diff --git a/CMakeLists.txt b/CMakeLists.txt
index e676292..c039682 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -29,18 +29,18 @@ endif()
 add_subdirectory(softfloat)
 
 # library files
-FILE(GLOB TGC_SOURCES    ${CMAKE_CURRENT_SOURCE_DIR}/src/iss/*.cpp) 
+FILE(GLOB TGC_SOURCES    ${CMAKE_CURRENT_SOURCE_DIR}/src/iss/arch/*.cpp) 
 FILE(GLOB TGC_VM_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/src/vm/interp/vm_*.cpp)
 
 set(LIB_SOURCES 
     src/vm/fp_functions.cpp
-    src/plugin/instruction_count.cpp
+    src/iss/plugin/instruction_count.cpp
     
     ${TGC_SOURCES}
     ${TGC_VM_SOURCES}
 )
 if(TARGET RapidJSON)
-    list(APPEND LIB_SOURCES src/plugin/cycle_estimate.cpp src/plugin/pctrace.cpp)
+    list(APPEND LIB_SOURCES src/iss/plugin/cycle_estimate.cpp src/iss/plugin/pctrace.cpp)
 endif()
 
 if(WITH_LLVM)
@@ -69,7 +69,7 @@ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
     target_compile_options(${PROJECT_NAME} PRIVATE /wd4293)
 endif()
-target_include_directories(${PROJECT_NAME} PUBLIC incl)
+target_include_directories(${PROJECT_NAME} PUBLIC src)
 target_link_libraries(${PROJECT_NAME} PUBLIC softfloat scc-util jsoncpp Boost::coroutine)
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     target_link_libraries(${PROJECT_NAME} PUBLIC -Wl,--whole-archive dbt-rise-core -Wl,--no-whole-archive)
diff --git a/incl/iss/arch/.gitignore b/src/iss/arch/.gitignore
similarity index 100%
rename from incl/iss/arch/.gitignore
rename to src/iss/arch/.gitignore
diff --git a/incl/iss/arch/hwl.h b/src/iss/arch/hwl.h
similarity index 100%
rename from incl/iss/arch/hwl.h
rename to src/iss/arch/hwl.h
diff --git a/incl/iss/arch/riscv_hart_common.h b/src/iss/arch/riscv_hart_common.h
similarity index 100%
rename from incl/iss/arch/riscv_hart_common.h
rename to src/iss/arch/riscv_hart_common.h
diff --git a/incl/iss/arch/riscv_hart_m_p.h b/src/iss/arch/riscv_hart_m_p.h
similarity index 100%
rename from incl/iss/arch/riscv_hart_m_p.h
rename to src/iss/arch/riscv_hart_m_p.h
diff --git a/incl/iss/arch/riscv_hart_msu_vp.h b/src/iss/arch/riscv_hart_msu_vp.h
similarity index 100%
rename from incl/iss/arch/riscv_hart_msu_vp.h
rename to src/iss/arch/riscv_hart_msu_vp.h
diff --git a/incl/iss/arch/riscv_hart_mu_p.h b/src/iss/arch/riscv_hart_mu_p.h
similarity index 100%
rename from incl/iss/arch/riscv_hart_mu_p.h
rename to src/iss/arch/riscv_hart_mu_p.h
diff --git a/src/iss/tgc_c.cpp b/src/iss/arch/tgc_c.cpp
similarity index 99%
rename from src/iss/tgc_c.cpp
rename to src/iss/arch/tgc_c.cpp
index 35a27d0..a014ac7 100644
--- a/src/iss/tgc_c.cpp
+++ b/src/iss/arch/tgc_c.cpp
@@ -32,7 +32,7 @@
 
 #include "util/ities.h"
 #include <util/logging.h>
-#include <iss/arch/tgc_c.h>
+#include "tgc_c.h"
 #include <cstdio>
 #include <cstring>
 #include <fstream>
diff --git a/incl/iss/arch/tgc_c.h b/src/iss/arch/tgc_c.h
similarity index 100%
rename from incl/iss/arch/tgc_c.h
rename to src/iss/arch/tgc_c.h
diff --git a/incl/iss/arch/tgc_mapper.h b/src/iss/arch/tgc_mapper.h
similarity index 100%
rename from incl/iss/arch/tgc_mapper.h
rename to src/iss/arch/tgc_mapper.h
diff --git a/incl/iss/debugger/riscv_target_adapter.h b/src/iss/debugger/riscv_target_adapter.h
similarity index 100%
rename from incl/iss/debugger/riscv_target_adapter.h
rename to src/iss/debugger/riscv_target_adapter.h
diff --git a/incl/iss/factory.h b/src/iss/factory.h
similarity index 100%
rename from incl/iss/factory.h
rename to src/iss/factory.h
diff --git a/src/plugin/cycle_estimate.cpp b/src/iss/plugin/cycle_estimate.cpp
similarity index 97%
rename from src/plugin/cycle_estimate.cpp
rename to src/iss/plugin/cycle_estimate.cpp
index 553a772..3174f30 100644
--- a/src/plugin/cycle_estimate.cpp
+++ b/src/iss/plugin/cycle_estimate.cpp
@@ -32,14 +32,14 @@
  *       eyck@minres.com - initial API and implementation
  ******************************************************************************/
 
-#include "iss/plugin/cycle_estimate.h"
+#include "cycle_estimate.h"
 
 #include <iss/arch_if.h>
 #include <util/logging.h>
 #include <rapidjson/document.h>
 #include <rapidjson/istreamwrapper.h>
-#include "rapidjson/writer.h"
-#include "rapidjson/stringbuffer.h"
+#include <rapidjson/writer.h>
+#include <rapidjson/stringbuffer.h>
 #include <rapidjson/ostreamwrapper.h>
 #include <rapidjson/error/en.h>
 #include <fstream>
diff --git a/incl/iss/plugin/cycle_estimate.h b/src/iss/plugin/cycle_estimate.h
similarity index 100%
rename from incl/iss/plugin/cycle_estimate.h
rename to src/iss/plugin/cycle_estimate.h
diff --git a/src/plugin/instruction_count.cpp b/src/iss/plugin/instruction_count.cpp
similarity index 97%
rename from src/plugin/instruction_count.cpp
rename to src/iss/plugin/instruction_count.cpp
index aba30eb..0b54e21 100644
--- a/src/plugin/instruction_count.cpp
+++ b/src/iss/plugin/instruction_count.cpp
@@ -32,8 +32,8 @@
  *       eyck@minres.com - initial API and implementation
  ******************************************************************************/
 
-#include "iss/plugin/instruction_count.h"
-#include "iss/instrumentation_if.h"
+#include "instruction_count.h"
+#include <iss/instrumentation_if.h>
 
 #include <iss/arch_if.h>
 #include <util/logging.h>
diff --git a/incl/iss/plugin/instruction_count.h b/src/iss/plugin/instruction_count.h
similarity index 100%
rename from incl/iss/plugin/instruction_count.h
rename to src/iss/plugin/instruction_count.h
diff --git a/src/plugin/pctrace.cpp b/src/iss/plugin/pctrace.cpp
similarity index 98%
rename from src/plugin/pctrace.cpp
rename to src/iss/plugin/pctrace.cpp
index d3d099b..7f25652 100644
--- a/src/plugin/pctrace.cpp
+++ b/src/iss/plugin/pctrace.cpp
@@ -1,11 +1,11 @@
 #include <iss/arch_if.h>
-#include <iss/plugin/pctrace.h>
+#include "pctrace.h"
 #include <util/logging.h>
 #include <util/ities.h>
 #include <rapidjson/document.h>
 #include <rapidjson/istreamwrapper.h>
-#include "rapidjson/writer.h"
-#include "rapidjson/stringbuffer.h"
+#include <rapidjson/writer.h>
+#include <rapidjson/stringbuffer.h>
 #include <rapidjson/ostreamwrapper.h>
 #include <rapidjson/error/en.h>
 #include <fstream>
diff --git a/incl/iss/plugin/pctrace.h b/src/iss/plugin/pctrace.h
similarity index 100%
rename from incl/iss/plugin/pctrace.h
rename to src/iss/plugin/pctrace.h
diff --git a/src/main.cpp b/src/main.cpp
index d8d6bd6..0d4fe2f 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -35,14 +35,14 @@
 
 #include <boost/lexical_cast.hpp>
 #include <boost/program_options.hpp>
-#include <iss/arch/tgc_mapper.h>
+#include "iss/arch/tgc_mapper.h"
 #ifdef WITH_LLVM
 #include <iss/llvm/jit_helper.h>
 #endif
 #include <iss/log_categories.h>
-#include <iss/plugin/cycle_estimate.h>
-#include <iss/plugin/instruction_count.h>
-#include <iss/plugin/pctrace.h>
+#include "iss/plugin/cycle_estimate.h"
+#include "iss/plugin/instruction_count.h"
+#include "iss/plugin/pctrace.h"
 #include <iss/plugin/loader.h>
 #if defined(HAS_LUA)
 #include <iss/plugin/lua.h>
diff --git a/src/sysc/core_complex.cpp b/src/sysc/core_complex.cpp
index 53ff0cb..118767e 100644
--- a/src/sysc/core_complex.cpp
+++ b/src/sysc/core_complex.cpp
@@ -38,7 +38,7 @@
 #include <iss/iss.h>
 #include <iss/vm_types.h>
 #include <iss/plugin/loader.h>
-#include <sysc/core_complex.h>
+#include "core_complex.h"
 #include <iss/arch/tgc_mapper.h>
 #include <scc/report.h>
 #include <util/ities.h>
diff --git a/incl/sysc/core_complex.h b/src/sysc/core_complex.h
similarity index 100%
rename from incl/sysc/core_complex.h
rename to src/sysc/core_complex.h