diff --git a/hw/fpga/constraints/pynq-z2/constraints.xdc b/hw/fpga/constraints/pynq-z2/constraints.xdc
index ed3a6e89a..38e2f6b39 100644
--- a/hw/fpga/constraints/pynq-z2/constraints.xdc
+++ b/hw/fpga/constraints/pynq-z2/constraints.xdc
@@ -1 +1 @@
-create_clock -add -name sys_clk_pin -period 10.00 -waveform {0 5} [get_ports {clk_i}];
+create_clock -add -name sys_clk_pin -period 8.00 -waveform {0 5} [get_ports {clk_i}];
diff --git a/sw/CMakeLists.txt b/sw/CMakeLists.txt
index 9639d6cfc..ef5743c66 100644
--- a/sw/CMakeLists.txt
+++ b/sw/CMakeLists.txt
@@ -63,19 +63,19 @@ FILE(GLOB_RECURSE new_list FOLLOW_SYMLINKS ${SOURCE_PATH}*.h)
 SET(dir_list_str "")
 FOREACH(file_path ${new_list})
   SET(add 0) # This variable is set to 1 if the file_pth needs to be added to the list
-  if(${file_path} MATCHES "${ROOT_PROJECT}device/")
-    if(${file_path} MATCHES "${ROOT_PROJECT}device/target/") # Add it if its not in target, or if its in target/${TARGET}
-      if(${file_path} MATCHES "${ROOT_PROJECT}device/target/${TARGET}")
+  if(${file_path} MATCHES "${SOURCE_PATH}device/")
+    if(${file_path} MATCHES "${SOURCE_PATH}device/target/") # Add it if its not in target, or if its in target/${TARGET}
+      if(${file_path} MATCHES "${SOURCE_PATH}device/target/${TARGET}")
         SET(add 1)
       endif()
     else()
       SET(add 1)
     endif()
-  elseif(${file_path} MATCHES ${PROJECT})
+  elseif(${file_path} MATCHES ${SOURCE_PATH}applications/${PROJECT}/)
     SET(add 1)
-  elseif( ( ${file_path} MATCHES "${ROOT_PROJECT}freertos/" ) AND ( ${PROJECT} MATCHES "freertos" ) )
+  elseif( ( ${file_path} MATCHES "${SOURCE_PATH}freertos/" ) AND ( ${PROJECT} MATCHES "freertos" ) )
     SET(add 1)
-  elseif( ${file_path} MATCHES "${ROOT_PROJECT}external/" )
+  elseif( ${file_path} MATCHES "${SOURCE_PATH}external/" )
     SET(add 1)
   endif()
 
@@ -124,14 +124,14 @@ SET( c_dir_list "" )
 SET( app_found 0 )
 FOREACH(file_path IN LISTS new_list)
   SET(add 0) # This variable is set to 1 if the file_pth needs to be added to the list
-  if(${file_path} MATCHES "${ROOT_PROJECT}device/")
+  if(${file_path} MATCHES "${SOURCE_PATH}device/")
     SET(add 1)
-  elseif( ${file_path} MATCHES "${ROOT_PROJECT}external/" )
+  elseif( ${file_path} MATCHES "${SOURCE_PATH}external/" )
     SET(add 1)
-  elseif( ( ${file_path} MATCHES "/${PROJECT}/" ) AND ( NOT ${file_path} MATCHES ${MAINFILE} ) )
-    SET(add 1)
-    elseif( ( ${file_path} MATCHES "/${PROJECT}/" ) AND ( ${file_path} MATCHES ${MAINFILE} ) )
+  elseif( ${file_path} MATCHES "${SOURCE_PATH}applications/${PROJECT}/.*${MAINFILE}\." ) # look for main.*
     SET(app_found 1)
+  elseif( ${file_path} MATCHES "${SOURCE_PATH}applications/${PROJECT}/" ) # other sources
+    SET(add 1)
   endif()
 
   if( add EQUAL 1 ) # If the file path mathced one of the criterion, add it to the list
@@ -155,7 +155,7 @@ if( app_found EQUAL 0 )
     SET(add 0) # This variable is set to 1 if the file_pth needs to be added to the list
     if(${file_path} MATCHES "${ROOT_PROJECT}device/")
       SET(add 1)
-    elseif( ( ${file_path} MATCHES "/${PROJECT}/" ) AND ( NOT ${file_path} MATCHES ${MAINFILE} ) )
+    elseif( ( ${file_path} MATCHES "${ROOT_PROJECT}/applications/${PROJECT}/" ) AND ( NOT ${file_path} MATCHES "${ROOT_PROJECT}applications/${PROJECT}/.*${MAINFILE}\." ) )
       SET(add 1)
     endif()