Visual Studio template ignores some project settings that are in template

Question

I created a new template, which I can use. However it only uses some project settings

I made a project with a working libSDL hi world example. I exported as a template, but template doesn't save some of my settings: ( It 'saves' them, but new projects ignore them. )

Ignored settings:

include header folders:
    for .h files
    for .lib files
linker args: SDLmain.lib SDL.lib
windows subsystem: /SUBSYSTEM:WINDOWS

Here's the saved /template/sdl/sdl.vcxproj file, and the settings actually appear in it yet they are ignored.

<?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>{8DDA73A6-86DD-4B03-BA9B-54BE878B648C}</ProjectGuid>
    <RootNamespace>$safeprojectname$</RootNamespace>
  </PropertyGroup>
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
    <ConfigurationType>Application</ConfigurationType>
    <UseDebugLibraries>true</UseDebugLibraries>
    <PlatformToolset>v110</PlatformToolset>
    <CharacterSet>MultiByte</CharacterSet>
  </PropertyGroup>
  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
    <ConfigurationType>Application</ConfigurationType>
    <UseDebugLibraries>false</UseDebugLibraries>
    <PlatformToolset>v110</PlatformToolset>
    <WholeProgramOptimization>true</WholeProgramOptimization>
    <CharacterSet>MultiByte</CharacterSet>
  </PropertyGroup>
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
  <ImportGroup Label="ExtensionSettings">
  </ImportGroup>
  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
  </ImportGroup>
  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
  </ImportGroup>
  <PropertyGroup Label="UserMacros" />
  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
    <IncludePath>C:\cpp_libs\SDL-1.2.15\include;$(IncludePath)</IncludePath>
    <ReferencePath>C:\cpp_libs\SDL-1.2.15\lib\x86;$(ReferencePath)</ReferencePath>
    <LibraryPath>C:\cpp_libs\SDL-1.2.15\lib\x86;$(LibraryPath)</LibraryPath>
    <SourcePath>C:\cpp_libs\SDL-1.2.15\include;$(SourcePath)</SourcePath>
  </PropertyGroup>
  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
    <ClCompile>
      <WarningLevel>Level3</WarningLevel>
      <Optimization>Disabled</Optimization>
    </ClCompile>
    <Link>
      <GenerateDebugInformation>true</GenerateDebugInformation>
    </Link>
  </ItemDefinitionGroup>
  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
    <ClCompile>
      <WarningLevel>Level3</WarningLevel>
      <Optimization>MaxSpeed</Optimization>
      <FunctionLevelLinking>true</FunctionLevelLinking>
      <IntrinsicFunctions>true</IntrinsicFunctions>
    </ClCompile>
    <Link>
      <GenerateDebugInformation>true</GenerateDebugInformation>
      <EnableCOMDATFolding>true</EnableCOMDATFolding>
      <OptimizeReferences>true</OptimizeReferences>
      <AdditionalDependencies>SDLmain.lib;SDL.lib;%(AdditionalDependencies)</AdditionalDependencies>
      <SubSystem>Windows</SubSystem>
    </Link>
  </ItemDefinitionGroup>
  <ItemGroup>
    <ClCompile Include="Source.cpp" />
  </ItemGroup>
  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
  <ImportGroup Label="ExtensionTargets">
  </ImportGroup>
</Project>

Answer 1

It's likely that the project system is actually removing these items as the file is being created: when you create a new project, Visual Studio runs a wizard in the background which can affect what actually ends up in the newly-created .vcxproj file.

These wizards are specific to the project type so you can actually supply your own via the <WizardExtension> element in the .vstemplate file. Of course by overriding the project creation logic, you may lose certain functionality/behaviour (unless there's a way of inheriting the original wizard's base assembly).

Alternately, a solution which I've used in the past is to create a VSPackage which handles the SolutionEvents_ProjectAdded method (in DTE.SolutionEvents). This method gets called whenever a new project is created or added to the solution, so you could potentially use that to set your project up as needed.

Note that you would need a way to ensure that it only affects projects of your specific type; a flag in the .vcxproj template file would do this.