diff --git a/bin/irpf90 b/bin/irpf90
index e537e26..d9d2360 120000
--- a/bin/irpf90
+++ b/bin/irpf90
@@ -1 +1 @@
-../src/irpf90.exe
\ No newline at end of file
+../src/irpf90_python.exe
\ No newline at end of file
diff --git a/example/Makefile b/example/Makefile
index 0a69231..2b8aa7f 100644
--- a/example/Makefile
+++ b/example/Makefile
@@ -1,4 +1,4 @@
-IRPF90 = ~/irpf90/bin/irpf90  -a -d
+IRPF90 = python ../src/irpf90.py -I input -a -d
 FC     = gfortran
 FCFLAGS= -O2
 
diff --git a/man/man1/irpf90.1.gz b/man/man1/irpf90.1.gz
index ebc370e..c4212e3 100644
Binary files a/man/man1/irpf90.1.gz and b/man/man1/irpf90.1.gz differ
diff --git a/src/command_line.py b/src/command_line.py
index 11facfa..4524ecf 100644
--- a/src/command_line.py
+++ b/src/command_line.py
@@ -73,6 +73,8 @@ class CommandLine(object):
       self._include_dir = []
       for o,a in self.opts:
         if o in [ "-I", '--'+options['I'][0] ]:
+          if a[-1] != '/':
+            a = a+'/'
           self._include_dir.append(a)
     return self._include_dir
   include_dir = property(fget=include_dir)
diff --git a/src/init.py b/src/init.py
index ceb4719..4fd25d1 100644
--- a/src/init.py
+++ b/src/init.py
@@ -30,6 +30,7 @@ import os
 import util
 import makefile
 import irpf90_t
+from command_line import command_line
 
 initialized = False
 
@@ -49,26 +50,34 @@ def init():
     except OSError:
       os.mkdir(dir)
 
+  for dir in command_line.include_dir:
+    dir = irpf90_t.irpdir+dir
+    try:
+      wd = os.getcwd()
+      os.chdir(dir)
+      os.chdir(wd)
+    except OSError:
+      os.mkdir(dir)
+
   # Create makefile
   makefile.create()
   
   # Copy current files in the irpdir
-  for filename in os.listdir(os.getcwd()):
-    if not filename[0].startswith(".") and not os.path.isdir(filename):
-      try:
-        file  = open(filename,"r")
-      except IOError:
-        print "Warning : Unable to read file %s."%(filename)
-      else:
-        buffer = file.readlines()
-        file.close()
-        if not util.same_file(irpf90_t.irpdir+filename,buffer):
+  for dir in ['./']+command_line.include_dir:
+    for filename in os.listdir(dir):
+      filename = dir+filename
+      if not filename[0].startswith(".") and not os.path.isdir(filename):
+        try:
           file  = open(filename,"r")
+        except IOError:
+          print "Warning : Unable to read file %s."%(filename)
+        else:
           buffer = file.read()
           file.close()
-          file = open(irpf90_t.irpdir+filename,"w")
-          file.write(buffer)
-          file.close()
+          if not util.same_file(irpf90_t.irpdir+filename,buffer):
+            file = open(irpf90_t.irpdir+filename,"w")
+            file.write(buffer)
+            file.close()
 
   initialized = True
 
diff --git a/src/irpf90_t.py b/src/irpf90_t.py
index 6aaa30a..1068ada 100644
--- a/src/irpf90_t.py
+++ b/src/irpf90_t.py
@@ -350,10 +350,9 @@ def create_irpf90_files():
     return filename.endswith(".irp.f") and not filename.startswith('.')
   result = filter ( is_irpf90_file, os.listdir(os.getcwd()) )
   for dir in command_line.include_dir:
-    result += map(lambda x: dir+'/'+x, filter ( is_irpf90_file, os.listdir(dir) ) )
+    result += map(lambda x: dir+x, filter ( is_irpf90_file, os.listdir(dir) ) )
   return result
 irpf90_files = create_irpf90_files()
-print irpf90_files
 
 
 
diff --git a/src/makefile.py b/src/makefile.py
index 9cf2858..03ea7fd 100644
--- a/src/makefile.py
+++ b/src/makefile.py
@@ -68,26 +68,30 @@ def run():
       mod.append(m)
 
     file = open('irpf90.make','w')
-
-    result = "SRC += %sirp_stack.irp.F90"%(irpdir)
+    result = ""
+    result += "FC+=-I %s "%(irpdir)
+    for i in command_line.include_dir:
+       result += "-I %s%s "%(irpdir,i)
+    result += "\n"
+    result += "SRC += %sirp_stack.irp.F90"%(irpdir)
     result += " %sirp_touches.irp.F90"%(irpdir)
     if command_line.do_openmp:
       result += " %sirp_locks.irp.F90"%(irpdir)
     if command_line.do_profile:
       result += " %sirp_profile.irp.F90"%(irpdir)
     for m in mod:
-      result += " %s%s.irp.F90"%(irpdir,m.name[:-4])
-      result += " %s%s.irp.module.F90"%(irpdir,m.name[:-4])
+      result += " %s%s.irp.F90"%(irpdir,m.filename)
+      result += " %s%s.irp.module.F90"%(irpdir,m.filename)
     print >>file, result
 
     result = "OBJ += %sirp_stack.irp.o"%(irpdir)
     for m in mod:
       if not m.is_main:
-        result += " %s%s.irp.o"%(irpdir,m.name[:-4])
-        result += " %s%s.irp.module.o"%(irpdir,m.name[:-4])
+        result += " %s%s.irp.o"%(irpdir,m.filename)
+        result += " %s%s.irp.module.o"%(irpdir,m.filename)
     print >>file, result
 
-    print >>file, "OBJ1 = $(patsubst %%, %s%%,$(notdir $(OBJ))) %sirp_touches.irp.o"%(irpdir,irpdir),
+    print >>file, "OBJ1 = $(OBJ) %sirp_touches.irp.o"%(irpdir),
     if command_line.do_profile:
       print >>file, " %sirp_profile.irp.o"%(irpdir), " irp_rdtsc.o",
     if command_line.do_openmp:
@@ -106,14 +110,14 @@ def run():
     print >>file, "ifdef USE_IRPF90_A"
     for m in mod:
       if m.is_main:
-        exe = m.name[:-4]
+        exe = m.filename
         print >>file, "%s: %s%s.irp.o %s%s.irp.module.o irpf90.a"%(exe,irpdir,exe,irpdir,exe)
         print >>file, "\t$(FC) -o $@ %s$@.irp.o %s$@.irp.module.o irpf90.a $(LIB)"%(irpdir,irpdir)
         print >>file, "\t@$(MAKE) -s move"
     print >>file, "else"
     for m in mod:
       if m.is_main:
-        exe = m.name[:-4]
+        exe = m.filename
         print >>file, "%s: %s%s.irp.o %s%s.irp.module.o $(OBJ1)"%(exe,irpdir,exe,irpdir,exe)
         print >>file, "\t$(FC) -o $@ %s$@.irp.o %s$@.irp.module.o $(OBJ1) $(LIB)"%(irpdir,irpdir)
         print >>file, "\t@$(MAKE) -s move"
@@ -121,14 +125,16 @@ def run():
 
     buffer = ""
     for m in mod:
-      filename = "%s%s.irp.o: %s%s.irp.module.o"%(irpdir,m.name[:-4],irpdir,m.name[:-4])
-      mds = map (lambda x: " %s%s.irp.module.o"%(irpdir,x[:-4]),m.needed_modules)
+      filename = "%s%s.irp.o: %s%s.irp.module.o"%(irpdir,m.filename,irpdir,m.filename)
+      needed_modules = filter( lambda x: modules[x].name in m.needed_modules, modules )
+      needed_files = map(lambda x: modules[x].filename, needed_modules)
+      mds = map (lambda x: " %s%s.irp.module.o"%(irpdir,x),needed_files)
       print >>file, filename," ".join(mds)," ".join(m.includes)
       if not m.is_main:
         buffer += "\t - @echo '"+filename+" ".join(mds)+"' >> %sdist_Makefile\n"%(irpdir)
     print >>file, "%sirp_touches.irp.o:"%(irpdir),
     mds = filter(lambda x: not x.is_main,mod)
-    mds = map(lambda x: " %s%s.irp.o %s%s.irp.o"%(irpdir,x.name[:-4],irpdir,x.name[:-4]),mds)
+    mds = map(lambda x: " %s%s.irp.o %s%s.irp.o"%(irpdir,x.filename,irpdir,x.filename),mds)
     print >>file," ".join(mds)
     if command_line.do_profile:
       print >>file, "%sirp_profile.irp.o:"%(irpdir),
@@ -165,18 +171,19 @@ def run():
 #   print >>file, "\t- @cp %s$*.irp.F90 dist/$*/| DO_NOTHING="%(irpdir)
 #   print >>file, "\t- cd dist ; tar -zcvf ../$*.tar.gz $*\n"
 
-    print >>file, irpdir+"%.irp.module.o: "+irpdir+"%.irp.module.F90"
-    print >>file, "\t$(FC) $(FCFLAGS) -c "+irpdir+"$*.irp.module.F90 -o "+irpdir+"$*.irp.module.o"
-    print >>file, irpdir+"%.irp.o: "+irpdir+"%.irp.module.o "+irpdir+"%.irp.F90"
-    print >>file, "\t$(FC) $(FCFLAGS) -c "+irpdir+"$*.irp.F90 -o "+irpdir+"$*.irp.o"
-    print >>file, irpdir+"%.irp.o: "+irpdir+"%.irp.F90"
-    print >>file, "\t$(FC) $(FCFLAGS) -c "+irpdir+"$*.irp.F90 -o "+irpdir+"$*.irp.o"
-    print >>file, irpdir+"%.o: %.F90"
-    print >>file, "\t$(FC) $(FCFLAGS) -c $*.F90 -o "+irpdir+"$*.o"
-    print >>file, irpdir+"%.o: %.f90\n\t$(FC) $(FCFLAGS) -c $*.f90 -o "+irpdir+"$*.o"
-    print >>file, irpdir+"%.o: %.f\n\t$(FC) $(FCFLAGS) -c $*.f -o "+irpdir+"$*.o"
-    print >>file, irpdir+"%.o: %.F\n\t$(FC) $(FCFLAGS) -c $*.F -o "+irpdir+"$*.o"
-    print >>file, irpdir+"%.irp.F90: irpf90.make\n"
+    for dir in [ irpdir ] + map(lambda x: irpdir+x, command_line.include_dir):
+      print >>file, dir+"%.irp.module.o: "+dir+"%.irp.module.F90"
+      print >>file, "\t$(FC) $(FCFLAGS) -c "+dir+"$*.irp.module.F90 -o "+dir+"$*.irp.module.o"
+      print >>file, dir+"%.irp.o: "+dir+"%.irp.module.o "+dir+"%.irp.F90"
+      print >>file, "\t$(FC) $(FCFLAGS) -c "+dir+"$*.irp.F90 -o "+dir+"$*.irp.o"
+      print >>file, dir+"%.irp.o: "+dir+"%.irp.F90"
+      print >>file, "\t$(FC) $(FCFLAGS) -c "+dir+"$*.irp.F90 -o "+dir+"$*.irp.o"
+      print >>file, dir+"%.o: %.F90"
+      print >>file, "\t$(FC) $(FCFLAGS) -c $*.F90 -o "+dir+"$*.o"
+      print >>file, dir+"%.o: %.f90\n\t$(FC) $(FCFLAGS) -c $*.f90 -o "+dir+"$*.o"
+      print >>file, dir+"%.o: %.f\n\t$(FC) $(FCFLAGS) -c $*.f -o "+dir+"$*.o"
+      print >>file, dir+"%.o: %.F\n\t$(FC) $(FCFLAGS) -c $*.F -o "+dir+"$*.o"
+      print >>file, dir+"%.irp.F90: irpf90.make\n"
     print >>file, "move:\n\t@mv -f *.mod IRPF90_temp/ 2> /dev/null | DO_NOTHING=\n"
     print >>file, "irpf90.a: $(OBJ1)\n\t$(AR) crf irpf90.a $(OBJ1)\n"
     print >>file, "clean:\n\trm -rf $(EXE) $(OBJ1) irpf90.a $(ALL_OBJ1) $(ALL)\n"
diff --git a/src/module.py b/src/module.py
index 0711ed4..4bb9f49 100644
--- a/src/module.py
+++ b/src/module.py
@@ -46,7 +46,8 @@ class Fmodule(object):
 
   def __init__(self,text,filename):
     self.text = put_info(text,filename)
-    self.name = "%s_mod"%(filename[:-6])
+    self.filename = filename[:-6]
+    self.name = "%s_mod"%(self.filename).replace('/','__')
 
   def is_main(self):
     if '_is_main' not in self.__dict__:
diff --git a/src/modules.py b/src/modules.py
index ec060a2..2974442 100644
--- a/src/modules.py
+++ b/src/modules.py
@@ -42,7 +42,7 @@ modules = create_modules()
 ######################################################################
 def write_module(m):
   # Module data
-  filename = irpdir+m.name[0:-4]+".irp.module.F90"
+  filename = irpdir+m.filename+".irp.module.F90"
   text = m.header + m.head 
   text = map(lambda x: "%s\n"%(x),text)
   if not same_file(filename,text):
@@ -52,7 +52,7 @@ def write_module(m):
     file.close()
 
   # Subroutines
-  filename = irpdir+m.name[0:-4]+".irp.F90"
+  filename = irpdir+m.filename+".irp.F90"
   text = m.header + m.generated_text + m.residual_text
   text = map(lambda x: "%s\n"%(x),text)
   if not same_file(filename,text):
diff --git a/src/preprocessed_text.py b/src/preprocessed_text.py
index 7e7ae4a..4941ea2 100644
--- a/src/preprocessed_text.py
+++ b/src/preprocessed_text.py
@@ -664,7 +664,11 @@ def change_includes(text):
      if len(txt) != 3:
        print txt
        error.fail(line,"Error in include statement")
-     filename = txt[1].strip()
+     directory = (("./"+line.filename).rsplit('/',1)[0]+'/')[2:]
+     if directory == "":
+        filename = txt[1].strip()
+     else:
+        filename = directory+txt[1].strip()
      try:
        file = open(filename,'r')
        file.close()
diff --git a/src/util.py b/src/util.py
index 54421e3..f5935d2 100644
--- a/src/util.py
+++ b/src/util.py
@@ -35,7 +35,10 @@ def lower(x):
 
 def same_file(filename,txt):
   assert isinstance(filename,str)
-  assert type(txt) == list
+  if (type(txt) == list):
+    buffer = ''.join(txt)
+  else:
+    buffer = txt
 
   try:
     file = open(filename,"r")
@@ -44,12 +47,10 @@ def same_file(filename,txt):
   stream = file.read()
   file.close()
 
-  buffer = ''.join(txt)
- 
   if len(stream) != len(buffer):
     return False
   if stream != buffer:
-      return False
+    return False
   return True
 
 def build_dim(dim):
diff --git a/src/variable.py b/src/variable.py
index f9eb512..817aba9 100644
--- a/src/variable.py
+++ b/src/variable.py
@@ -200,7 +200,7 @@ class Variable(object):
   ############################################################
   def fmodule(self):
     if '_fmodule' not in self.__dict__:
-      self._fmodule = self.line.filename[0].split('.irp.f')[0]+'_mod'
+      self._fmodule = self.line.filename[0].replace('/','__').split('.irp.f')[0]+'_mod'
     return self._fmodule
   fmodule = property(fmodule)
 
diff --git a/src/version.py b/src/version.py
index 26ccef1..253dc6a 100644
--- a/src/version.py
+++ b/src/version.py
@@ -1 +1 @@
-version = "1.2.22"
+version = "1.3.00"