diff --git a/IPython/core/displayhook.py b/IPython/core/displayhook.py
index 262fe7e..b0f83e3 100644
--- a/IPython/core/displayhook.py
+++ b/IPython/core/displayhook.py
@@ -250,7 +250,7 @@ class DisplayHook(Configurable):
     def log_output(self, result):
         """Log the output."""
         if self.shell.logger.log_output:
-            self.shell.logger.log_write(repr(result),'output')
+            self.shell.logger.log_write(repr(result), 'output')
 
     def finish_displayhook(self):
         """Finish up all displayhook activities."""
diff --git a/IPython/core/history.py b/IPython/core/history.py
index 9ee3dca..e013a6b 100644
--- a/IPython/core/history.py
+++ b/IPython/core/history.py
@@ -36,6 +36,7 @@ class HistoryManager(object):
     def __init__(self, shell):
         """Create a new history manager associated with a shell instance.
         """
+        # We need a pointer back to the shell for various tasks.
         self.shell = shell
         
         # List of input with multi-line handling.
@@ -64,6 +65,13 @@ class HistoryManager(object):
         # Objects related to shadow history management
         self._init_shadow_hist()
     
+        # Variables used to store the three last inputs from the user.  On each
+        # new history update, we populate the user's namespace with these,
+        # shifted as necessary.
+        self._i00, self._i, self._ii, self._iii = '','','',''
+
+        # Object is fully initialized, we can now call methods on it.
+        
         # Fill the history zero entry, user counter starts at 1
         self.store_inputs('\n', '\n')
 
@@ -158,8 +166,9 @@ class HistoryManager(object):
         return hist
 
     def store_inputs(self, source, source_raw=None):
-        """Store source and raw input in history.
-
+        """Store source and raw input in history and create input cache
+        variables _i*.
+        
         Parameters
         ----------
         source : str
@@ -175,6 +184,20 @@ class HistoryManager(object):
         self.input_hist_raw.append(source_raw)
         self.shadow_hist.add(source)
 
+        # update the auto _i variables
+        self._iii = self._ii
+        self._ii = self._i
+        self._i = self._i00
+        self._i00 = source_raw
+
+        # hackish access to user namespace to create _i1,_i2... dynamically
+        new_i = '_i%s' % self.shell.execution_count
+        to_main = {'_i': self._i,
+                   '_ii': self._ii,
+                   '_iii': self._iii,
+                   new_i : self._i00 }
+        self.shell.user_ns.update(to_main)
+
     def sync_inputs(self):
         """Ensure raw and translated histories have same length."""
         if len(self.input_hist) != len (self.input_hist_raw):
@@ -403,7 +426,7 @@ def rep_f(self, arg):
     try:
         lines = self.extract_input_slices(args, True)
         print("lines", lines)
-        self.runlines(lines)
+        self.run_cell(lines)
     except ValueError:
         print("Not found in recent history:", args)
         
diff --git a/IPython/core/interactiveshell.py b/IPython/core/interactiveshell.py
index 649c049..51c1112 100644
--- a/IPython/core/interactiveshell.py
+++ b/IPython/core/interactiveshell.py
@@ -430,11 +430,12 @@ class InteractiveShell(Configurable, Magic):
         self.dir_stack = []
 
     def init_logger(self):
-        self.logger = Logger(self, logfname='ipython_log.py', logmode='rotate')
-        # local shortcut, this is used a LOT
-        self.log = self.logger.log
+        self.logger = Logger(self.home_dir, logfname='ipython_log.py',
+                             logmode='rotate')
 
     def init_logstart(self):
+        """Initialize logging in case it was requested at the command line.
+        """
         if self.logappend:
             self.magic_logstart(self.logappend + ' append')
         elif self.logfile:
@@ -1839,7 +1840,6 @@ class InteractiveShell(Configurable, Magic):
         # code out there that may rely on this).
         self.prefilter = self.prefilter_manager.prefilter_lines
 
-
     def auto_rewrite_input(self, cmd):
         """Print to the screen the rewritten form of the user's command.
 
@@ -2026,12 +2026,11 @@ class InteractiveShell(Configurable, Magic):
         with prepended_to_syspath(dname):
             try:
                 with open(fname) as thefile:
-                    script = thefile.read()
-                    # self.runlines currently captures all exceptions
-                    # raise in user code.  It would be nice if there were
+                    # self.run_cell currently captures all exceptions
+                    # raised in user code.  It would be nice if there were
                     # versions of runlines, execfile that did raise, so
                     # we could catch the errors.
-                    self.runlines(script, clean=True)
+                    self.run_cell(thefile.read())
             except:
                 self.showtraceback()
                 warn('Unknown failure executing file: <%s>' % fname)
@@ -2099,6 +2098,7 @@ class InteractiveShell(Configurable, Magic):
         # Store raw and processed history
         self.history_manager.store_inputs(ipy_cell, cell)
 
+        self.logger.log(ipy_cell, cell)
         # dbg code!!!
         if 0:
             def myapp(self, val):  # dbg
diff --git a/IPython/core/macro.py b/IPython/core/macro.py
index 676e083..4a05180 100644
--- a/IPython/core/macro.py
+++ b/IPython/core/macro.py
@@ -20,9 +20,7 @@ class Macro(IPyAutocall):
     """
 
     def __init__(self,data):
-
-        # store the macro value, as a single string which can be evaluated by
-        # runlines()
+        # store the macro value, as a single string which can be executed
         self.value = ''.join(data).rstrip()+'\n'
         
     def __str__(self):
@@ -34,7 +32,7 @@ class Macro(IPyAutocall):
     def __call__(self,*args):
         IPython.utils.io.Term.cout.flush()
         self._ip.user_ns['_margv'] = args
-        self._ip.runlines(self.value)
+        self._ip.run_cell(self.value)
     
     def __getstate__(self):
         """ needed for safe pickling via %store """
diff --git a/IPython/core/magic.py b/IPython/core/magic.py
index 31ba558..c63b054 100644
--- a/IPython/core/magic.py
+++ b/IPython/core/magic.py
@@ -41,11 +41,6 @@ except ImportError:
     except ImportError:
         profile = pstats = None
 
-# print_function was added to __future__ in Python2.6, remove this when we drop
-# 2.5 compatibility
-if not hasattr(__future__,'CO_FUTURE_PRINT_FUNCTION'):
-    __future__.CO_FUTURE_PRINT_FUNCTION = 65536
-
 import IPython
 from IPython.core import debugger, oinspect
 from IPython.core.error import TryNext
@@ -2331,7 +2326,7 @@ Currently the magic system has the following functions:\n"""
         else:
             print 'done. Executing edited code...'
             if opts_r:
-                self.shell.runlines(file_read(filename))
+                self.shell.run_cell(file_read(filename))
             else:
                 self.shell.safe_execfile(filename,self.shell.user_ns,
                                          self.shell.user_ns)
@@ -2992,7 +2987,7 @@ Defaulting color scheme to 'NoColor'"""
                    (input.startswith(start) or input.startswith(start_magic)):
                 #print 'match',`input`  # dbg
                 print 'Executing:',input,
-                self.shell.runlines(input)
+                self.shell.run_cell(input)
                 return
         print 'No previous input matching `%s` found.' % start
 
diff --git a/IPython/core/prefilter.py b/IPython/core/prefilter.py
index e427091..5f36f94 100755
--- a/IPython/core/prefilter.py
+++ b/IPython/core/prefilter.py
@@ -373,10 +373,6 @@ class PrefilterManager(Configurable):
         # print "prefilter_line: ", line, continue_prompt
         # All handlers *must* return a value, even if it's blank ('').
 
-        # Lines are NOT logged here. Handlers should process the line as
-        # needed, update the cache AND log it (so that the input cache array
-        # stays synced).
-
         # save the line away in case we crash, so the post-mortem handler can
         # record it
         self.shell._last_input_line = line
@@ -792,7 +788,6 @@ class PrefilterHandler(Configurable):
             ):
             line = ''
 
-        self.shell.log(line, line, continue_prompt)
         return line
 
     def __str__(self):
@@ -811,7 +806,6 @@ class AliasHandler(PrefilterHandler):
         line_out = '%sget_ipython().system(%s)' % (line_info.pre_whitespace,
                                          make_quoted_expr(transformed))
         
-        self.shell.log(line_info.line, line_out, line_info.continue_prompt)
         return line_out
 
 
@@ -840,8 +834,6 @@ class ShellEscapeHandler(PrefilterHandler):
             cmd = line.lstrip().lstrip(ESC_SHELL)
             line_out = '%sget_ipython().system(%s)' % (line_info.pre_whitespace,
                                              make_quoted_expr(cmd))
-        # update cache/log and return
-        self.shell.log(line, line_out, line_info.continue_prompt)
         return line_out
 
 
@@ -856,7 +848,6 @@ class MagicHandler(PrefilterHandler):
         the_rest = line_info.the_rest
         cmd = '%sget_ipython().magic(%s)' % (line_info.pre_whitespace,
                                    make_quoted_expr(ifun + " " + the_rest))
-        self.shell.log(line_info.line, cmd, line_info.continue_prompt)
         return cmd
 
 
@@ -877,7 +868,6 @@ class AutoHandler(PrefilterHandler):
 
         # This should only be active for single-line input!
         if continue_prompt:
-            self.shell.log(line,line,continue_prompt)
             return line
 
         force_auto = isinstance(obj, IPyAutocall)
@@ -918,9 +908,6 @@ class AutoHandler(PrefilterHandler):
         if auto_rewrite:
             self.shell.auto_rewrite_input(newcmd)
             
-        # log what is now valid Python, not the actual user input (without the
-        # final newline)
-        self.shell.log(line,newcmd,continue_prompt)
         return newcmd
 
 
@@ -947,7 +934,6 @@ class HelpHandler(PrefilterHandler):
                 line = line[1:]
             elif line[-1]==ESC_HELP:
                 line = line[:-1]
-            self.shell.log(line, '#?'+line, line_info.continue_prompt)
             if line:
                 #print 'line:<%r>' % line  # dbg
                 self.shell.magic_pinfo(line)
diff --git a/IPython/frontend/terminal/ipapp.py b/IPython/frontend/terminal/ipapp.py
index d52052a..442e98a 100755
--- a/IPython/frontend/terminal/ipapp.py
+++ b/IPython/frontend/terminal/ipapp.py
@@ -571,7 +571,7 @@ class IPythonApp(Application):
                     try:
                         self.log.info("Running code in user namespace: %s" %
                                       line)
-                        self.shell.runlines(line)
+                        self.shell.run_cell(line)
                     except:
                         self.log.warn("Error in executing line in user "
                                       "namespace: %s" % line)
@@ -616,7 +616,7 @@ class IPythonApp(Application):
             try:
                 self.log.info("Running code given at command line (-c): %s" %
                               line)
-                self.shell.runlines(line)
+                self.shell.run_cell(line)
             except:
                 self.log.warn("Error in executing line in user namespace: %s" %
                               line)
diff --git a/IPython/lib/demo.py b/IPython/lib/demo.py
index 580588f..a2e82ea 100644
--- a/IPython/lib/demo.py
+++ b/IPython/lib/demo.py
@@ -248,7 +248,7 @@ class Demo(object):
         self.ip_ns       = ip.user_ns
         self.ip_colorize = ip.pycolorize
         self.ip_showtb   = ip.showtraceback
-        self.ip_runlines = ip.runlines
+        self.ip_run_cell = ip.run_cell
         self.shell       = ip
 
         # load user data and initialize data structures
@@ -411,7 +411,7 @@ class Demo(object):
             print >>IPython.utils.io.Term.cout, block,
         sys.stdout.flush()
 
-    def runlines(self,source):
+    def run_cell(self,source):
         """Execute a string with one or more lines of code"""
 
         exec source in self.user_ns
@@ -449,7 +449,7 @@ class Demo(object):
             try:
                 save_argv = sys.argv
                 sys.argv = self.sys_argv
-                self.runlines(next_block)
+                self.run_cell(next_block)
                 self.post_cmd()
             finally:
                 sys.argv = save_argv
@@ -496,10 +496,10 @@ class IPythonDemo(Demo):
     class requires the input to be valid, pure Python code.
     """
 
-    def runlines(self,source):
+    def run_cell(self,source):
         """Execute a string with one or more lines of code"""
 
-        self.shell.runlines(source)
+        self.shell.run_cell(source)
         
 class LineDemo(Demo):
     """Demo where each line is executed as a separate block.
diff --git a/IPython/zmq/ipkernel.py b/IPython/zmq/ipkernel.py
index b07776f..0282979 100755
--- a/IPython/zmq/ipkernel.py
+++ b/IPython/zmq/ipkernel.py
@@ -214,14 +214,8 @@ class Kernel(Configurable):
                 # statements in that code will obviously still execute.
                 shell.runcode(code)
             else:
-                # FIXME: runlines calls the exception handler itself.
+                # FIXME: the shell calls the exception handler itself.
                 shell._reply_content = None
-
-                # For now leave this here until we're sure we can stop using it
-                #shell.runlines(code)
-
-                # Experimental: cell mode!  Test more before turning into
-                # default and removing the hacks around runlines.
                 shell.run_cell(code)
         except:
             status = u'error'