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C# MSBuild not including the NuGet packages (works in Visual Studio 17)

I am using PackageReference in my .csproj file and my build works in Visual Studio (2017). I'm building with .net 4.5 I have looked at this:
(MSBuild not adding a /reference for nuget PackageReference when building with jenkins)
I was at first having the issue on our build server so I tried it locally on my computer. I do a restore and then the build (or rebuild). the error is:
(CoreCompile target) ->
Properties\AssemblyInfo.cs(25,12): error CS0246: The type or namespace name 'log4net' could not be found (are you missing a using directive or an assembly reference?)
And in my project I have
<ItemGroup>
<PackageReference Include="log4net">
<Version>2.0.12</Version>
</PackageReference>
Thanks in advance.
Update
I created a simple solution/project that just includes one Nuget Package. I also created it with the latest framework in case that had any bearing on the issue. Again, it builds in VS2017 but fails using MSBuild the .csproj file is
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
<ProjectGuid>{9A64612A-63A2-4CA5-8470-75DD978D7449}</ProjectGuid>
<OutputType>Exe</OutputType>
<RootNamespace>testNetwonNugetProject</RootNamespace>
<AssemblyName>testNetwonNugetProject</AssemblyName>
<TargetFrameworkVersion>v4.8</TargetFrameworkVersion>
<FileAlignment>512</FileAlignment>
<AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
<Deterministic>true</Deterministic>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<ItemGroup>
<Reference Include="System" />
<Reference Include="System.Core" />
<Reference Include="System.Xml.Linq" />
<Reference Include="System.Data.DataSetExtensions" />
<Reference Include="Microsoft.CSharp" />
<Reference Include="System.Data" />
<Reference Include="System.Net.Http" />
<Reference Include="System.Xml" />
</ItemGroup>
<ItemGroup>
<Compile Include="Program.cs" />
<Compile Include="Properties\AssemblyInfo.cs" />
</ItemGroup>
<ItemGroup>
<None Include="App.config" />
</ItemGroup>
<ItemGroup>
<PackageReference Include="Newtonsoft.Json">
<Version>13.0.1</Version>
</PackageReference>
</ItemGroup>
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
</Project>
I verified that on restore the files are added to the project obj folder as well as user/roaming/nuget and user/.nuget/packages. I get the same error message as above.

Deploy click-once application with Azure Devops?

I have an error when deploying my click-once project with Azure DevOps Pipeline. I don't see where is my error.
First, I can build and publish my click-once application manually from Visual Studio. I have no issue.
When I use Azure DevOps Pipeline to build and publish my click-once application I get an error:
[error]C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\MSBuild\15.0\Bin\Microsoft.Common.CurrentVersion.targets(780,5):
Error : The OutputPath property is not set for project
'******.vbproj'. Please check to make sure that you have specified a
valid combination of Configuration and Platform for this project.
Configuration='release' Platform='any cpu'. You may be seeing this
message because you are trying to build a project without a solution
file, and have specified a non-default Configuration or Platform that
doesn't exist for this project.
The OutputPath property is not set for project. Well, I don't know. Let me give you my project file:
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="14.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
<ProjectGuid>{****}</ProjectGuid>
<OutputType>WinExe</OutputType>
<AppDesignerFolder>Properties</AppDesignerFolder>
<RootNamespace>****.*****4</RootNamespace>
<AssemblyName>****.*****4</AssemblyName>
<TargetFrameworkVersion>v4.7.2</TargetFrameworkVersion>
<FileAlignment>512</FileAlignment>
<ProjectTypeGuids>{60dc8134-eba5-43b8-bcc9-bb4bc16c2548};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
<WarningLevel>4</WarningLevel>
<AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
<IsWebBootstrapper>true</IsWebBootstrapper>
<NuGetPackageImportStamp>
</NuGetPackageImportStamp>
<TargetFrameworkProfile />
<PublishFilePath>$(PublishDir)install*****4.html</PublishFilePath>
<PublishUrl>\\server15\c%24\inetpub\wwwroot\*****4Install %28Staging%29\</PublishUrl>
<Install>true</Install>
<InstallFrom>Web</InstallFrom>
<UpdateEnabled>true</UpdateEnabled>
<UpdateMode>Foreground</UpdateMode>
<UpdateInterval>7</UpdateInterval>
<UpdateIntervalUnits>Days</UpdateIntervalUnits>
<UpdatePeriodically>false</UpdatePeriodically>
<UpdateRequired>true</UpdateRequired>
<MapFileExtensions>true</MapFileExtensions>
<InstallUrl>http://*****4install-staging.newsprintgroup.com/</InstallUrl>
<ProductName>***** Application</ProductName>
<PublisherName>NewsPrint Group</PublisherName>
<MinimumRequiredVersion>4.15.0.0</MinimumRequiredVersion>
<CreateWebPageOnPublish>true</CreateWebPageOnPublish>
<WebPage>install*****4.html</WebPage>
<ApplicationRevision>1</ApplicationRevision>
<ApplicationVersion>4.15.9.1</ApplicationVersion>
<UseApplicationTrust>false</UseApplicationTrust>
<CreateDesktopShortcut>true</CreateDesktopShortcut>
<PublishWizardCompleted>true</PublishWizardCompleted>
<BootstrapperEnabled>true</BootstrapperEnabled>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup>
<ManifestCertificateThumbprint>57DF31CB3510678332744572F14AD9BAAC60178E</ManifestCertificateThumbprint>
</PropertyGroup>
<PropertyGroup>
<ManifestKeyFile>****.*****4_1_TemporaryKey.pfx</ManifestKeyFile>
</PropertyGroup>
<PropertyGroup>
<GenerateManifests>true</GenerateManifests>
</PropertyGroup>
<PropertyGroup>
<SignManifests>false</SignManifests>
</PropertyGroup>
<ItemGroup>
(...)
</ItemGroup>
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
<Import Project="$(SlowCheetahTargets)" Condition="Exists('$(SlowCheetahTargets)')" Label="SlowCheetah" />
<Import Project="..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets" Condition="Exists('..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" />
<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
<PropertyGroup>
<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
</PropertyGroup>
<Error Condition="!Exists('..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets'))" />
<Error Condition="!Exists('..\packages\SlowCheetah.2.5.48\build\SlowCheetah.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\SlowCheetah.2.5.48\build\SlowCheetah.targets'))" />
</Target>
<Import Project="..\packages\SlowCheetah.2.5.48\build\SlowCheetah.targets" Condition="Exists('..\packages\SlowCheetah.2.5.48\build\SlowCheetah.targets')" />
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
Other similar extension points exist, see Microsoft.Common.targets.
<Target Name="BeforeBuild">
</Target>
<Target Name="AfterBuild">
</Target>
-->
</Project>

This error only relevant with your incorrect configuration about the Platform in the
task. It should caused by the value you specified to Platform could not be recognized by the task. Without the Platform value, the server prompt the error message Please check to make sure that you have specified a valid combination of Configuration and Platform for this project.
Since what you used in the task is .*proj file instead of .sln file, to solve the error you are facing, here you need use AnyCPU rather than a normal value any cpu.
In this doc, it point out that corresponding to different file designation methods, you should use the different task configurations:

No references were found in the windows sdk (Windows 1903)

I want to create simple toast notification to action center in windows 10 from a WPF app using this article.
But I got problem on Step 2:
Right click on the project => Add => Reference... => Windows => Core
What I checked:
Windows 10 SDK Installation:
Same issue with a WPF project
And this is my csproj file:
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
<ProjectGuid>{A5A389ED-4BBB-4EF4-A8A4-45DD3D0AF9AE}</ProjectGuid>
<OutputType>WinExe</OutputType>
<RootNamespace>WpfApp3</RootNamespace>
<AssemblyName>WpfApp3</AssemblyName>
<TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
<TargetPlatformVersion>10.0.10240.0</TargetPlatformVersion>
<FileAlignment>512</FileAlignment>
<ProjectTypeGuids>{60dc8134-eba5-43b8-bcc9-bb4bc16c2548};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
<WarningLevel>4</WarningLevel>
<AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
<Deterministic>true</Deterministic>
<TargetFrameworkProfile />
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<PlatformTarget>AnyCPU</PlatformTarget>
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<ItemGroup>
<Reference Include="System" />
<Reference Include="System.Data" />
<Reference Include="System.Xml" />
<Reference Include="Microsoft.CSharp" />
<Reference Include="System.Core" />
<Reference Include="System.Xml.Linq" />
<Reference Include="System.Data.DataSetExtensions" />
<Reference Include="System.Net.Http" />
<Reference Include="System.Xaml">
<RequiredTargetFramework>4.0</RequiredTargetFramework>
</Reference>
<Reference Include="WindowsBase" />
<Reference Include="PresentationCore" />
<Reference Include="PresentationFramework" />
</ItemGroup>
<ItemGroup>
<ApplicationDefinition Include="App.xaml">
<Generator>MSBuild:Compile</Generator>
<SubType>Designer</SubType>
</ApplicationDefinition>
<Page Include="MainWindow.xaml">
<Generator>MSBuild:Compile</Generator>
<SubType>Designer</SubType>
</Page>
<Compile Include="App.xaml.cs">
<DependentUpon>App.xaml</DependentUpon>
<SubType>Code</SubType>
</Compile>
<Compile Include="MainWindow.xaml.cs">
<DependentUpon>MainWindow.xaml</DependentUpon>
<SubType>Code</SubType>
</Compile>
</ItemGroup>
<ItemGroup>
<Compile Include="Properties\AssemblyInfo.cs">
<SubType>Code</SubType>
</Compile>
<Compile Include="Properties\Resources.Designer.cs">
<AutoGen>True</AutoGen>
<DesignTime>True</DesignTime>
<DependentUpon>Resources.resx</DependentUpon>
</Compile>
<Compile Include="Properties\Settings.Designer.cs">
<AutoGen>True</AutoGen>
<DependentUpon>Settings.settings</DependentUpon>
<DesignTimeSharedInput>True</DesignTimeSharedInput>
</Compile>
<EmbeddedResource Include="Properties\Resources.resx">
<Generator>ResXFileCodeGenerator</Generator>
<LastGenOutput>Resources.Designer.cs</LastGenOutput>
</EmbeddedResource>
<None Include="Properties\Settings.settings">
<Generator>SettingsSingleFileGenerator</Generator>
<LastGenOutput>Settings.Designer.cs</LastGenOutput>
</None>
</ItemGroup>
<ItemGroup>
<None Include="App.config" />
</ItemGroup>
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
</Project>
This error occurs after the update to Windows 1903, because Visual studio can not access C:\Windows\System32\WinMetadata

On updating to the May 2019 release of Windows 10 the directory C:\WINDOWS\SysWOW64\WinMetadata is removed and this is where Visual Studio is 2017 and 2019 is looking for all of the files.
There is 2 way to solve this:
1. Click Browse in reference manager and chose your reference from C:\WINDOWS\System32\WinMetadata.
2. Copy WinMetadata folder from C:\WINDOWS\System32\WinMetadata to C:\WINDOWS\SysWOW64\WinMetadata. and then re-open reference manager.

Looks like the parent bug is documented at https://developercommunity.visualstudio.com/content/problem/446490/visual-studio-cant-see-winmetadatadirectory-in-cwi.html
For me I clicked browse and used this path %windir%\Sysnative\WinMetadata and it worked for me. Windows 10 1903 \ VS 17

I've reproduced your issue. The node <TargetPlatformVersion> should be below the existing node <TargetFrameworkVersion> node.
<TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
<TargetPlatformVersion>10.0.10240.0</TargetPlatformVersion>
But there is the separate PropertyGroup with this node in your project file.

Visual Studio can not access the C:\Windows\System32\WinMetadata directory to load the windows SDK on Windows 1903.
So a downgrade from windows 1903 to 1803 solved this issue.
I have reported this problem on the visual studio developer community page.

Windows 1903:
Copy WinMetadata folder from (hidden folder) C:\WINDOWS\sysnative\WinMetadata to C:\WINDOWS\SysWOW64\WinMetadata.
Re-open reference manager.

​The folder %windir%\Sysnative\WinMetadata does not seem to exist on my Windows 1903 (OS Build 18362.900).
My workaround was to make a local copy of the required files in %windir%\System32\WinMetadata (e.g. under a lib folder in your solution) and reference them from there.
In my case, this is how I got a hold of the Windows.Data.winmd and Windows.UI.winmd files (couldn't find them on NuGet).

What is a .psproj file?

I cloned a repo and in it I got a .psproj file. I tried opening in Visual Studio 2017 (since notepad++ showed it contained xml much like VS Solutions). In VS also it opened showing internal xml and not as a proj/solution file. Same outcome with VS Code.
So my question is
What is a psproj file?
Since it was contained in a PowerShell folder, so is my assumption correct that it is a powershell project file?
What is the IDE to view these projects?
The file's contents:
<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<SchemaVersion>2.0</SchemaVersion>
<ProjectGuid>6CAFC0C6-A428-4d30-A9F9-700E829FEA51</ProjectGuid>
<OutputType>Exe</OutputType>
<RootNamespace>MyApplication</RootNamespace>
<AssemblyName>MyApplication</AssemblyName>
<Name>Bootstrapper</Name>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<ItemGroup />
<ItemGroup>
<Compile Include="Script.ps1" />
</ItemGroup>
<Import Project="$(MSBuildBinPath)\Microsoft.CSharp.targets" />
<Target Name="Build" />
</Project>

It's a powershell project file, but not for Visual Studio, it's for Powershell Studio. The powershell projects for visual studio are .pssproj. It took me forever to figure this out because everyone here was too busy arguing about whether this was a valid question to pro

Ok so going by the comments on questions, it is a powershell project file.
To enable your VS to understand such files, one needs to install respective extension to your VS2015 or VS2017 or VS2013
Nice article on this is here

How can a project be built as a portable or a normal class library depending on the selected configuration?

Context: We have a common library project called 'THEPROJECT' that is shared with a Xamarin mobile solution and a web project in visual studio. This shared library is a PCL Profile259 due to restrictions in Xamarin. In our web application solution we would like to mark the data models with the appropriate attributes for DataContext to work correctly (as we want to use LinqToSql).
Attempted Solution: We decided to look into the project for 'THEPROJECT' and change the msbuild in a way that would allow it to exist in a state of portable library / normal class library depending on the selected configuration in visual studio.
We have looked at the solution in this post however it is only part of the solution. We can get the project to exist as one or the other, however it requires a manual change to the project file. Now we get the error loading the following project. The for a portable project must be '.NETPortable'.
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<Configuration Condition=" '$(Configuration)' == '' ">DebugDesktop</Configuration>
<Platform Condition="'$(Platform)' == ''">AnyCPU</Platform>
<ProjectGuid>{426E7BD8-9DA8-4E15-9512-72E7C632B037}</ProjectGuid>
<OutputType>Library</OutputType>
<AppDesignerFolder>Properties</AppDesignerFolder>
<RootNamespace>THEPROJECT</RootNamespace>
<AssemblyName>THEPROJECT</AssemblyName>
<TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
<MinimumVisualStudioVersion>10.0</MinimumVisualStudioVersion>
<BuildMode>Desktop</BuildMode>
</PropertyGroup>
<!-- Define the Build Configurations -->
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'DebugDesktop|AnyCPU' ">
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Desktop\Debug\</OutputPath>
<DefineConstants>TRACE;DEBUG;</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
<ConsolePause>false</ConsolePause>
<BuildMode>Desktop</BuildMode>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'ReleaseDesktop|AnyCPU' ">
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Desktop\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
<BuildMode>Desktop</BuildMode>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'DebugPCL|AnyCPU' ">
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\PCL\Debug\</OutputPath>
<DefineConstants>TRACE;DEBUG;</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
<ConsolePause>false</ConsolePause>
<BuildMode>Portable</BuildMode>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'ReleasePCL|AnyCPU' ">
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\PCL\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
<BuildMode>Portable</BuildMode>
</PropertyGroup>
<!-- Determine the correct properties for PCL/Desktop -->
<Choose>
<When Condition=" '$(BuildMode)' == 'Portable' ">
<PropertyGroup>
<ProjectTypeGuids>{786C830F-07A1-408B-BD7F-6EE04809D6DB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
<TargetFrameworkProfile>Profile259</TargetFrameworkProfile>
<TargetFrameworkIdentifier>.NETPortable</TargetFrameworkIdentifier>
<DynamicImportPath>$(MSBuildExtensionsPath32)\Microsoft\Portable\$(TargetFrameworkVersion)\Microsoft.Portable.CSharp.targets</DynamicImportPath>
</PropertyGroup>
</When>
<When Condition=" '$(BuildMode)' == 'Desktop' ">
<PropertyGroup>
<FileAlignment>512</FileAlignment>
<TargetFrameworkProfile />
<DynamicImportPath>$(MSBuildToolsPath)\Microsoft.CSharp.targets</DynamicImportPath>
</PropertyGroup>
<ItemGroup>
<Reference Include="System.Data.Linq" />
</ItemGroup>
</When>
</Choose>
<ItemGroup>
<Reference Include="Newtonsoft.Json, Version=8.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
<HintPath>..\..\mobileapplication\packages\Newtonsoft.Json.8.0.2\lib\portable-net40+sl5+wp80+win8+wpa81\Newtonsoft.Json.dll</HintPath>
<Private>True</Private>
</Reference>
<Reference Include="System" />
<Reference Include="System.Core" />
<Reference Include="System.Xml.Linq" />
<Reference Include="Microsoft.CSharp" />
<Reference Include="System.Xml" />
</ItemGroup>
<ItemGroup>
<ProjectReference Include="..\..\sqlite-net-extensions\SQLiteNetExtensions\SQLiteNetExtensions-PCL.csproj">
<Project>{f723017d-ede5-49cc-a84f-881c067c6004}</Project>
<Name>SQLiteNetExtensions-PCL</Name>
</ProjectReference>
<ProjectReference Include="..\..\sqlitenetpcl\src\SQLite.Net\SQLite.Net.csproj">
<Project>{4971d437-0694-4297-a8cc-146ce08c3bd9}</Project>
<Name>SQLite.Net</Name>
</ProjectReference>
</ItemGroup>
<Import Project="$(DynamicImportPath)" />
<!-- Source/Resx etc... -->
</Project>

To answer the question about making a project be "Portable" or "Normal" depending on the configuration, when the error that pops up is something about the <TargetFrameworkIdentifier> must be .NETPortable:
Remove all the <ProjectTypeGuids> from the configuration.
Those project type GUIDs give Visual Studio some GUI things that have to do with portable projects only, so when the configuration is not portable it causes the error you got. But since you're comfortable editing the XML, you obviously don't need that stuff. Plus you can continue to use the GUI to edit project properties with the project type GUIDs removed.
At least as of Visual Studio 2015.

When you create a Portable Class Library you need to create your library as a Windows 8.1 Portable Library you can't use Universal Libraries for this, which it sounds like you did by the constraints of Xamarin. The Windows 8.1 Portable Library is a kind of hybrid library that allows classic .net to communicate with the new lightweight versions of .net.
The issue with the Portable Class Library is it can't reference a a Classic Class Library via project reference, you can only reference it via DLL reference. You do not need to mess around with the XML if you are uncomfortable editing that file just find the compiled DLL and add the reference manually. If you choose to do this you will need to manually update the build dependencies or you may have broken references.
It seems like the issue isn't entirely in your .csproj but it is also in your project.json. I have been noticing visual studio not generating the proper project.json file. I have to tinker with the targets in the UI to get it to generate correctly. Once I get the initial project.json to generate I have no other issues.
Prior to doing anything we need to wire up our Portable Class Library to handle a Classic Class Library. The first step is updating the target framework from the properties to target .net 4.5 or whatever version you prefer.
Once you do this confirm that the project.json file looks something like this:
{
"supports": {},
"dependencies": {},
"frameworks": {
".NETPortable,Version=v4.5,Profile=Profile259": {}
}
}
Once your Portable Class Library is targeting the correct version you can then add a DLL reference to the compiled .net 4.5 assembly. I have made no additional changes to the csproj file for the portable class library but here is the source to that so you can take a look.
Notice how the ClassLibrary1 is referenced:
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="14.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
<PropertyGroup>
<MinimumVisualStudioVersion>11.0</MinimumVisualStudioVersion>
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
<ProjectGuid>{7C4EB968-4C17-438C-B981-97EDC865F312}</ProjectGuid>
<OutputType>Library</OutputType>
<AppDesignerFolder>Properties</AppDesignerFolder>
<RootNamespace>PortableLibrary</RootNamespace>
<AssemblyName>PortableLibrary</AssemblyName>
<DefaultLanguage>en-US</DefaultLanguage>
<FileAlignment>512</FileAlignment>
<ProjectTypeGuids>{786C830F-07A1-408B-BD7F-6EE04809D6DB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
<TargetFrameworkProfile>Profile259</TargetFrameworkProfile>
<TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<DebugSymbols>true</DebugSymbols>
<DebugType>full</DebugType>
<Optimize>false</Optimize>
<OutputPath>bin\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
</PropertyGroup>
<ItemGroup>
<Compile Include="Class1.cs" />
<Compile Include="Properties\AssemblyInfo.cs" />
</ItemGroup>
<ItemGroup>
<Reference Include="ClassLibrary1">
<HintPath>..\ClassLibrary1\bin\Debug\ClassLibrary1.dll</HintPath>
</Reference>
</ItemGroup>
<ItemGroup>
<None Include="project.json" />
</ItemGroup>
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\Portable\$(TargetFrameworkVersion)\Microsoft.Portable.CSharp.targets" />
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
Other similar extension points exist, see Microsoft.Common.targets.
<Target Name="BeforeBuild">
</Target>
<Target Name="AfterBuild">
</Target>
-->
</Project>
This should eliminate issues assuming your web project is ASP.NET Core 1.0. If you are running a Classic ASP.NET application you may still have to create the build rules.
TLDR:
Looks like there is an issue with your project.json file, make sure it is getting generated correctly and you can't directly reference .net 4.5 via project reference you have to reference the DLL.