Replace update_version shell script with a python script, which is much better at handling XML rewrite. Update the PHP version too. As part of rewrite, some XML file format will change a little, but the semantics is still the same so it should be okay.
diff --git a/update_version.py b/update_version.py
new file mode 100755
index 0000000..148e62b
--- /dev/null
+++ b/update_version.py
@@ -0,0 +1,247 @@
+#!/usr/bin/env python
+
+import datetime
+import re
+import sys
+from xml.dom import minidom
+
+if len(sys.argv) < 2:
+  print """
+[ERROR] Please specify a version.
+
+Example:
+./update_version.py 2.1.3
+"""
+  exit(1)
+
+NEW_VERSION = sys.argv[1]
+NEW_VERSION_INFO = NEW_VERSION.split('.')
+if len(NEW_VERSION_INFO) != 3:
+  print """
+[ERROR] Version must be in the format <MAJOR>.<MINOR>.<MICRO>
+
+Example:
+./update_version.py 2.1.3
+"""
+  exit(1)
+
+
+def Find(elem, tagname):
+  for child in elem.childNodes:
+    if child.nodeName == tagname:
+      return child
+  return None
+
+
+def FindAndClone(elem, tagname):
+  return Find(elem, tagname).cloneNode(True)
+
+
+def ReplaceText(elem, text):
+  elem.firstChild.replaceWholeText(text)
+
+
+def RewriteXml(filename, rewriter, add_xml_prefix=True):
+  document = minidom.parse(filename)
+  rewriter(document)
+  # document.toxml() always prepend the XML version without inserting new line.
+  # We wants to preserve as much of the original formatting as possible, so we
+  # will remove the default XML version and replace it with our custom one when
+  # whever necessary.
+  content = document.toxml().replace('<?xml version="1.0" ?>', '')
+  file_handle = open(filename, 'wb')
+  if add_xml_prefix:
+    file_handle.write('<?xml version="1.0" encoding="UTF-8"?>\n')
+  file_handle.write(content)
+  file_handle.close()
+
+
+def RewriteTextFile(filename, line_rewriter):
+  lines = open(filename, 'r').readlines()
+  updated_lines = []
+  for line in lines:
+    updated_lines.append(line_rewriter(line))
+  if lines == updated_lines:
+    print '%s was not updated. Please double check.' % filename
+  f = open(filename, 'w')
+  f.write(''.join(updated_lines))
+  f.close()
+
+
+def UpdateConfigure():
+  RewriteTextFile('configure.ac',
+    lambda line : re.sub(
+      r'^AC_INIT\(\[Protocol Buffers\],\[.*\],\[protobuf@googlegroups.com\],\[protobuf\]\)$',
+      ('AC_INIT([Protocol Buffers],[%s],[protobuf@googlegroups.com],[protobuf])'
+        % NEW_VERSION),
+      line))
+
+
+def UpdateCpp():
+  cpp_version = '%s00%s00%s' % (
+    NEW_VERSION_INFO[0], NEW_VERSION_INFO[1], NEW_VERSION_INFO[2])
+  def RewriteCpp(line):
+    line = re.sub(
+      r'^#define GOOGLE_PROTOBUF_VERSION .*$',
+      '#define GOOGLE_PROTOBUF_VERSION %s' % cpp_version,
+      line)
+    if NEW_VERSION_INFO[2] == '0':
+      line = re.sub(
+        r'^#define GOOGLE_PROTOBUF_MIN_LIBRARY_VERSION .*$',
+        '#define GOOGLE_PROTOBUF_MIN_LIBRARY_VERSION %s' % cpp_version,
+        line)
+      line = re.sub(
+        r'^#define GOOGLE_PROTOBUF_MIN_PROTOC_VERSION .*$',
+        '#define GOOGLE_PROTOBUF_MIN_PROTOC_VERSION %s' % cpp_version,
+        line)
+      line = re.sub(
+        r'^static const int kMinHeaderVersionForLibrary = .*$',
+        'static const int kMinHeaderVersionForLibrary = %s;' % cpp_version,
+        line)
+      line = re.sub(
+        r'^static const int kMinHeaderVersionForProtoc = .*$',
+        'static const int kMinHeaderVersionForProtoc = %s;' % cpp_version,
+        line)
+    return line
+  RewriteTextFile('src/google/protobuf/stubs/common.h', RewriteCpp)
+
+
+def UpdateCsharp():
+  RewriteXml('csharp/src/Google.Protobuf/Google.Protobuf.csproj',
+    lambda document : ReplaceText(
+      Find(Find(document.documentElement, 'PropertyGroup'), 'VersionPrefix'),
+      NEW_VERSION),
+    add_xml_prefix=False)
+
+  RewriteXml('csharp/Google.Protobuf.Tools.nuspec',
+    lambda document : ReplaceText(
+      Find(Find(document.documentElement, 'metadata'), 'version'),
+      NEW_VERSION))
+
+
+def UpdateJava():
+  RewriteXml('java/pom.xml',
+    lambda document : ReplaceText(
+      Find(document.documentElement, 'version'), NEW_VERSION))
+
+  RewriteXml('java/core/pom.xml',
+    lambda document : ReplaceText(
+      Find(Find(document.documentElement, 'parent'), 'version'),
+      NEW_VERSION))
+
+  RewriteXml('java/util/pom.xml',
+    lambda document : ReplaceText(
+      Find(Find(document.documentElement, 'parent'), 'version'),
+      NEW_VERSION))
+
+  RewriteXml('protoc-artifacts/pom.xml',
+    lambda document : ReplaceText(
+      Find(document.documentElement, 'version'), NEW_VERSION))
+
+
+def UpdateJavaScript():
+  RewriteTextFile('js/package.json',
+    lambda line : re.sub(
+      r'^  "version": ".*",$',
+      '  "version": "%s",' % NEW_VERSION,
+      line))
+
+
+def UpdateMakefile():
+  protobuf_version_offset = 11
+  expected_major_version = '3'
+  if NEW_VERSION_INFO[0] != expected_major_version:
+    print """[ERROR] Major protobuf version has changed. Please update
+update_version.py to readjust the protobuf_version_offset and
+expected_major_version such that the PROTOBUF_VERSION in src/Makefile.am is
+always increasing.
+    """
+    exit(1)
+
+  protobuf_version_info = '%s:%s:0' % (
+    int(NEW_VERSION_INFO[1]) + protobuf_version_offset, NEW_VERSION_INFO[2])
+  RewriteTextFile('src/Makefile.am',
+    lambda line : re.sub(
+      r'^PROTOBUF_VERSION = .*$',
+      'PROTOBUF_VERSION = %s' % protobuf_version_info,
+      line))
+
+
+def UpdateObjectiveC():
+  RewriteTextFile('Protobuf.podspec',
+    lambda line : re.sub(
+      r"^  s.version  = '.*'$",
+      "  s.version  = '%s'" % NEW_VERSION,
+      line))
+
+
+def UpdatePhp():
+  def Callback(document):
+    def CreateNode(tagname, indent, children):
+      elem = document.createElement(tagname)
+      indent += 1
+      for child in children:
+        elem.appendChild(document.createTextNode('\n' + (' ' * indent)))
+        elem.appendChild(child)
+      indent -= 1
+      elem.appendChild(document.createTextNode('\n' + (' ' * indent)))
+      return elem
+
+    root = document.documentElement
+    version = Find(root, 'version')
+    ReplaceText(Find(version, 'release'), NEW_VERSION)
+    ReplaceText(Find(version, 'api'), NEW_VERSION)
+    now = datetime.datetime.now()
+    ReplaceText(Find(root, 'date'), now.strftime('%Y-%m-%d'))
+    ReplaceText(Find(root, 'time'), now.strftime('%H:%M:%S'))
+    changelog = Find(root, 'changelog')
+    for old_version in changelog.getElementsByTagName('version'):
+      if Find(old_version, 'release').firstChild.nodeValue == NEW_VERSION:
+        print ('[WARNING] Version %s already exists in the change log.'
+          % NEW_VERSION)
+        return
+    changelog.appendChild(document.createTextNode(' '))
+    stability = Find(root, 'stability')
+    release = CreateNode('release', 2, [
+        CreateNode('version', 3, [
+          FindAndClone(version, 'release'),
+          FindAndClone(version, 'api')
+        ]),
+        CreateNode('stability', 3, [
+          FindAndClone(stability, 'release'),
+          FindAndClone(stability, 'api')
+        ]),
+        FindAndClone(root, 'date'),
+        FindAndClone(root, 'time'),
+        FindAndClone(root, 'license'),
+        FindAndClone(root, 'notes')
+      ])
+    changelog.appendChild(release)
+    changelog.appendChild(document.createTextNode('\n '))
+  RewriteXml('php/ext/google/protobuf/package.xml', Callback)
+
+def UpdatePython():
+  RewriteTextFile('python/google/protobuf/__init__.py',
+    lambda line : re.sub(
+      r"^__version__ = '.*'$",
+      "__version__ = '%s'" % NEW_VERSION,
+      line))
+
+def UpdateRuby():
+  RewriteTextFile('ruby/google-protobuf.gemspec',
+    lambda line : re.sub(
+      r'^  s.version     = ".*"$',
+      '  s.version     = "%s"' % NEW_VERSION,
+      line))
+
+
+UpdateConfigure()
+UpdateCsharp()
+UpdateCpp()
+UpdateJava()
+UpdateJavaScript()
+UpdateMakefile()
+UpdateObjectiveC()
+UpdatePhp()
+UpdatePython()
+UpdateRuby()