Why git diff shows identical files as modified?

Question

The files have the same hash, but git thinks the file has been modified on every single line except the last line. This is from a rsync -azP clone of git working directory. I did this to move a svn to git (git svn fetch, then git svn rebase) repository to another host.

the host where the git repository was on => Ubuntu 12.04.5 LTS, git 2.6.4 rsync destination CentOS 7.2.1511 (Core), git 1.8.3.1

in both files lines end in ^M$

I suspect this is caused by git config or git bug.

git diff src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj
diff --git a/src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj b/src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj
index e6491ab..8b7ec22 100644
--- a/src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj
+++ b/src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj
@@ -1,69 +1,69 @@
-<U+FEFF><?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <ItemGroup Label="ProjectConfigurations">
-    <ProjectConfiguration Include="Debug|Win32">
-      <Configuration>Debug</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-    <ProjectConfiguration Include="Release|Win32">
-      <Configuration>Release</Configuration>
-      <Platform>Win32</Platform>
-    </ProjectConfiguration>
-  </ItemGroup>
-  <PropertyGroup Label="Globals">
-    <ProjectGuid>{8598C2C8-34C4-47A1-99B0-7C295A890615}</ProjectGuid>
-    <RootNamespace>msvc-generate</RootNamespace>
-    <Keyword>MakeFileProj</Keyword>
-  </PropertyGroup>
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
-    <ConfigurationType>Makefile</ConfigurationType>
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
-    <ConfigurationType>Makefile</ConfigurationType>
-  </PropertyGroup>
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
-  <ImportGroup Label="ExtensionSettings">
-  </ImportGroup>
-  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
-    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')
-  </ImportGroup>
-  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
-    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')
-  </ImportGroup>
-  <PropertyGroup Label="UserMacros" />
-  <PropertyGroup>
-    <_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
-    <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</OutDir>
-    <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</IntDir>
-    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>
-    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>
-    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>
-    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">config-msvc-version.h</NMakeOutput>
-    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">WIN32;_DEBUG;$(NMakePreprocessorDefinitions)</NMakePre
-    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>
-    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>
-    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>
-    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssemblie
-    <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</OutDir>
-    <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</IntDir>
-    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>
-    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>
-    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>
-    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">config-msvc-version.h</NMakeOutput>
-    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">WIN32;NDEBUG;$(NMakePreprocessorDefinitions)</NMakeP
-    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>
-    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>
-    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>
-    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssembl
-  </PropertyGroup>
-  <ItemDefinitionGroup>
-  </ItemDefinitionGroup>
-  <ItemGroup>
-    <None Include="Makefile.mak" />
-    <None Include="msc-generate.js" />
-  </ItemGroup>
-  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
-  <ImportGroup Label="ExtensionTargets">
-  </ImportGroup>
+<U+FEFF><?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <ItemGroup Label="ProjectConfigurations">
+    <ProjectConfiguration Include="Debug|Win32">
+      <Configuration>Debug</Configuration>
+      <Platform>Win32</Platform>
+    </ProjectConfiguration>
+    <ProjectConfiguration Include="Release|Win32">
+      <Configuration>Release</Configuration>
+      <Platform>Win32</Platform>
+    </ProjectConfiguration>
+  </ItemGroup>
+  <PropertyGroup Label="Globals">
+    <ProjectGuid>{8598C2C8-34C4-47A1-99B0-7C295A890615}</ProjectGuid>
+    <RootNamespace>msvc-generate</RootNamespace>
+    <Keyword>MakeFileProj</Keyword>
+  </PropertyGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
+    <ConfigurationType>Makefile</ConfigurationType>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
+    <ConfigurationType>Makefile</ConfigurationType>
+  </PropertyGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+  <ImportGroup Label="ExtensionSettings">
+  </ImportGroup>
+  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')
+  </ImportGroup>
+  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')
+  </ImportGroup>
+  <PropertyGroup Label="UserMacros" />
+  <PropertyGroup>
+    <_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
+    <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</OutDir>
+    <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</IntDir>
+    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>
+    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>
+    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>
+    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">config-msvc-version.h</NMakeOutput>
+    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">WIN32;_DEBUG;$(NMakePreprocessorDefinitions)</NMakePre
+    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>
+    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>
+    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>
+    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssemblie
+    <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</OutDir>
+    <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</IntDir>
+    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>
+    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>
+    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>
+    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">config-msvc-version.h</NMakeOutput>
+    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">WIN32;NDEBUG;$(NMakePreprocessorDefinitions)</NMakeP
+    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>
+    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>
+    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>
+    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssembl
+  </PropertyGroup>
+  <ItemDefinitionGroup>
+  </ItemDefinitionGroup>
+  <ItemGroup>
+    <None Include="Makefile.mak" />
+    <None Include="msc-generate.js" />
+  </ItemGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+  <ImportGroup Label="ExtensionTargets">
+  </ImportGroup>
 </Project>
\ No newline at end of file

Edit1:

od -t x1 output from both files are exactly the same

Encoding, line break permissions are exactly the same too

src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj: XML document, UTF-8 Unicode (with BOM) text, with CRLF line terminators

Edit2

Both files are the same in cat -A, how is this related to autocrlf?

$ cat -A src/router/openvpn/build/msvc/msvc-generate/msvc-generate.vcxproj
M-oM-;M-?<?xml version="1.0" encoding="utf-8"?>^M$
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">^M$
  <ItemGroup Label="ProjectConfigurations">^M$
    <ProjectConfiguration Include="Debug|Win32">^M$
      <Configuration>Debug</Configuration>^M$
      <Platform>Win32</Platform>^M$
    </ProjectConfiguration>^M$
    <ProjectConfiguration Include="Release|Win32">^M$
      <Configuration>Release</Configuration>^M$
      <Platform>Win32</Platform>^M$
    </ProjectConfiguration>^M$
  </ItemGroup>^M$
  <PropertyGroup Label="Globals">^M$
    <ProjectGuid>{8598C2C8-34C4-47A1-99B0-7C295A890615}</ProjectGuid>^M$
    <RootNamespace>msvc-generate</RootNamespace>^M$
    <Keyword>MakeFileProj</Keyword>^M$
  </PropertyGroup>^M$
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />^M$
  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">^M$
    <ConfigurationType>Makefile</ConfigurationType>^M$
  </PropertyGroup>^M$
  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">^M$
    <ConfigurationType>Makefile</ConfigurationType>^M$
  </PropertyGroup>^M$
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />^M$
  <ImportGroup Label="ExtensionSettings">^M$
  </ImportGroup>^M$
  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">^M$
    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />^M$
  </ImportGroup>^M$
  <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">^M$
    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />^M$
  </ImportGroup>^M$
  <PropertyGroup Label="UserMacros" />^M$
  <PropertyGroup>^M$
    <_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>^M$
    <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</OutDir>^M$
    <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Configuration)\</IntDir>^M$
    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>^M$
    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>^M$
    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>^M$
    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">config-msvc-version.h</NMakeOutput>^M$
    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">WIN32;_DEBUG;$(NMakePreprocessorDefinitions)</NMakePreprocessorDefinitions>^M$
    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>^M$
    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>^M$
    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>^M$
    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssemblies>^M$
    <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</OutDir>^M$
    <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Configuration)\</IntDir>^M$
    <NMakeBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak all</NMakeBuildCommandLine>^M$
    <NMakeReBuildCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean all</NMakeReBuildCommandLine>^M$
    <NMakeCleanCommandLine Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">nmake -f Makefile.mak clean</NMakeCleanCommandLine>^M$
    <NMakeOutput Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">config-msvc-version.h</NMakeOutput>^M$
    <NMakePreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">WIN32;NDEBUG;$(NMakePreprocessorDefinitions)</NMakePreprocessorDefinitions>^M$
    <NMakeIncludeSearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeIncludeSearchPath)</NMakeIncludeSearchPath>^M$
    <NMakeForcedIncludes Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedIncludes)</NMakeForcedIncludes>^M$
    <NMakeAssemblySearchPath Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeAssemblySearchPath)</NMakeAssemblySearchPath>^M$
    <NMakeForcedUsingAssemblies Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(NMakeForcedUsingAssemblies)</NMakeForcedUsingAssemblies>^M$
  </PropertyGroup>^M$
  <ItemDefinitionGroup>^M$
  </ItemDefinitionGroup>^M$
  <ItemGroup>^M$
    <None Include="Makefile.mak" />^M$
    <None Include="msc-generate.js" />^M$
  </ItemGroup>^M$
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />^M$
  <ImportGroup Label="ExtensionTargets">^M$
  </ImportGroup>^M$
</Project>

Answer 1

You need to set your core.autocrlf.

core.autocrlf = true

Text files checked-out from the repository that have only LF EOL characters are normalized to CRLF in your working tree; files that contain CRLF in the repository will not be touched

Text files that have only LF EOL characters in the repository, are normalized from CRLF to LF when committed back to the repository. Files that contain CRLF in the repository will be committed untouched.

core.autocrlf = input

Text files checked-out from the repository will keep original EOL characters in your working tree.

Text files in your working tree with CRLF EOL characters are normalized to LF when committed back to the repository.

core.autocrlf = false

core.eol dictates EOL characters in the text files of your working tree.

core.eol = native by default, which means Windows EOLs are CRLF and Unix-based OS are LF in working trees.