diff --git a/Cura/skeinforge_application/alterations/end.gcode b/Cura/alterations/end.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/end.gcode
rename to Cura/alterations/end.gcode
diff --git a/Cura/skeinforge_application/alterations/example_cool_end.gcode b/Cura/alterations/example_cool_end.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_cool_end.gcode
rename to Cura/alterations/example_cool_end.gcode
diff --git a/Cura/skeinforge_application/alterations/example_cool_start.gcode b/Cura/alterations/example_cool_start.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_cool_start.gcode
rename to Cura/alterations/example_cool_start.gcode
diff --git a/Cura/skeinforge_application/alterations/example_end.gcode b/Cura/alterations/example_end.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_end.gcode
rename to Cura/alterations/example_end.gcode
diff --git a/Cura/skeinforge_application/alterations/example_home.gcode b/Cura/alterations/example_home.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_home.gcode
rename to Cura/alterations/example_home.gcode
diff --git a/Cura/skeinforge_application/alterations/example_replace.csv b/Cura/alterations/example_replace.csv
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_replace.csv
rename to Cura/alterations/example_replace.csv
diff --git a/Cura/skeinforge_application/alterations/example_replace_M108.csv b/Cura/alterations/example_replace_M108.csv
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_replace_M108.csv
rename to Cura/alterations/example_replace_M108.csv
diff --git a/Cura/skeinforge_application/alterations/example_start.gcode b/Cura/alterations/example_start.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_start.gcode
rename to Cura/alterations/example_start.gcode
diff --git a/Cura/skeinforge_application/alterations/example_support_end.gcode b/Cura/alterations/example_support_end.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_support_end.gcode
rename to Cura/alterations/example_support_end.gcode
diff --git a/Cura/skeinforge_application/alterations/example_support_start.gcode b/Cura/alterations/example_support_start.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/example_support_start.gcode
rename to Cura/alterations/example_support_start.gcode
diff --git a/Cura/skeinforge_application/alterations/start.gcode b/Cura/alterations/start.gcode
similarity index 100%
rename from Cura/skeinforge_application/alterations/start.gcode
rename to Cura/alterations/start.gcode
diff --git a/Cura/fabmetheus_utilities/settings.py b/Cura/fabmetheus_utilities/settings.py
index d9573c3..567b5a8 100644
--- a/Cura/fabmetheus_utilities/settings.py
+++ b/Cura/fabmetheus_utilities/settings.py
@@ -105,7 +105,7 @@ def getProfileInformation():
 		},'inset': {
 			'Add_Custom_Code_for_Temperature_Reading': DEFSET,
 			'Infill_in_Direction_of_Bridge': "True",
-			'Infill_Width': getProfileSetting("nozzle_size"),
+			'Infill_Width': storedSetting("nozzle_size"),
 			'Loop_Order_Choice': DEFSET,
 			'Overlap_Removal_Width_over_Perimeter_Width_ratio': DEFSET,
 			'Turn_Extruder_Heater_Off_at_Shut_Down': DEFSET,
@@ -133,7 +133,7 @@ def getProfileInformation():
 			'Line': ifSettingIs('infill_type', 'Line'),
 			'Infill_Perimeter_Overlap_ratio': storedPercentSetting('fill_overlap'),
 			'Infill_Solidity_ratio': storedPercentSetting('fill_density'),
-			'Infill_Width': getProfileSetting("nozzle_size"),
+			'Infill_Width': storedSetting("nozzle_size"),
 			'Sharpest_Angle_degrees': DEFSET,
 			'Solid_Surface_Thickness_layers': calculateSolidLayerCount,
 			'Start_From_Choice': DEFSET,
@@ -410,27 +410,8 @@ def getAlterationFileLines(fileName):
 def getAlterationLines(fileName):
 	return archive.getTextLines(getAlterationFile(fileName))
 
-def getAlterationFile(fileName, allowMagicPrefix = True):
-	"Get the file from the fileName or the lowercase fileName in the alterations directories."
-	#print ('getAlterationFile:', fileName)
-	prefix = ''
-	if allowMagicPrefix:
-		if fileName == 'start.gcode':
-			#For the start code, hack the temperature and the steps per E value into it. So the temperature is reached before the start code extrusion.
-			#We also set our steps per E here, if configured.
-			eSteps = float(profile.getPreference('steps_per_e'))
-			if eSteps > 0:
-				prefix += 'M92 E'+str(eSteps)+'\n'
-			temp = float(profile.getProfileSetting('print_temperature'))
-			if temp > 0:
-				prefix += 'M109 S'+str(temp)+'\n'
-		elif fileName == 'replace.csv':
-			prefix = 'M101\nM103\n'
-	alterationsDirectory = archive.getSkeinforgePath('alterations')
-	fullFilename = os.path.join(alterationsDirectory, fileName)
-	if os.path.isfile(fullFilename):
-		return prefix + archive.getFileText( fullFilename )
-	return prefix
+def getAlterationFile(fileName):
+	return profile.getAlterationFileContents(fileName)
 
 ####################################
 ## Configuration settings classes ##
diff --git a/Cura/newui/alterationPanel.py b/Cura/newui/alterationPanel.py
index 453cdd4..c25a1dd 100644
--- a/Cura/newui/alterationPanel.py
+++ b/Cura/newui/alterationPanel.py
@@ -1,14 +1,13 @@
 import wx
 import sys,math,threading,os
 
-from fabmetheus_utilities import settings
-from fabmetheus_utilities import archive
+from newui import profile
 
 class alterationPanel(wx.Panel):
 	def __init__(self, parent):
 		wx.Panel.__init__(self, parent,-1)
 
-		self.alterationFileList = ['start.gcode', 'end.gcode', 'cool_start.gcode', 'cool_end.gcode']
+		self.alterationFileList = ['start.gcode', 'end.gcode', 'cool_start.gcode', 'cool_end.gcode', 'replace.csv']
 		self.currentFile = None
 
 		self.textArea = wx.TextCtrl(self, style=wx.TE_MULTILINE|wx.TE_DONTWRAP|wx.TE_PROCESS_TAB)
@@ -32,11 +31,11 @@ class alterationPanel(wx.Panel):
 		self.currentFile = self.list.GetSelection()
 
 	def loadFile(self, filename):
-		self.textArea.SetValue(unicode(settings.getAlterationFile(filename, False), "utf-8"))
+		self.textArea.SetValue(unicode(profile.getAlterationFileContents(filename, False), "utf-8"))
 
 	def OnFocusLost(self, e):
 		if self.currentFile == self.list.GetSelection():
-			filename = os.path.join(archive.getSkeinforgePath('alterations'), self.alterationFileList[self.list.GetSelection()])
+			filename = profile.getAlterationFilePath(self.alterationFileList[self.list.GetSelection()])
 			f = open(filename, "wb")
 			f.write(self.textArea.GetValue().encode("utf-8"))
 			f.close()
diff --git a/Cura/newui/gcodeInterpreter.py b/Cura/newui/gcodeInterpreter.py
index 5424cfe..334d475 100644
--- a/Cura/newui/gcodeInterpreter.py
+++ b/Cura/newui/gcodeInterpreter.py
@@ -54,7 +54,9 @@ class gcode():
 				pathType = line[6:].strip()
 				if pathType != "CUSTOM":
 					startCodeDone = True
+					
 			if ';' in line:
+				#Slic3r GCode comment parser
 				comment = line[line.find(';')+1:].strip()
 				if comment == 'fill':
 					pathType = 'FILL'
@@ -65,6 +67,7 @@ class gcode():
 				if pathType != "CUSTOM":
 					startCodeDone = True
 				line = line[0:line.find(';')]
+			
 			G = self.getCodeInt(line, 'G')
 			if G is not None:
 				if G == 0 or G == 1:	#Move
diff --git a/Cura/newui/profile.py b/Cura/newui/profile.py
index 96e56ad..d523962 100644
--- a/Cura/newui/profile.py
+++ b/Cura/newui/profile.py
@@ -7,6 +7,10 @@ import os
 import traceback
 import math
 
+#########################################################
+## Profile and preferences functions
+#########################################################
+
 #Single place to store the defaults, so we have a consistent set of default settings.
 profileDefaultSettings = {
 	'nozzle_size': '0.4',
@@ -149,8 +153,9 @@ def putPreference(name, value):
 	globalPreferenceParser.set('preference', name, str(value))
 	globalPreferenceParser.write(open(getPreferencePath(), 'w'))
 
+#########################################################
 ## Utility functions to calculate common profile values
-
+#########################################################
 def calculateEdgeWidth():
 	wallThickness = float(getProfileSetting('wall_thickness'))
 	nozzleSize = float(getProfileSetting('nozzle_size'))
@@ -184,3 +189,35 @@ def calculateSolidLayerCount():
 	solidThickness = float(getProfileSetting('solid_layer_thickness'))
 	return int(math.ceil(solidThickness / layerHeight - 0.0001))
 
+#########################################################
+## Alteration file functions
+#########################################################
+def getCuraBasePath():
+	return os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
+
+def getAlterationFilePath(filename):
+	return os.path.join(getCuraBasePath(), "alterations", filename)
+
+def getAlterationFileContents(filename, allowMagicPrefix = True):
+	"Get the file from the fileName or the lowercase fileName in the alterations directories."
+	prefix = ''
+	if allowMagicPrefix:
+		if filename == 'start.gcode':
+			#For the start code, hack the temperature and the steps per E value into it. So the temperature is reached before the start code extrusion.
+			#We also set our steps per E here, if configured.
+			eSteps = float(getPreference('steps_per_e'))
+			if eSteps > 0:
+				prefix += 'M92 E'+str(eSteps)+'\n'
+			temp = float(getProfileSetting('print_temperature'))
+			if temp > 0:
+				prefix += 'M109 S'+str(temp)+'\n'
+		elif filename == 'replace.csv':
+			prefix = 'M101\nM103\n'
+	fullFilename = getAlterationFilePath(filename)
+	if os.path.isfile(fullFilename):
+		file = open(fullFilename, "r")
+		fileText = file.read()
+		file.close()
+		return prefix + fileText
+	return prefix
+
diff --git a/Cura/newui/sliceRun.py b/Cura/newui/sliceRun.py
index b4d30dc..d81f4aa 100644
--- a/Cura/newui/sliceRun.py
+++ b/Cura/newui/sliceRun.py
@@ -91,8 +91,8 @@ def getSliceCommand(filename):
 			'--fill-angle', '45',
 			'--fill-pattern', 'rectilinear',
 			'--solid-fill-pattern', 'rectilinear',
-			'--start-gcode', '',
-			'--end-gcode', '',
+			'--start-gcode', profile.getAlterationFilePath('start.gcode'),
+			'--end-gcode', profile.getAlterationFilePath('end.gcode'),
 			'--retract-length', profile.getProfileSetting('retraction_amount'),
 			'--retract-speed', str(int(float(profile.getProfileSetting('retraction_speed')))),
 			'--retract-restart-extra', profile.getProfileSetting('retraction_extra'),