-sections)
-
-# Build the runtime
-add_subdirectory(../snRuntime snRuntime)
-
-# Includes
-include_directories(${SNRUNTIME_INCLUDE_DIRS})
-
-# Programs
-add_snitch_executable(hello_world hello_world.c)
-add_snitch_executable(memory memory.c)
-
diff --git a/sw/examples/README.md b/sw/examples/README.md
deleted file mode 100644
index ad235f2e9..000000000
--- a/sw/examples/README.md
+++ /dev/null
@@ -1,29 +0,0 @@
-# Snitch Software Examples
-
-Build the examples with
-
-```bash
-mkdir build; cd build
-cmake -DCMAKE_TOOLCHAIN_FILE=toolchain-llvm -DSNITCH_RUNTIME=snRuntime-banshee ..
-make
-```
-
-Where
-- `CMAKE_TOOLCHAIN_FILE` can choose between the LLVM toolchain (`toolchain-llvm`) or GNU GCC (`toolchain-gcc`)
-- `SNITCH_RUNTIME` to choose between banshee simulator (`snRuntime-banshee`, default) and RTL simulator (`snRuntime-cluster`)
-
-To run with banshee
-```bash
-# Using the generated target
-make run-banshee-hello_world
-# Manually invoke banshee
-banshee --no-opt-llvm --no-opt-jit hello_world --num-cores=4 --num-clusters=1
-```
-
-To run with verilator RTL simulator
-```bash
-# Using the generated target
-make run-rtl-hello_world
-# Manually invoke RTL simulator
-../../../hw/system/snitch_cluster/bin/snitch_cluster.vlt  hello_world
-```
diff --git a/sw/examples/hello_world.c b/sw/examples/hello_world.c
deleted file mode 100644
index 7d8b03095..000000000
--- a/sw/examples/hello_world.c
+++ /dev/null
@@ -1,30 +0,0 @@
-// Copyright 2020 ETH Zurich and University of Bologna.
-// Licensed under the Apache License, Version 2.0, see LICENSE for details.
-// SPDX-License-Identifier: Apache-2.0
-
-#include "printf.h"
-#include "snrt.h"
-
-int main() {
-    uint32_t core_idx = snrt_global_core_idx();
-    uint32_t core_num = snrt_global_core_num();
-
-    printf("# hart %d global core %d(%d) ", snrt_hartid(),
-           snrt_global_core_idx(), snrt_global_core_num());
-    printf("in cluster %d(%d) ", snrt_cluster_idx(), snrt_cluster_num());
-    printf("cluster core %d(%d) ", snrt_cluster_core_idx(),
-           snrt_cluster_core_num());
-    printf("compute core %d(%d) ", snrt_cluster_compute_core_idx(),
-           snrt_cluster_compute_core_num());
-    printf("dm core %d(%d) ", snrt_cluster_dm_core_idx(),
-           snrt_cluster_dm_core_num());
-    printf("compute: %d dm: %d ", snrt_is_compute_core(), snrt_is_dm_core());
-    printf("\n");
-
-    printf("# global mem [%#llx:%#llx] cluster mem [%#llx:%#llx] ",
-           snrt_global_memory().start, snrt_global_memory().end,
-           snrt_cluster_memory().start, snrt_cluster_memory().end);
-    printf("\n");
-
-    return 0;
-}
diff --git a/sw/examples/memory.c b/sw/examples/memory.c
deleted file mode 100644
index b32ee20be..000000000
--- a/sw/examples/memory.c
+++ /dev/null
@@ -1,48 +0,0 @@
-// Copyright 2020 ETH Zurich and University of Bologna.
-// Licensed under the Apache License, Version 2.0, see LICENSE for details.
-// SPDX-License-Identifier: Apache-2.0
-
-#include "printf.h"
-#include "snrt.h"
-
-__thread uint32_t private_int;
-
-int main() {
-    uint32_t core_idx = snrt_global_core_idx();
-    uint32_t core_num = snrt_global_core_num();
-
-    // Thread-private memory can be used with the __thread specifier. It makes
-    // use of TLS and buts initialized and non-initialized data in the TCDM
-    // memory region reserved for the stack. __thread variable must have global
-    // storage
-    private_int = 1000 + core_idx;
-    for (uint32_t i = 0; i < core_num; i++) {
-        if (i == core_idx)
-            printf("thread-private: %d at %#x\n", private_int, &private_int);
-        snrt_barrier();
-    }
-
-    // local storage is allocated on stack and also thread-private
-    uint32_t private_int_stack = 2000 + core_idx;
-    for (uint32_t i = 0; i < core_num; i++) {
-        if (i == core_idx)
-            printf("thread-private on stack: %d at %#x\n", private_int_stack,
-                   &private_int_stack);
-        snrt_barrier();
-    }
-
-    // Use snrt_l1alloc() to allocate a chunk of memory in the cluster-private
-    // TCMD L1 scratchpad memory. Free is currently not possible. Store the
-    // pointer in a static variable that is shared amongst the cluster cores
-    static void* p;
-    if (core_idx == 0) {
-        p = snrt_l1alloc(1024);
-        printf("Allocated at %#x\n", p);
-    }
-    for (uint32_t i = 0; i < core_num; i++) {
-        if (i == core_idx) printf("  %#x pointer location: %#x\n", p, &p);
-        snrt_barrier();
-    }
-
-    return 0;
-}
diff --git a/target/snitch_cluster/Makefile b/target/snitch_cluster/Makefile
index bcd86d5da..bb4f837c6 100644
--- a/target/snitch_cluster/Makefile
+++ b/target/snitch_cluster/Makefile
@@ -9,14 +9,16 @@
 # Makefile invocation #
 #######################
 
-DEBUG          ?= OFF  # ON to turn on debugging symbols and wave logging
-CFG_OVERRIDE   ?=      # Override default config file
-SELECT_RUNTIME ?=      # Select snRuntime implementation: "banshee" or "rtl" (default)
+# ON to turn on debugging symbols and wave logging
+DEBUG ?= OFF
+# Override default config file
+CFG_OVERRIDE ?=
+# Select snRuntime implementation: "banshee" or "rtl" (default)
+SELECT_RUNTIME ?= rtl
 
 .DEFAULT_GOAL := help
 .PHONY: all clean
-all: sw
-clean: clean-sw clean-work clean-vcs clean-logs clean-bender clean-generated
+clean: clean-work clean-vcs clean-logs clean-bender clean-generated
 
 ##########
 # Common #
@@ -24,7 +26,7 @@ clean: clean-sw clean-work clean-vcs clean-logs clean-bender clean-generated
 
 MKFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
 MKFILE_DIR  := $(dir $(MKFILE_PATH))
-ROOT        := ${MKFILE_DIR}../..
+ROOT        := $(realpath ${MKFILE_DIR}../..)
 SNITCH_ROOT := $(ROOT)
 
 TARGET = snitch_cluster
@@ -204,7 +206,7 @@ clean-work:
 	rm -rf work
 
 clean-bender:
-	rm -rf $(ROOT)/Bender.lock $(ROOT)/.bender/
+	rm -rf $(ROOT)/.bender/
 
 clean-logs:
 	rm -rf $(LOGS_DIR)
diff --git a/target/snitch_cluster/sw.mk b/target/snitch_cluster/sw.mk
index c9d6e7e7a..ca8246124 100644
--- a/target/snitch_cluster/sw.mk
+++ b/target/snitch_cluster/sw.mk
@@ -4,14 +4,14 @@
 #
 # Luca Colagrande <colluca@iis.ee.ethz.ch>
 
-MK_TARGET ?= all
-SELECT_RUNTIME ?= rtl
+###################
+# General targets #
+###################
 
-ifeq ($(SELECT_RUNTIME), banshee)
-RUNTIME = sw/runtime/banshee
-else
-RUNTIME = sw/runtime/rtl
-endif
+.PHONY: sw clean-sw
+
+all: sw
+clean: clean-sw
 
 ####################
 # Platform headers #
@@ -22,10 +22,10 @@ CLUSTER_GEN_HEADERS = snitch_cluster_cfg.h \
 
 REGGEN_HEADERS = snitch_cluster_peripheral.h
 
-TARGET_C_HDRS_DIR = sw/runtime/common
+TARGET_C_HDRS_DIR = $(ROOT)/target/snitch_cluster/sw/runtime/common
 TARGET_C_HDRS     = $(addprefix $(TARGET_C_HDRS_DIR)/,$(CLUSTER_GEN_HEADERS) $(REGGEN_HEADERS))
 
-# CLUSTERGEN headers
+# CLUSTERGEN headers,
 $(addprefix $(TARGET_C_HDRS_DIR)/,$(CLUSTER_GEN_HEADERS)): %.h: $(CFG) $(CLUSTER_GEN_PREREQ) %.h.tpl
 	@echo "[CLUSTERGEN] Generate $@"
 	$(CLUSTER_GEN) -c $< --outdir $(TARGET_C_HDRS_DIR) --template $@.tpl
@@ -34,12 +34,20 @@ $(addprefix $(TARGET_C_HDRS_DIR)/,$(CLUSTER_GEN_HEADERS)): %.h: $(CFG) $(CLUSTER
 $(TARGET_C_HDRS_DIR)/snitch_cluster_peripheral.h: $(ROOT)/hw/snitch_cluster/src/snitch_cluster_peripheral/snitch_cluster_peripheral_reg.hjson $(REGGEN)
 	$(call reggen_generate_header,$@,$<)
 
-########
-# Apps #
-########
+.PHONY: clean-headers
+clean-sw: clean-headers
+clean-headers:
+	rm -f $(TARGET_C_HDRS)
+
+##################
+# Subdirectories #
+##################
 
-APPS  = sw/apps/lto
-APPS += sw/apps/nop
+include sw/toolchain.mk
+include sw/runtime/runtime.mk
+include sw/tests/tests.mk
+
+APPS  = sw/apps/nop
 APPS += sw/apps/blas/axpy
 APPS += sw/apps/blas/gemm
 APPS += sw/apps/blas/dot
@@ -59,19 +67,7 @@ APPS += sw/apps/atax
 APPS += sw/apps/correlation
 APPS += sw/apps/covariance
 
-SUBDIRS = sw/runtime/banshee sw/runtime/rtl $(APPS) sw/tests
-
-.PHONY: sw clean-sw $(SUBDIRS)
-
-sw: $(SUBDIRS)
-clean-sw:
-	$(MAKE) sw MK_TARGET=clean
-	rm -f $(TARGET_C_HDRS)
-
-# Runtime libraries depend on platform headers
-sw/runtime/rtl sw/runtime/banshee: $(TARGET_C_HDRS)
-	$(MAKE) -C $@ $(MK_TARGET)
-
-# Apps depend on runtime libraries
-$(APPS) sw/tests: $(RUNTIME)
-	$(MAKE) -C $@ $(MK_TARGET)
+# Include Makefile from each app subdirectory
+$(foreach app,$(APPS), \
+	$(eval include $(app)/app.mk) \
+)
diff --git a/target/snitch_cluster/sw/apps/atax/Makefile b/target/snitch_cluster/sw/apps/atax/Makefile
deleted file mode 100644
index 1962a43fe..000000000
--- a/target/snitch_cluster/sw/apps/atax/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-include ../../../../../sw/apps/atax/Makefile
-include ../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/atax/app.mk b/target/snitch_cluster/sw/apps/atax/app.mk
new file mode 100644
index 000000000..87e94ca8a
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/atax/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := atax
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/apps/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/blas/axpy/Makefile b/target/snitch_cluster/sw/apps/blas/axpy/Makefile
deleted file mode 100644
index cc9164f30..000000000
--- a/target/snitch_cluster/sw/apps/blas/axpy/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-include ../../../../../../sw/blas/axpy/Makefile
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/blas/axpy/app.mk b/target/snitch_cluster/sw/apps/blas/axpy/app.mk
new file mode 100644
index 000000000..76c4f90e2
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/blas/axpy/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := axpy
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/blas/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/blas/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/blas/dot/Makefile b/target/snitch_cluster/sw/apps/blas/dot/Makefile
deleted file mode 100644
index 41e58a534..000000000
--- a/target/snitch_cluster/sw/apps/blas/dot/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Matteo Perotti <mperotti@iis.ee.ethz.ch>
-
-include ../../../../../../sw/blas/dot/Makefile
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/blas/dot/app.mk b/target/snitch_cluster/sw/apps/blas/dot/app.mk
new file mode 100644
index 000000000..2e62f6bdf
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/blas/dot/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := dot
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/blas/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/blas/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/blas/gemm/Makefile b/target/snitch_cluster/sw/apps/blas/gemm/Makefile
deleted file mode 100644
index 7625cda9c..000000000
--- a/target/snitch_cluster/sw/apps/blas/gemm/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Tim Fischer <fischeti@iis.ee.ethz.ch>
-
-include ../../../../../../sw/blas/gemm/Makefile
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/blas/gemm/app.mk b/target/snitch_cluster/sw/apps/blas/gemm/app.mk
new file mode 100644
index 000000000..5d2b54068
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/blas/gemm/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := gemm
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/blas/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/blas/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/blas/gemm/test/test.sh b/target/snitch_cluster/sw/apps/blas/gemm/test/test.sh
index fa0eb6979..236631b82 100755
--- a/target/snitch_cluster/sw/apps/blas/gemm/test/test.sh
+++ b/target/snitch_cluster/sw/apps/blas/gemm/test/test.sh
@@ -13,5 +13,5 @@ TEST_LIST=$(pwd)/run.yaml
 CFG_FILES=$(pwd)/cfg/"*"
 CMD="$ROOT/sw/blas/gemm/scripts/verify.py \${sim_bin} \${elf} --dump-results"
 
-$BUILD_PY sw/apps/blas/gemm --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
+$BUILD_PY gemm --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
 $RUN_PY $TEST_LIST --simulator vsim -j
diff --git a/target/snitch_cluster/sw/apps/common.mk b/target/snitch_cluster/sw/apps/common.mk
index 0b7a10ebd..1877d6ad5 100644
--- a/target/snitch_cluster/sw/apps/common.mk
+++ b/target/snitch_cluster/sw/apps/common.mk
@@ -1,93 +1,85 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
+# Copyright 2024 ETH Zurich and University of Bologna.
 # Licensed under the Apache License, Version 2.0, see LICENSE for details.
 # SPDX-License-Identifier: Apache-2.0
 #
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include
-# this Makefile from multiple different locations
-MK_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include $(MK_DIR)/../toolchain.mk
-
-###############
-# Directories #
-###############
-
-# Fixed paths in repository tree
-ROOT     := $(abspath $(MK_DIR)/../../../..)
-SNRT_DIR := $(ROOT)/sw/snRuntime
-ifeq ($(SELECT_RUNTIME), banshee)
-RUNTIME_DIR  := $(ROOT)/target/snitch_cluster/sw/runtime/banshee
-RISCV_CFLAGS += -DBIST
-else
-RUNTIME_DIR := $(ROOT)/target/snitch_cluster/sw/runtime/rtl
-endif
-
-# Paths relative to the app including this Makefile
-APP_BUILDDIR ?= $(abspath build)
+# Luca Colagrande <colluca@iis.ee.ethz.ch
 
 ###################
 # Build variables #
 ###################
 
-INCDIRS += $(RUNTIME_DIR)/src
-INCDIRS += $(RUNTIME_DIR)/../common
-INCDIRS += $(SNRT_DIR)/api
-INCDIRS += $(SNRT_DIR)/api/omp
-INCDIRS += $(SNRT_DIR)/src
-INCDIRS += $(SNRT_DIR)/src/omp
-INCDIRS += $(ROOT)/sw/blas
-INCDIRS += $(ROOT)/sw/deps/riscv-opcodes
+$(APP)_HEADERS += $(TARGET_C_HDRS)
 
-LIBS += $(RUNTIME_DIR)/build/libsnRuntime.a
+$(APP)_INCDIRS += $(SNRT_INCDIRS)
+$(APP)_INCDIRS += $(ROOT)/sw/deps/riscv-opcodes
 
-LIBDIRS  = $(dir $(LIBS))
-LIBNAMES = $(patsubst lib%,%,$(notdir $(basename $(LIBS))))
+$(APP)_RISCV_CFLAGS += $(RISCV_CFLAGS)
+$(APP)_RISCV_CFLAGS += $(addprefix -I,$($(APP)_INCDIRS))
+ifeq ($(SELECT_RUNTIME), banshee)
+$(APP)_RISCV_CFLAGS += -DBIST
+endif
+
+$(APP)_LIBS += $(SNRT_TARGET_DIR)/build/libsnRuntime.a
+
+$(APP)_LIBDIRS  = $(dir $($(APP)_LIBS))
+$(APP)_LIBNAMES = $(patsubst lib%,%,$(notdir $(basename $($(APP)_LIBS))))
 
-RISCV_LDFLAGS += -L$(abspath $(RUNTIME_DIR))
-RISCV_LDFLAGS += -T$(abspath $(SNRT_DIR)/base.ld)
-RISCV_LDFLAGS += $(addprefix -L,$(LIBDIRS))
-RISCV_LDFLAGS += $(addprefix -l,$(LIBNAMES))
+$(APP)_RISCV_LDFLAGS += $(RISCV_LDFLAGS)
+$(APP)_RISCV_LDFLAGS += -L$(abspath $(SNRT_TARGET_DIR)/..)
+$(APP)_RISCV_LDFLAGS += -T$(abspath $(SNRT_DIR)/base.ld)
+$(APP)_RISCV_LDFLAGS += $(addprefix -L,$($(APP)_LIBDIRS))
+$(APP)_RISCV_LDFLAGS += $(addprefix -l,$($(APP)_LIBNAMES))
 
 ###########
 # Outputs #
 ###########
 
-ELF         = $(abspath $(addprefix $(APP_BUILDDIR)/,$(addsuffix .elf,$(APP))))
-DEP         = $(abspath $(addprefix $(APP_BUILDDIR)/,$(addsuffix .d,$(APP))))
-DUMP        = $(abspath $(addprefix $(APP_BUILDDIR)/,$(addsuffix .dump,$(APP))))
-DWARF       = $(abspath $(addprefix $(APP_BUILDDIR)/,$(addsuffix .dwarf,$(APP))))
-ALL_OUTPUTS = $(ELF) $(DEP) $(DUMP) $(DWARF)
+ELF         := $(abspath $(addprefix $($(APP)_BUILD_DIR)/,$(addsuffix .elf,$(APP))))
+DEP         := $(abspath $(addprefix $($(APP)_BUILD_DIR)/,$(addsuffix .d,$(APP))))
+DUMP        := $(abspath $(addprefix $($(APP)_BUILD_DIR)/,$(addsuffix .dump,$(APP))))
+DWARF       := $(abspath $(addprefix $($(APP)_BUILD_DIR)/,$(addsuffix .dwarf,$(APP))))
+ALL_OUTPUTS := $(ELF) $(DEP) $(DUMP) $(DWARF)
 
 #########
 # Rules #
 #########
 
-.PHONY: all
-all: $(ALL_OUTPUTS)
+.PHONY: $(APP) clean-$(APP)
 
-.PHONY: clean
-clean:
-	rm -rf $(APP_BUILDDIR)
+sw: $(APP)
+clean-sw: clean-$(APP)
 
-.PHONY: $(APP)
-$(APP): $(ELF)
+$(APP): $(ALL_OUTPUTS)
 
-$(APP_BUILDDIR):
+clean-$(APP): BUILD_DIR := $($(APP)_BUILD_DIR)
+clean-$(APP):
+	rm -rf $(BUILD_DIR)
+
+$($(APP)_BUILD_DIR):
 	mkdir -p $@
 
-$(DEP): $(SRCS) | $(APP_BUILDDIR)
+$(DEP): ELF := $(ELF)
+$(ELF): SRCS := $(SRCS)
+# Guarantee that variables used in rule recipes (thus subject to deferred expansion)
+# have unique values, despite depending on variables with the same name across
+# applications, but which could have different values (e.g. the APP variable itself)
+$(DEP) $(ELF): RISCV_CFLAGS := $($(APP)_RISCV_CFLAGS)
+$(ELF): RISCV_LDFLAGS := $($(APP)_RISCV_LDFLAGS)
+
+$(DEP): $(SRCS) | $($(APP)_BUILD_DIR) $($(APP)_HEADERS)
 	$(RISCV_CC) $(RISCV_CFLAGS) -MM -MT '$(ELF)' $< > $@
 
-$(ELF): $(SRCS) $(DEP) $(LIBS) | $(APP_BUILDDIR)
+$(ELF): $(SRCS) $(DEP) $($(APP)_LIBS) | $($(APP)_BUILD_DIR)
 	$(RISCV_CC) $(RISCV_CFLAGS) $(RISCV_LDFLAGS) $(SRCS) -o $@
 
-$(DUMP): $(ELF) | $(APP_BUILDDIR)
+$(DUMP): $(ELF) | $($(APP)_BUILD_DIR)
 	$(RISCV_OBJDUMP) $(RISCV_OBJDUMP_FLAGS) $< > $@
 
-$(DWARF): $(ELF) | $(APP_BUILDDIR)
+$(DWARF): $(ELF) | $($(APP)_BUILD_DIR)
 	$(RISCV_DWARFDUMP) $< > $@
 
 ifneq ($(MAKECMDGOALS),clean)
+ifneq ($(MAKECMDGOALS),clean-sw)
 -include $(DEP)
 endif
+endif
diff --git a/target/snitch_cluster/sw/apps/correlation/Makefile b/target/snitch_cluster/sw/apps/correlation/Makefile
deleted file mode 100644
index e5588e8ad..000000000
--- a/target/snitch_cluster/sw/apps/correlation/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-include ../../../../../sw/apps/correlation/Makefile
-include ../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/correlation/app.mk b/target/snitch_cluster/sw/apps/correlation/app.mk
new file mode 100644
index 000000000..f2284a6ce
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/correlation/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := correlation
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/apps/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/covariance/Makefile b/target/snitch_cluster/sw/apps/covariance/Makefile
deleted file mode 100644
index e3016de89..000000000
--- a/target/snitch_cluster/sw/apps/covariance/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2024 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-include ../../../../../sw/apps/covariance/Makefile
-include ../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/covariance/app.mk b/target/snitch_cluster/sw/apps/covariance/app.mk
new file mode 100644
index 000000000..c177a9d61
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/covariance/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := covariance
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/apps/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/apps/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/batchnorm/Makefile b/target/snitch_cluster/sw/apps/dnn/batchnorm/Makefile
deleted file mode 100644
index f84fccea6..000000000
--- a/target/snitch_cluster/sw/apps/dnn/batchnorm/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= batchnorm
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
\ No newline at end of file
diff --git a/target/snitch_cluster/sw/apps/dnn/batchnorm/app.mk b/target/snitch_cluster/sw/apps/dnn/batchnorm/app.mk
new file mode 100644
index 000000000..016162a66
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/batchnorm/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := batchnorm
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/concat/Makefile b/target/snitch_cluster/sw/apps/dnn/concat/Makefile
deleted file mode 100644
index 088d29d66..000000000
--- a/target/snitch_cluster/sw/apps/dnn/concat/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= concat
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
\ No newline at end of file
diff --git a/target/snitch_cluster/sw/apps/dnn/concat/app.mk b/target/snitch_cluster/sw/apps/dnn/concat/app.mk
new file mode 100644
index 000000000..3fd2b8ee5
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/concat/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := concat
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/conv2d/Makefile b/target/snitch_cluster/sw/apps/dnn/conv2d/Makefile
deleted file mode 100644
index a9018b35d..000000000
--- a/target/snitch_cluster/sw/apps/dnn/conv2d/Makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Gianna Paulin <pauling@iis.ee.ethz.ch>
-# Viviane Potocnik <vivianep@iis.ee.ethz.ch>
-
-APP ?= conv2d
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/conv2d/app.mk b/target/snitch_cluster/sw/apps/dnn/conv2d/app.mk
new file mode 100644
index 000000000..5dcc592df
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/conv2d/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := conv2d
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/flashattention_2/Makefile b/target/snitch_cluster/sw/apps/dnn/flashattention_2/Makefile
deleted file mode 100644
index 75585b2d6..000000000
--- a/target/snitch_cluster/sw/apps/dnn/flashattention_2/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= flashattention_2
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/flashattention_2/app.mk b/target/snitch_cluster/sw/apps/dnn/flashattention_2/app.mk
new file mode 100644
index 000000000..a08ae6874
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/flashattention_2/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := flashattention_2
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/flashattention_2/test/test.sh b/target/snitch_cluster/sw/apps/dnn/flashattention_2/test/test.sh
index 704d8146d..35cbf23e2 100755
--- a/target/snitch_cluster/sw/apps/dnn/flashattention_2/test/test.sh
+++ b/target/snitch_cluster/sw/apps/dnn/flashattention_2/test/test.sh
@@ -12,5 +12,5 @@ TEST_LIST=$(pwd)/run.yaml
 CFG_FILES=$(pwd)/cfg/"*"
 CMD="$ROOT/sw/dnn/flashattention_2/scripts/verify.py \${sim_bin} \${elf} --dump-results"
 
-$BUILD_PY sw/apps/dnn/flashattention_2 --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
+$BUILD_PY flashattention_2 --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
 $RUN_PY $TEST_LIST --simulator vsim -j
diff --git a/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/Makefile b/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/Makefile
deleted file mode 100644
index 827014a08..000000000
--- a/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= fused_concat_linear
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/app.mk b/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/app.mk
new file mode 100644
index 000000000..c10af49be
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/fused_concat_linear/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := fused_concat_linear
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/fusedconv/Makefile b/target/snitch_cluster/sw/apps/dnn/fusedconv/Makefile
deleted file mode 100644
index 927d6b3e0..000000000
--- a/target/snitch_cluster/sw/apps/dnn/fusedconv/Makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Gianna Paulin <pauling@iis.ee.ethz.ch>
-# Viviane Potocnik <vivianep@iis.ee.ethz.ch>
-
-APP ?= fusedconv
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
\ No newline at end of file
diff --git a/target/snitch_cluster/sw/apps/dnn/fusedconv/app.mk b/target/snitch_cluster/sw/apps/dnn/fusedconv/app.mk
new file mode 100644
index 000000000..b269f5cdb
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/fusedconv/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := fusedconv
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/gelu/Makefile b/target/snitch_cluster/sw/apps/dnn/gelu/Makefile
deleted file mode 100644
index 4225a8cd8..000000000
--- a/target/snitch_cluster/sw/apps/dnn/gelu/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= gelu
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
\ No newline at end of file
diff --git a/target/snitch_cluster/sw/apps/dnn/gelu/app.mk b/target/snitch_cluster/sw/apps/dnn/gelu/app.mk
new file mode 100644
index 000000000..2032f0784
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/gelu/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := gelu
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/layernorm/Makefile b/target/snitch_cluster/sw/apps/dnn/layernorm/Makefile
deleted file mode 100644
index f8df5a08a..000000000
--- a/target/snitch_cluster/sw/apps/dnn/layernorm/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= layernorm
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/layernorm/app.mk b/target/snitch_cluster/sw/apps/dnn/layernorm/app.mk
new file mode 100644
index 000000000..d2dc68c75
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/layernorm/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := layernorm
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/maxpool/Makefile b/target/snitch_cluster/sw/apps/dnn/maxpool/Makefile
deleted file mode 100644
index e83838ca4..000000000
--- a/target/snitch_cluster/sw/apps/dnn/maxpool/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= maxpool
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
\ No newline at end of file
diff --git a/target/snitch_cluster/sw/apps/dnn/maxpool/app.mk b/target/snitch_cluster/sw/apps/dnn/maxpool/app.mk
new file mode 100644
index 000000000..3d7af9652
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/maxpool/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := maxpool
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/softmax/Makefile b/target/snitch_cluster/sw/apps/dnn/softmax/Makefile
deleted file mode 100644
index d4f685c7d..000000000
--- a/target/snitch_cluster/sw/apps/dnn/softmax/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= softmax
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/softmax/app.mk b/target/snitch_cluster/sw/apps/dnn/softmax/app.mk
new file mode 100644
index 000000000..7618d6c51
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/softmax/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := softmax
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/transpose/Makefile b/target/snitch_cluster/sw/apps/dnn/transpose/Makefile
deleted file mode 100644
index b1c819cfe..000000000
--- a/target/snitch_cluster/sw/apps/dnn/transpose/Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP ?= transpose
-
-include ../../../../../../sw/dnn/common.mk
-include ../../common.mk
-
-$(DEP): $(DATA_H)
diff --git a/target/snitch_cluster/sw/apps/dnn/transpose/app.mk b/target/snitch_cluster/sw/apps/dnn/transpose/app.mk
new file mode 100644
index 000000000..204ba4a0b
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/dnn/transpose/app.mk
@@ -0,0 +1,13 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := transpose
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/dnn/$(APP)/build
+SRC_DIR          := $(ROOT)/sw/dnn/$(APP)/src
+SRCS             := $(SRC_DIR)/main.c
+
+include $(ROOT)/sw/dnn/common.mk
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/dnn/transpose/test/test.sh b/target/snitch_cluster/sw/apps/dnn/transpose/test/test.sh
index 8794e3d11..02e85373c 100755
--- a/target/snitch_cluster/sw/apps/dnn/transpose/test/test.sh
+++ b/target/snitch_cluster/sw/apps/dnn/transpose/test/test.sh
@@ -12,5 +12,5 @@ TEST_LIST=$(pwd)/run.yaml
 CFG_FILES=$(pwd)/cfg/"*"
 CMD="$ROOT/sw/dnn/transpose/scripts/verify.py \${sim_bin} \${elf} --dump-results"
 
-$BUILD_PY sw/apps/dnn/transpose --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
+$BUILD_PY transpose --cfg $CFG_FILES --testlist $TEST_LIST --testlist-cmd "$CMD"
 $RUN_PY $TEST_LIST --simulator vsim -j
diff --git a/target/snitch_cluster/sw/apps/lto/Makefile b/target/snitch_cluster/sw/apps/lto/Makefile
deleted file mode 100644
index a55bcac8a..000000000
--- a/target/snitch_cluster/sw/apps/lto/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-include ../../../../../sw/apps/lto/Makefile
-include ../common.mk
diff --git a/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/Makefile b/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/Makefile
deleted file mode 100644
index ed455b3b5..000000000
--- a/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-PI_ESTIMATION_DIR = ../../../../../../sw/apps/montecarlo/pi_estimation
-PRNG_DIR          = ../../../../../../sw/apps/prng
-
-APP     ?= pi_estimation
-SRCS    ?= $(PI_ESTIMATION_DIR)/main.c
-INCDIRS += $(PI_ESTIMATION_DIR) $(PRNG_DIR)
-
-include ../../common.mk
diff --git a/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/app.mk b/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/app.mk
new file mode 100644
index 000000000..998456aa0
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/app.mk
@@ -0,0 +1,15 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+PI_ESTIMATION_DIR := $(ROOT)/sw/apps/montecarlo/pi_estimation
+PRNG_DIR          := $(ROOT)/sw/apps/prng
+
+APP              := pi_estimation
+SRCS             := $(PI_ESTIMATION_DIR)/main.c
+$(APP)_INCDIRS   := $(PI_ESTIMATION_DIR) $(PRNG_DIR)
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/montecarlo/pi_estimation/build
+
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/nop/Makefile b/target/snitch_cluster/sw/apps/nop/Makefile
deleted file mode 100644
index 1218113c9..000000000
--- a/target/snitch_cluster/sw/apps/nop/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-APP  = nop
-SRCS = src/$(APP).c
-
-include ../common.mk
diff --git a/target/snitch_cluster/sw/apps/nop/app.mk b/target/snitch_cluster/sw/apps/nop/app.mk
new file mode 100644
index 000000000..9f3938f37
--- /dev/null
+++ b/target/snitch_cluster/sw/apps/nop/app.mk
@@ -0,0 +1,11 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+APP              := nop
+SRCS             := $(ROOT)/target/snitch_cluster/sw/apps/$(APP)/src/main.c
+$(APP)_BUILD_DIR ?= $(ROOT)/target/snitch_cluster/sw/apps/$(APP)/build
+
+include $(ROOT)/target/snitch_cluster/sw/apps/common.mk
diff --git a/target/snitch_cluster/sw/apps/nop/src/nop.c b/target/snitch_cluster/sw/apps/nop/src/main.c
similarity index 100%
rename from target/snitch_cluster/sw/apps/nop/src/nop.c
rename to target/snitch_cluster/sw/apps/nop/src/main.c
diff --git a/target/snitch_cluster/sw/runtime/banshee/Makefile b/target/snitch_cluster/sw/runtime/banshee/Makefile
deleted file mode 100644
index ae9ff7f77..000000000
--- a/target/snitch_cluster/sw/runtime/banshee/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-SRCS  = snitch_cluster_start.S
-SRCS += snrt.c
-
-include ../common/common.mk
diff --git a/target/snitch_cluster/sw/runtime/common/common.mk b/target/snitch_cluster/sw/runtime/common/common.mk
deleted file mode 100644
index 08d7d15c2..000000000
--- a/target/snitch_cluster/sw/runtime/common/common.mk
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include
-# this Makefile from multiple different locations
-MK_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include $(MK_DIR)/../../toolchain.mk
-
-###############
-# Directories #
-###############
-
-# Fixed paths in repository tree
-ROOT     = $(abspath $(MK_DIR)/../../../../..)
-SNRT_DIR = $(ROOT)/sw/snRuntime
-
-# Paths relative to the runtime including this Makefile
-BUILDDIR = $(abspath build)
-SRC_DIR  = $(abspath src)
-
-###################
-# Build variables #
-###################
-
-INCDIRS += $(SNRT_DIR)/src
-INCDIRS += $(SNRT_DIR)/api
-INCDIRS += $(SNRT_DIR)/src/omp
-INCDIRS += $(SNRT_DIR)/api/omp
-INCDIRS += $(SNRT_DIR)/vendor/riscv-opcodes
-INCDIRS += $(ROOT)/target/snitch_cluster/sw/runtime/common
-
-###########
-# Outputs #
-###########
-
-OBJS        = $(addprefix $(BUILDDIR)/,$(addsuffix .o,$(basename $(notdir $(SRCS)))))
-DEPS        = $(addprefix $(BUILDDIR)/,$(addsuffix .d,$(basename $(notdir $(SRCS)))))
-LIB         = $(BUILDDIR)/libsnRuntime.a
-DUMP        = $(BUILDDIR)/libsnRuntime.dump
-ALL_OUTPUTS = $(LIB) $(DUMP)
-
-#########
-# Rules #
-#########
-
-.PHONY: all
-all: $(ALL_OUTPUTS)
-
-.PHONY: clean
-clean:
-	rm -rf $(BUILDDIR)
-
-$(BUILDDIR):
-	mkdir -p $@
-
-$(BUILDDIR)/%.o: $(SRC_DIR)/%.S | $(BUILDDIR)
-	$(RISCV_CC) $(RISCV_CFLAGS) -c $< -o $@
-
-$(BUILDDIR)/%.o: $(SRC_DIR)/%.c | $(BUILDDIR)
-	$(RISCV_CC) $(RISCV_CFLAGS) -c $< -o $@
-
-$(BUILDDIR)/%.d: $(SRC_DIR)/%.c | $(BUILDDIR)
-	$(RISCV_CC) $(RISCV_CFLAGS) -MM -MT '$(@:.d=.o)' $< > $@
-
-$(LIB): $(OBJS) | $(BUILDDIR)
-	$(RISCV_AR) $(RISCV_ARFLAGS) $@ $^
-
-$(DUMP): $(LIB) | $(BUILDDIR)
-	$(RISCV_OBJDUMP) -D $< > $@
-
-ifneq ($(MAKECMDGOALS),clean)
--include $(DEPS)
-endif
diff --git a/target/snitch_cluster/sw/runtime/banshee/memory.ld b/target/snitch_cluster/sw/runtime/memory.ld
similarity index 100%
rename from target/snitch_cluster/sw/runtime/banshee/memory.ld
rename to target/snitch_cluster/sw/runtime/memory.ld
diff --git a/target/snitch_cluster/sw/runtime/rtl/Makefile b/target/snitch_cluster/sw/runtime/rtl/Makefile
deleted file mode 100644
index ae9ff7f77..000000000
--- a/target/snitch_cluster/sw/runtime/rtl/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-SRCS  = snitch_cluster_start.S
-SRCS += snrt.c
-
-include ../common/common.mk
diff --git a/target/snitch_cluster/sw/runtime/rtl/memory.ld b/target/snitch_cluster/sw/runtime/rtl/memory.ld
deleted file mode 100644
index 985c7cfd8..000000000
--- a/target/snitch_cluster/sw/runtime/rtl/memory.ld
+++ /dev/null
@@ -1,8 +0,0 @@
-/* Copyright 2020 ETH Zurich and University of Bologna. */
-/* Solderpad Hardware License, Version 0.51, see LICENSE for details. */
-/* SPDX-License-Identifier: SHL-0.51 */
-
-MEMORY
-{
-    L3 (rwxa) : ORIGIN = 0x80000000, LENGTH = 0x80000000
-}
diff --git a/target/snitch_cluster/sw/runtime/runtime.mk b/target/snitch_cluster/sw/runtime/runtime.mk
new file mode 100644
index 000000000..8f15ebab1
--- /dev/null
+++ b/target/snitch_cluster/sw/runtime/runtime.mk
@@ -0,0 +1,82 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+###############
+# Directories #
+###############
+
+SNRT_DIR        = $(ROOT)/sw/snRuntime
+SNRT_TARGET_DIR = $(ROOT)/target/snitch_cluster/sw/runtime/$(SELECT_RUNTIME)
+SNRT_BUILDDIR   = $(SNRT_TARGET_DIR)/build
+SNRT_SRCDIR     = $(SNRT_TARGET_DIR)/src
+
+###################
+# Build variables #
+###################
+
+SNRT_SRCS  = snitch_cluster_start.S
+SNRT_SRCS += snrt.c
+
+SNRT_INCDIRS += $(SNRT_DIR)/src
+SNRT_INCDIRS += $(SNRT_DIR)/api
+SNRT_INCDIRS += $(SNRT_DIR)/src/omp
+SNRT_INCDIRS += $(SNRT_DIR)/api/omp
+SNRT_INCDIRS += $(SNRT_DIR)/vendor/riscv-opcodes
+SNRT_INCDIRS += $(SNRT_SRCDIR)
+SNRT_INCDIRS += $(SNRT_TARGET_DIR)/../common
+
+SNRT_RISCV_CFLAGS += $(RISCV_CFLAGS)
+SNRT_RISCV_CFLAGS += $(addprefix -I,$(SNRT_INCDIRS))
+
+###########
+# Outputs #
+###########
+
+SNRT_OBJS    = $(addprefix $(SNRT_BUILDDIR)/,$(addsuffix .o,$(basename $(notdir $(SNRT_SRCS)))))
+SNRT_DEPS    = $(addprefix $(SNRT_BUILDDIR)/,$(addsuffix .d,$(basename $(notdir $(SNRT_SRCS)))))
+SNRT_LIB     = $(SNRT_BUILDDIR)/libsnRuntime.a
+SNRT_DUMP    = $(SNRT_BUILDDIR)/libsnRuntime.dump
+SNRT_OUTPUTS = $(SNRT_LIB) $(SNRT_DUMP)
+
+#########
+# Rules #
+#########
+
+.PHONY: runtime clean-runtime
+
+sw: runtime
+clean-sw: clean-runtime
+
+runtime: $(SNRT_OUTPUTS)
+
+clean-runtime:
+	rm -rf $(SNRT_BUILDDIR)
+
+$(SNRT_BUILDDIR):
+	mkdir -p $@
+
+$(SNRT_BUILDDIR)/%.o: $(SNRT_SRCDIR)/%.S | $(SNRT_BUILDDIR)
+	$(RISCV_CC) $(SNRT_RISCV_CFLAGS) -c $< -o $@
+
+$(SNRT_BUILDDIR)/%.o: $(SNRT_SRCDIR)/%.c | $(SNRT_BUILDDIR)
+	$(RISCV_CC) $(SNRT_RISCV_CFLAGS) -c $< -o $@
+
+$(SNRT_BUILDDIR)/%.d: $(SNRT_SRCDIR)/%.c | $(SNRT_BUILDDIR)
+	$(RISCV_CC) $(SNRT_RISCV_CFLAGS) -MM -MT '$(@:.d=.o)' $< > $@
+
+$(SNRT_LIB): $(SNRT_OBJS) | $(SNRT_BUILDDIR)
+	$(RISCV_AR) $(RISCV_ARFLAGS) $@ $^
+
+$(SNRT_DUMP): $(SNRT_LIB) | $(SNRT_BUILDDIR)
+	$(RISCV_OBJDUMP) $(RISCV_OBJDUMP_FLAGS) $< > $@
+
+$(SNRT_DEPS): | $(TARGET_C_HDRS)
+
+ifneq ($(MAKECMDGOALS),clean)
+ifneq ($(MAKECMDGOALS),clean-sw)
+-include $(SNRT_DEPS)
+endif
+endif
diff --git a/target/snitch_cluster/sw/tests/Makefile b/target/snitch_cluster/sw/tests/Makefile
deleted file mode 100644
index 87a488e9a..000000000
--- a/target/snitch_cluster/sw/tests/Makefile
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 2023 ETH Zurich and University of Bologna.
-# Licensed under the Apache License, Version 2.0, see LICENSE for details.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Luca Colagrande <colluca@iis.ee.ethz.ch>
-
-# Usage of absolute paths is required to externally include
-# this Makefile from multiple different locations
-MK_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include $(MK_DIR)/../toolchain.mk
-
-###############
-# Directories #
-###############
-
-ROOT        = $(abspath ../../../..)
-SNRT_DIR    = $(ROOT)/sw/snRuntime
-SRC_DIR     = $(ROOT)/sw/tests
-BUILDDIR    = $(ROOT)/target/snitch_cluster/sw/tests/build
-ifeq ($(SELECT_RUNTIME), banshee)
-RUNTIME_DIR = $(ROOT)/target/snitch_cluster/sw/runtime/banshee
-else
-RUNTIME_DIR = $(ROOT)/target/snitch_cluster/sw/runtime/rtl
-endif
-
-###################
-# Build variables #
-###################
-
-INCDIRS += $(RUNTIME_DIR)/src
-INCDIRS += $(RUNTIME_DIR)/../common
-INCDIRS += $(SNRT_DIR)/api
-INCDIRS += $(SNRT_DIR)/api/omp
-INCDIRS += $(SNRT_DIR)/src
-INCDIRS += $(SNRT_DIR)/src/omp
-INCDIRS += $(SNRT_DIR)/vendor/riscv-opcodes
-
-RISCV_LDFLAGS += -L$(abspath $(RUNTIME_DIR))
-RISCV_LDFLAGS += -T$(abspath $(SNRT_DIR)/base.ld)
-RISCV_LDFLAGS += -L$(abspath $(RUNTIME_DIR)/build/)
-RISCV_LDFLAGS += -lsnRuntime
-
-###########
-# Outputs #
-###########
-
-APPS        = $(basename $(notdir $(wildcard $(SRC_DIR)/*.c)))
-ELFS        = $(abspath $(addprefix $(BUILDDIR)/,$(addsuffix .elf,$(APPS))))
-DEPS        = $(abspath $(addprefix $(BUILDDIR)/,$(addsuffix .d,$(APPS))))
-DUMPS       = $(abspath $(addprefix $(BUILDDIR)/,$(addsuffix .dump,$(APPS))))
-DWARFS      = $(abspath $(addprefix $(BUILDDIR)/,$(addsuffix .dwarf,$(APPS))))
-ALL_OUTPUTS = $(ELFS)
-
-ifeq ($(DEBUG), ON)
-ALL_OUTPUTS += $(DUMPS) $(DWARFS)
-endif
-
-#########
-# Rules #
-#########
-
-.PHONY: all
-all: $(ALL_OUTPUTS)
-
-.PHONY: clean
-clean:
-	rm -rf $(BUILDDIR)
-
-$(BUILDDIR):
-	mkdir -p $@
-
-$(BUILDDIR)/%.d: $(SRC_DIR)/%.c | $(BUILDDIR)
-	$(RISCV_CC) $(RISCV_CFLAGS) -MM -MT '$(BUILDDIR)/$*.elf' $< > $@
-
-$(BUILDDIR)/%.elf: $(SRC_DIR)/%.c $(BUILDDIR)/%.d | $(BUILDDIR)
-	$(RISCV_CC) $(RISCV_CFLAGS) $(RISCV_LDFLAGS) $(SRC_DIR)/$*.c -o $@
-
-$(BUILDDIR)/%.dump: $(BUILDDIR)/%.elf | $(BUILDDIR)
-	$(RISCV_OBJDUMP) $(RISCV_OBJDUMP_FLAGS) $< > $@
-
-$(BUILDDIR)/%.dwarf: $(BUILDDIR)/%.elf | $(BUILDDIR)
-	$(RISCV_DWARFDUMP) --all $< > $@
-
-ifneq ($(MAKECMDGOALS),clean)
--include $(DEPS)
-endif
diff --git a/target/snitch_cluster/sw/tests/tests.mk b/target/snitch_cluster/sw/tests/tests.mk
new file mode 100644
index 000000000..35afa66ea
--- /dev/null
+++ b/target/snitch_cluster/sw/tests/tests.mk
@@ -0,0 +1,77 @@
+# Copyright 2023 ETH Zurich and University of Bologna.
+# Licensed under the Apache License, Version 2.0, see LICENSE for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Luca Colagrande <colluca@iis.ee.ethz.ch>
+
+###############
+# Directories #
+###############
+
+TESTS_SRCDIR   = $(ROOT)/sw/tests
+TESTS_BUILDDIR = $(ROOT)/target/snitch_cluster/sw/tests/build
+
+###################
+# Build variables #
+###################
+
+TESTS_RISCV_CFLAGS += $(RISCV_CFLAGS)
+TESTS_RISCV_CFLAGS += $(addprefix -I,$(SNRT_INCDIRS))
+
+TESTS_RISCV_LDFLAGS += $(RISCV_LDFLAGS)
+TESTS_RISCV_LDFLAGS += -L$(abspath $(SNRT_TARGET_DIR)/..)
+TESTS_RISCV_LDFLAGS += -T$(abspath $(SNRT_DIR)/base.ld)
+TESTS_RISCV_LDFLAGS += -L$(SNRT_TARGET_DIR)/build
+TESTS_RISCV_LDFLAGS += -lsnRuntime
+
+###########
+# Outputs #
+###########
+
+TEST_NAMES   = $(basename $(notdir $(wildcard $(TESTS_SRCDIR)/*.c)))
+TEST_ELFS    = $(abspath $(addprefix $(TESTS_BUILDDIR)/,$(addsuffix .elf,$(TEST_NAMES))))
+TEST_DEPS    = $(abspath $(addprefix $(TESTS_BUILDDIR)/,$(addsuffix .d,$(TEST_NAMES))))
+TEST_DUMPS   = $(abspath $(addprefix $(TESTS_BUILDDIR)/,$(addsuffix .dump,$(TEST_NAMES))))
+TEST_DWARFS  = $(abspath $(addprefix $(TESTS_BUILDDIR)/,$(addsuffix .dwarf,$(TEST_NAMES))))
+TEST_OUTPUTS = $(TEST_ELFS)
+
+ifeq ($(DEBUG), ON)
+TEST_OUTPUTS += $(DUMPS) $(DWARFS)
+endif
+
+#########
+# Rules #
+#########
+
+.PHONY: tests clean-tests
+
+sw: tests
+clean-sw: clean-tests
+
+tests: $(TEST_OUTPUTS)
+
+clean-tests:
+	rm -rf $(TESTS_BUILDDIR)
+
+$(TESTS_BUILDDIR):
+	mkdir -p $@
+
+$(TESTS_BUILDDIR)/%.d: $(TESTS_SRCDIR)/%.c | $(TESTS_BUILDDIR)
+	$(RISCV_CC) $(TESTS_RISCV_CFLAGS) -MM -MT '$(TESTS_BUILDDIR)/$*.elf' $< > $@
+
+$(TESTS_BUILDDIR)/%.elf: $(TESTS_SRCDIR)/%.c $(SNRT_LIB) $(TESTS_BUILDDIR)/%.d | $(TESTS_BUILDDIR)
+	$(RISCV_CC) $(TESTS_RISCV_CFLAGS) $(TESTS_RISCV_LDFLAGS) $(TESTS_SRCDIR)/$*.c -o $@
+
+$(TESTS_BUILDDIR)/%.dump: $(TESTS_BUILDDIR)/%.elf | $(TESTS_BUILDDIR)
+	$(RISCV_OBJDUMP) $(RISCV_OBJDUMP_FLAGS) $< > $@
+
+$(TESTS_BUILDDIR)/%.dwarf: $(TESTS_BUILDDIR)/%.elf | $(TESTS_BUILDDIR)
+	$(RISCV_DWARFDUMP) $< > $@
+
+$(TEST_DEPS): | $(TARGET_C_HDRS)
+
+ifneq ($(MAKECMDGOALS),clean)
+ifneq ($(MAKECMDGOALS),clean-sw)
+-include $(TEST_DEPS)
+endif
+endif
diff --git a/target/snitch_cluster/sw/toolchain.mk b/target/snitch_cluster/sw/toolchain.mk
index a57f229d2..9cadb8c44 100644
--- a/target/snitch_cluster/sw/toolchain.mk
+++ b/target/snitch_cluster/sw/toolchain.mk
@@ -26,8 +26,7 @@ RISCV_OBJDUMP   ?= $(LLVM_BINROOT)/llvm-objdump
 RISCV_DWARFDUMP ?= $(LLVM_BINROOT)/llvm-dwarfdump
 
 # Compiler flags
-RISCV_CFLAGS += $(addprefix -I,$(INCDIRS))
-RISCV_CFLAGS += -mcpu=snitch
+RISCV_CFLAGS := -mcpu=snitch
 RISCV_CFLAGS += -menable-experimental-extensions
 RISCV_CFLAGS += -mabi=ilp32d
 RISCV_CFLAGS += -mcmodel=medany
@@ -47,13 +46,13 @@ RISCV_CFLAGS += -DOPENOCD_SEMIHOSTING
 endif
 
 # Linker flags
-RISCV_LDFLAGS += -fuse-ld=$(RISCV_LD)
+RISCV_LDFLAGS := -fuse-ld=$(RISCV_LD)
 RISCV_LDFLAGS += -nostartfiles
 RISCV_LDFLAGS += -lm
 
 # Archiver flags
-RISCV_ARFLAGS = rcs
+RISCV_ARFLAGS := rcs
 
 # Objdump flags
-RISCV_OBJDUMP_FLAGS += --mcpu=snitch
+RISCV_OBJDUMP_FLAGS := --mcpu=snitch
 RISCV_OBJDUMP_FLAGS += -D
diff --git a/target/snitch_cluster/util/build.py b/target/snitch_cluster/util/build.py
index 11fe5cb95..f8a084ac9 100755
--- a/target/snitch_cluster/util/build.py
+++ b/target/snitch_cluster/util/build.py
@@ -13,15 +13,14 @@
 It assumes a build system with a specific interface which most existing
 kernels comply with. In particular, it assumes the following:
 
-- the data generation can be configured through a YAML file. The path to
-this file is provided to the build system in the `DATA_CFG` environment
-variable.
-- the generated data is written to a header file at the path specified by
-the `DATA_H` environment variable.
-- all build artifacts are created in the directory specified by the
-`APP_BUILDDIR` environment variable.
 - the build command should be a make target defined by the Snitch cluster
 target.
+- the data generation can be configured through a JSON file. The path to
+this file is provided to the build system in the `$(APP)_DATA_CFG`
+environment variable, where `$(APP)` coincides with the build command
+name.
+- all build artifacts are created in the directory specified by the
+`$(APP)_BUILD_DIR` environment variable.
 
 This utility takes a list of data configuration files as input and builds
 the application with the data generated from each configuration. Build
@@ -59,21 +58,20 @@ def parser():
     return parser
 
 
-def extend_environment(env=None, **kwargs):
+def extend_environment(vars, env=None):
     if env is None:
         env = os.environ.copy()
-    env.update(kwargs)
+    env.update(vars)
     return env
 
 
 # Build software target with a specific data configuration
 def build(target, cfg):
     # Define configuration-specific variables for build system
-    env = extend_environment(
-        DATA_CFG=cfg,
-        DATA_H=Path(f'include/{cfg.stem}/data.h').resolve(),
-        APP_BUILDDIR=Path(f'build/{cfg.stem}').resolve()
-    )
+    env = extend_environment({
+        f'{target}_DATA_CFG': cfg,
+        f'{target}_BUILD_DIR': Path(f'build/{cfg.stem}').resolve()
+    })
 
     # Build the software
     mk_dir = Path(__file__).resolve().parent.parent