diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autogenstep.cpp qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autogenstep.cpp
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autogenstep.cpp	2015-04-14 19:57:23.551710900 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autogenstep.cpp	2015-04-14 19:57:53.638531400 +0100
@@ -34,6 +34,7 @@
 #include "autotoolsproject.h"
 #include "autotoolsbuildconfiguration.h"
 #include "autotoolsprojectconstants.h"
+#include "shellprocessparameters.h"
 
 #include <projectexplorer/buildsteplist.h>
 #include <projectexplorer/target.h>
@@ -107,11 +107,12 @@
 
     ProcessParameters *pp = processParameters();
     pp->setMacroExpander(bc->macroExpander());
-    pp->setEnvironment(bc->environment());
     const QString projectDir(bc->target()->project()->projectDirectory().toString());
     pp->setWorkingDirectory(projectDir);
-    pp->setCommand("./autogen.sh");
-    pp->setArguments(additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(pp,
+                                                       bc->environment(),
+                                                       QLatin1String("./autogen.sh"),
+                                                       additionalArguments());
     pp->resolveAll();
 
     return AbstractProcessStep::init(earlierSteps);
@@ -223,11 +225,12 @@
 
     ProcessParameters param;
     param.setMacroExpander(bc->macroExpander());
-    param.setEnvironment(bc->environment());
     const QString projectDir(bc->target()->project()->projectDirectory().toString());
     param.setWorkingDirectory(projectDir);
-    param.setCommand("./autogen.sh");
-    param.setArguments(m_autogenStep->additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(&param,
+                                                       bc->environment(),
+                                                       QLatin1String("./autogen.sh"),
+                                                       m_autogenStep->additionalArguments());
     m_summaryText = param.summary(displayName());
     emit updateSummary();
 }
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autoreconfstep.cpp qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autoreconfstep.cpp
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autoreconfstep.cpp	2015-04-14 19:57:23.552210900 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autoreconfstep.cpp	2015-04-14 19:57:53.676036200 +0100
@@ -34,6 +34,7 @@
 #include "autotoolsproject.h"
 #include "autotoolsbuildconfiguration.h"
 #include "autotoolsprojectconstants.h"
+#include "shellprocessparameters.h"
 
 #include <projectexplorer/buildsteplist.h>
 #include <projectexplorer/target.h>
@@ -157,11 +158,12 @@
 
     ProcessParameters *pp = processParameters();
     pp->setMacroExpander(bc->macroExpander());
-    pp->setEnvironment(bc->environment());
     const QString projectDir(bc->target()->project()->projectDirectory().toString());
     pp->setWorkingDirectory(projectDir);
-    pp->setCommand("autoreconf");
-    pp->setArguments(additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(pp,
+                                                       bc->environment(),
+                                                       QLatin1String("autoreconf"),
+                                                       additionalArguments());
     pp->resolveAll();
 
     return AbstractProcessStep::init(earlierSteps);
@@ -270,11 +272,12 @@
 
     ProcessParameters param;
     param.setMacroExpander(bc->macroExpander());
-    param.setEnvironment(bc->environment());
     const QString projectDir(bc->target()->project()->projectDirectory().toString());
     param.setWorkingDirectory(projectDir);
-    param.setCommand("autoreconf");
-    param.setArguments(m_autoreconfStep->additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(&param,
+                                                       bc->environment(),
+                                                       QLatin1String("autoreconf"),
+                                                       m_autoreconfStep->additionalArguments());
     m_summaryText = param.summary(displayName());
     emit updateSummary();
 }
diff -urN qt-creator-opensource-src-3.4.0.orig/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.pro qt-creator-opensource-src-3.4.0/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.pro
--- qt-creator-opensource-src-3.4.0.orig/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.pro	2015-04-21 16:56:56.000000000 +0100
+++ qt-creator-opensource-src-3.4.0/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.pro	2015-04-24 00:37:06.163960200 +0100
@@ -14,7 +14,8 @@
           autoreconfstep.h\
           configurestep.h\
           makefileparserthread.h\
-          makefileparser.h
+          makefileparser.h \
+          shellprocessparameters.h
 SOURCES = autotoolsprojectplugin.cpp\
           autotoolsopenprojectwizard.cpp\
           autotoolsmanager.cpp\
@@ -28,4 +29,5 @@
           autoreconfstep.cpp\
           configurestep.cpp\
           makefileparserthread.cpp\
-          makefileparser.cpp
+          makefileparser.cpp\
+          shellprocessparameters.cpp
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.qbs qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.qbs
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.qbs	2015-04-14 19:57:23.592716100 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/autotoolsprojectmanager.qbs	2015-04-14 19:57:53.873561300 +0100
@@ -41,5 +41,7 @@
         "makefileparserthread.h",
         "makestep.cpp",
         "makestep.h",
+        "shellprocessparameters.cpp",
+        "shellprocessparameters.h",
     ]
 }
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/configurestep.cpp qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/configurestep.cpp
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/configurestep.cpp	2015-04-14 19:57:23.594216300 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/configurestep.cpp	2015-04-14 19:57:53.912566200 +0100
@@ -34,6 +34,7 @@
 #include "autotoolsproject.h"
 #include "autotoolsbuildconfiguration.h"
 #include "autotoolsprojectconstants.h"
+#include "shellprocessparameters.h"
 
 #include <projectexplorer/buildsteplist.h>
 #include <projectexplorer/target.h>
@@ -172,10 +173,11 @@
 
     ProcessParameters *pp = processParameters();
     pp->setMacroExpander(bc->macroExpander());
-    pp->setEnvironment(bc->environment());
     pp->setWorkingDirectory(bc->buildDirectory().toString());
-    pp->setCommand(projectDirRelativeToBuildDir(bc) + "configure");
-    pp->setArguments(additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(pp,
+                                                       bc->environment(), 
+                                                       projectDirRelativeToBuildDir(bc) + QLatin1String("configure"),
+                                                       additionalArguments());
     pp->resolveAll();
 
     return AbstractProcessStep::init(earlierSteps);
@@ -295,10 +297,11 @@
 
     ProcessParameters param;
     param.setMacroExpander(bc->macroExpander());
-    param.setEnvironment(bc->environment());
     param.setWorkingDirectory(bc->buildDirectory().toString());
-    param.setCommand(projectDirRelativeToBuildDir(bc) + "configure");
-    param.setArguments(m_configureStep->additionalArguments());
+    ShellScriptProcessParametersSetCommandAndArguments(&param,
+                                                       bc->environment(),
+                                                       projectDirRelativeToBuildDir(bc) + QLatin1String("configure"),
+                                                       m_configureStep->additionalArguments());
     m_summaryText = param.summaryInWorkdir(displayName());
     emit updateSummary();
 }
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/makestep.cpp qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/makestep.cpp
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/makestep.cpp	2015-04-14 19:57:23.637221700 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/makestep.cpp	2015-04-14 19:57:53.927568100 +0100
@@ -34,6 +34,7 @@
 #include "autotoolsproject.h"
 #include "autotoolsprojectconstants.h"
 #include "autotoolsbuildconfiguration.h"
+#include "shellprocessparameters.h"
 
 #include <projectexplorer/buildsteplist.h>
 #include <projectexplorer/target.h>
@@ -138,10 +139,8 @@
     pp->setMacroExpander(bc->macroExpander());
     Utils::Environment env = bc->environment();
     Utils::Environment::setupEnglishOutput(&env);
-    pp->setEnvironment(env);
     pp->setWorkingDirectory(bc->buildDirectory().toString());
-    pp->setCommand(tcList.at(0)->makeCommand(bc->environment()));
-    pp->setArguments(arguments);
+    ShellScriptProcessParametersSetMakeCommandAndArguments(pp, env, tcList.at(0), bc, arguments);
     pp->resolveAll();
 
     setOutputParser(new GnuMakeParser());
@@ -262,10 +265,8 @@
 
         ProcessParameters param;
         param.setMacroExpander(m_makeStep->macroExpander());
-        param.setEnvironment(bc->environment());
         param.setWorkingDirectory(bc->buildDirectory().toString());
-        param.setCommand(tcList.at(0)->makeCommand(bc->environment()));
-        param.setArguments(arguments);
+        ShellScriptProcessParametersSetMakeCommandAndArguments(&param, bc->environment(), tcList.at(0), bc, arguments);
         m_summaryText = param.summary(displayName());
     } else {
         m_summaryText = QLatin1String("<b>") + ToolChainKitInformation::msgNoToolChainInTarget()  + QLatin1String("</b>");
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/shellprocessparameters.cpp qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/shellprocessparameters.cpp
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/shellprocessparameters.cpp	1970-01-01 01:00:00.000000000 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/shellprocessparameters.cpp	2015-04-14 20:04:01.013682100 +0100
@@ -0,0 +1,89 @@
+/**************************************************************************
+**
+** Copyright (C) 2014 Ray Donnelly.
+** Author: Ray Donnelly (mingw.android@gmail.com)
+** Contact: http://www.qt-project.org/legal
+**
+** This file is part of Qt Creator.
+**
+** Commercial License Usage
+** Licensees holding valid commercial Qt licenses may use this file in
+** accordance with the commercial license agreement provided with the
+** Software or, alternatively, in accordance with the terms contained in
+** a written agreement between you and Digia.  For licensing terms and
+** conditions see http://qt.digia.com/licensing.  For further information
+** use the contact form at http://qt.digia.com/contact-us.
+**
+** GNU Lesser General Public License Usage
+** Alternatively, this file may be used under the terms of the GNU Lesser
+** General Public License version 2.1 as published by the Free Software
+** Foundation and appearing in the file LICENSE.LGPL included in the
+** packaging of this file.  Please review the following information to
+** ensure the GNU Lesser General Public License version 2.1 requirements
+** will be met: http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html.
+**
+** In addition, as a special exception, Digia gives you certain additional
+** rights.  These rights are described in the Digia Qt LGPL Exception
+** version 1.1, included in the file LGPL_EXCEPTION.txt in this package.
+**
+****************************************************************************/
+
+#include <QString>
+#include <QProcess>
+#include <QDir>
+#include <QFileInfo>
+
+#include "shellprocessparameters.h"
+
+using namespace Utils;
+using namespace ProjectExplorer;
+
+void ShellScriptProcessParametersSetCommandAndArguments(ProcessParameters *procParams,
+                                                        Environment const& env,
+                                                        QString command, QString args)
+{
+#if defined(Q_OS_WIN)
+    /* MSYS2 specific. This could be improved with a setting in Tools->Options */
+    QString sh_dir = QFileInfo(QCoreApplication::applicationDirPath()
+                               + QLatin1String("\\..\\..\\usr\\bin")).absoluteFilePath();
+    QString sh_exe = QFileInfo(sh_dir
+                               + QLatin1String("\\sh.exe")).absoluteFilePath();
+    QString sh_dir_native = QDir::toNativeSeparators(sh_dir);
+    Utils::Environment envCopy(env);
+    if (!env.path().contains(FileName::fromString(sh_dir)) && !env.path().contains(FileName::fromString(sh_dir_native))) {
+        envCopy.prependOrSetPath(sh_dir);
+    }
+    procParams->setEnvironment(envCopy);
+    procParams->setCommand(sh_exe);
+    procParams->setArguments(QLatin1String("-c \"")
+                             + command
+                             + QLatin1String(" ")
+                             + args
+                             + QLatin1String("\""));
+#else
+    procParams->setEnvironment(env);
+    procParams->setCommand(command);
+    procParams->setArguments(args);
+#endif
+}
+
+void ShellScriptProcessParametersSetMakeCommandAndArguments(ProcessParameters *procParams,
+                                                            Environment const& env,
+                                                            ToolChain const* toolchain,
+                                                            BuildConfiguration *buildConfig,
+                                                            QString args)
+{
+#if defined(Q_OS_WIN)
+    Q_UNUSED(buildConfig);
+    Q_UNUSED(toolchain);
+    QString makeCommand = QLatin1String("make");
+#else
+    QString makeCommand = (toolchain && buildConfig)
+                           ? toolchain->makeCommand(buildConfig->environment())
+                           : QLatin1String("make");
+#endif
+    ShellScriptProcessParametersSetCommandAndArguments(procParams,
+                                                       env,
+                                                       makeCommand,
+                                                       args);
+}
diff -urN qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/shellprocessparameters.h qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/shellprocessparameters.h
--- qt-creator-opensource-src-3.3.2.orig/src/plugins/autotoolsprojectmanager/shellprocessparameters.h	1970-01-01 01:00:00.000000000 +0100
+++ qt-creator-opensource-src-3.3.2/src/plugins/autotoolsprojectmanager/shellprocessparameters.h	2015-04-14 19:57:53.980574800 +0100
@@ -0,0 +1,49 @@
+/**************************************************************************
+**
+** Copyright (C) 2014 Ray Donnelly.
+** Author: Ray Donnelly (mingw.android@gmail.com)
+** Contact: http://www.qt-project.org/legal
+**
+** This file is part of Qt Creator.
+**
+** Commercial License Usage
+** Licensees holding valid commercial Qt licenses may use this file in
+** accordance with the commercial license agreement provided with the
+** Software or, alternatively, in accordance with the terms contained in
+** a written agreement between you and Digia.  For licensing terms and
+** conditions see http://qt.digia.com/licensing.  For further information
+** use the contact form at http://qt.digia.com/contact-us.
+**
+** GNU Lesser General Public License Usage
+** Alternatively, this file may be used under the terms of the GNU Lesser
+** General Public License version 2.1 as published by the Free Software
+** Foundation and appearing in the file LICENSE.LGPL included in the
+** packaging of this file.  Please review the following information to
+** ensure the GNU Lesser General Public License version 2.1 requirements
+** will be met: http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html.
+**
+** In addition, as a special exception, Digia gives you certain additional
+** rights.  These rights are described in the Digia Qt LGPL Exception
+** version 1.1, included in the file LGPL_EXCEPTION.txt in this package.
+**
+****************************************************************************/
+
+#ifndef SHELLPROCESSPARAMETERS_H
+#define SHELLPROCESSPARAMETERS_H
+
+#include <projectexplorer/processparameters.h>
+#include <projectexplorer/toolchain.h>
+#include "autotoolsbuildconfiguration.h"
+
+void ShellScriptProcessParametersSetCommandAndArguments(ProjectExplorer::ProcessParameters *pp,
+                                                        Utils::Environment const& env,
+                                                        QString command,
+                                                        QString args);
+
+void ShellScriptProcessParametersSetMakeCommandAndArguments(ProjectExplorer::ProcessParameters *procParams,
+                                                            Utils::Environment const& env,
+                                                            ProjectExplorer::ToolChain const* toolchain,
+                                                            ProjectExplorer::BuildConfiguration *buildConfig,
+                                                            QString args);
+
+#endif // SHELLPROCESSPARAMETERS_H