Some warning messages from Cake are showing twice since v1.0.0

### What You Are Seeing?

It seems the automatic bootstrapping of Cake in v1.0.0-rc0001 causes warnings to appear twice:


### What is Expected?


### What version of Cake are you using?

1.0.0-rc0001

### Are you running on a 32 or 64 bit system?

64-bit

### What environment are you running on? Windows? Linux? Mac?

Windows 10

### Are you running on a CI Server? If so, which one?

No

### How Did You Get This To Happen? (Steps to Reproduce)

```cmd
mkdir cake-tool-1-0-0--rc0001
cd cake-tool-1-0-0--rc0001
dotnet new tool-manifest --force
dotnet tool install cake.tool --version 1.0.0-rc0001
echo #load "optional.cake" > build.cake
dotnet cake --version
dotnet cake
```

### Output Log

Click to expand and see the log...

```
Looking for modules...
No scripts found at C:/augustoproiete/cake-tool-1-0-0--rc0001/optional.cake.
No modules found to install.
Module directory does not exist.
Analyzing build script...
Analyzing C:/augustoproiete/cake-tool-1-0-0--rc0001/build.cake...
No scripts found at C:/augustoproiete/cake-tool-1-0-0--rc0001/optional.cake.
Processing build script...
Adding assembly reference to System.Private.CoreLib.dll...
Adding assembly reference to System.Linq.Expressions.dll...
Adding assembly reference to Microsoft.CSharp.dll...
Adding assembly reference to Cake.Core.dll...
Adding assembly reference to Cake.Common.dll...
Adding assembly reference to System.Runtime.dll...
Adding assembly reference to System.Collections.dll...
Adding assembly reference to System.Linq.dll...
Adding assembly reference to System.Console.dll...
Adding assembly reference to System.Text.RegularExpressions.dll...
Adding assembly reference to System.Security.Cryptography.Algorithms.dll...
Adding assembly reference to System.Diagnostics.Process.dll...
Adding assembly reference to System.IO.FileSystem.dll...
Adding assembly reference to System.Collections.Concurrent.dll...
Adding assembly reference to Microsoft.Win32.Registry.dll...
Adding assembly reference to System.Threading.dll...
Adding assembly reference to System.Security.Cryptography.Primitives.dll...
Adding assembly reference to System.Runtime.InteropServices.RuntimeInformation.dll...
Adding assembly reference to System.ComponentModel.Primitives.dll...
Adding assembly reference to System.Runtime.InteropServices.dll...
Adding assembly reference to System.Threading.Thread.dll...
Adding assembly reference to System.Xml.ReaderWriter.dll...
Adding assembly reference to System.Xml.XDocument.dll...
Adding assembly reference to System.Runtime.Serialization.Primitives.dll...
Adding assembly reference to System.Runtime.Serialization.Json.dll...
Adding assembly reference to System.Net.Http.dll...
Adding assembly reference to System.IO.Compression.dll...
Adding assembly reference to System.ComponentModel.TypeConverter.dll...
Adding assembly reference to System.Text.Encoding.Extensions.dll...
Adding assembly reference to System.Runtime.Serialization.Xml.dll...
Adding assembly reference to System.Net.Primitives.dll...
Adding assembly reference to System.IO.Compression.ZipFile.dll...
Importing namespace Cake.Common...
Importing namespace Cake.Common.Build...
Importing namespace Cake.Common.Build.AppVeyor...
Importing namespace Cake.Common.Build.AppVeyor.Data...
Importing namespace Cake.Common.Build.AzurePipelines...
Importing namespace Cake.Common.Build.AzurePipelines.Data...
Importing namespace Cake.Common.Build.Bamboo...
Importing namespace Cake.Common.Build.Bamboo.Data...
Importing namespace Cake.Common.Build.BitbucketPipelines...
Importing namespace Cake.Common.Build.BitbucketPipelines.Data...
Importing namespace Cake.Common.Build.Bitrise...
Importing namespace Cake.Common.Build.Bitrise.Data...
Importing namespace Cake.Common.Build.ContinuaCI...
Importing namespace Cake.Common.Build.ContinuaCI.Data...
Importing namespace Cake.Common.Build.GitHubActions...
Importing namespace Cake.Common.Build.GitHubActions.Data...
Importing namespace Cake.Common.Build.GitLabCI...
Importing namespace Cake.Common.Build.GitLabCI.Data...
Importing namespace Cake.Common.Build.GoCD...
Importing namespace Cake.Common.Build.GoCD.Data...
Importing namespace Cake.Common.Build.Jenkins...
Importing namespace Cake.Common.Build.Jenkins.Data...
Importing namespace Cake.Common.Build.MyGet...
Importing namespace Cake.Common.Build.TeamCity...
Importing namespace Cake.Common.Build.TravisCI...
Importing namespace Cake.Common.Build.TravisCI.Data...
Importing namespace Cake.Common.Diagnostics...
Importing namespace Cake.Common.IO...
Importing namespace Cake.Common.IO.Paths...
Importing namespace Cake.Common.Net...
Importing namespace Cake.Common.Security...
Importing namespace Cake.Common.Solution...
Importing namespace Cake.Common.Solution.Project...
Importing namespace Cake.Common.Solution.Project.Properties...
Importing namespace Cake.Common.Solution.Project.XmlDoc...
Importing namespace Cake.Common.Text...
Importing namespace Cake.Common.Tools.Cake...
Importing namespace Cake.Common.Tools.Chocolatey...
Importing namespace Cake.Common.Tools.Chocolatey.ApiKey...
Importing namespace Cake.Common.Tools.Chocolatey.Config...
Importing namespace Cake.Common.Tools.Chocolatey.Download...
Importing namespace Cake.Common.Tools.Chocolatey.Features...
Importing namespace Cake.Common.Tools.Chocolatey.Install...
Importing namespace Cake.Common.Tools.Chocolatey.New...
Importing namespace Cake.Common.Tools.Chocolatey.Pack...
Importing namespace Cake.Common.Tools.Chocolatey.Pin...
Importing namespace Cake.Common.Tools.Chocolatey.Push...
Importing namespace Cake.Common.Tools.Chocolatey.Sources...
Importing namespace Cake.Common.Tools.Chocolatey.Uninstall...
Importing namespace Cake.Common.Tools.Chocolatey.Upgrade...
Importing namespace Cake.Common.Tools.DotCover...
Importing namespace Cake.Common.Tools.DotCover.Analyse...
Importing namespace Cake.Common.Tools.DotCover.Cover...
Importing namespace Cake.Common.Tools.DotCover.Merge...
Importing namespace Cake.Common.Tools.DotCover.Report...
Importing namespace Cake.Common.Tools.DotNetCore...
Importing namespace Cake.Common.Tools.DotNetCore.Build...
Importing namespace Cake.Common.Tools.DotNetCore.BuildServer...
Importing namespace Cake.Common.Tools.DotNetCore.Clean...
Importing namespace Cake.Common.Tools.DotNetCore.Execute...
Importing namespace Cake.Common.Tools.DotNetCore.MSBuild...
Importing namespace Cake.Common.Tools.DotNetCore.NuGet.Delete...
Importing namespace Cake.Common.Tools.DotNetCore.NuGet.Push...
Importing namespace Cake.Common.Tools.DotNetCore.NuGet.Source...
Importing namespace Cake.Common.Tools.DotNetCore.Pack...
Importing namespace Cake.Common.Tools.DotNetCore.Publish...
Importing namespace Cake.Common.Tools.DotNetCore.Restore...
Importing namespace Cake.Common.Tools.DotNetCore.Run...
Importing namespace Cake.Common.Tools.DotNetCore.Test...
Importing namespace Cake.Common.Tools.DotNetCore.Tool...
Importing namespace Cake.Common.Tools.DotNetCore.VSTest...
Importing namespace Cake.Common.Tools.DupFinder...
Importing namespace Cake.Common.Tools.Fixie...
Importing namespace Cake.Common.Tools.GitLink...
Importing namespace Cake.Common.Tools.GitReleaseManager...
Importing namespace Cake.Common.Tools.GitReleaseManager.AddAssets...
Importing namespace Cake.Common.Tools.GitReleaseManager.Close...
Importing namespace Cake.Common.Tools.GitReleaseManager.Create...
Importing namespace Cake.Common.Tools.GitReleaseManager.Discard...
Importing namespace Cake.Common.Tools.GitReleaseManager.Export...
Importing namespace Cake.Common.Tools.GitReleaseManager.Label...
Importing namespace Cake.Common.Tools.GitReleaseManager.Open...
Importing namespace Cake.Common.Tools.GitReleaseManager.Publish...
Importing namespace Cake.Common.Tools.GitReleaseNotes...
Importing namespace Cake.Common.Tools.GitVersion...
Importing namespace Cake.Common.Tools.ILMerge...
Importing namespace Cake.Common.Tools.ILRepack...
Importing namespace Cake.Common.Tools.InnoSetup...
Importing namespace Cake.Common.Tools.InspectCode...
Importing namespace Cake.Common.Tools.MSBuild...
Importing namespace Cake.Common.Tools.MSpec...
Importing namespace Cake.Common.Tools.MSTest...
Importing namespace Cake.Common.Tools.NSIS...
Importing namespace Cake.Common.Tools.NuGet...
Importing namespace Cake.Common.Tools.NuGet.Add...
Importing namespace Cake.Common.Tools.NuGet.Delete...
Importing namespace Cake.Common.Tools.NuGet.Init...
Importing namespace Cake.Common.Tools.NuGet.Install...
Importing namespace Cake.Common.Tools.NuGet.List...
Importing namespace Cake.Common.Tools.NuGet.Pack...
Importing namespace Cake.Common.Tools.NuGet.Push...
Importing namespace Cake.Common.Tools.NuGet.Restore...
Importing namespace Cake.Common.Tools.NuGet.SetApiKey...
Importing namespace Cake.Common.Tools.NuGet.SetProxy...
Importing namespace Cake.Common.Tools.NuGet.Sources...
Importing namespace Cake.Common.Tools.NuGet.Update...
Importing namespace Cake.Common.Tools.NUnit...
Importing namespace Cake.Common.Tools.OctopusDeploy...
Importing namespace Cake.Common.Tools.OpenCover...
Importing namespace Cake.Common.Tools.ReportGenerator...
Importing namespace Cake.Common.Tools.ReportUnit...
Importing namespace Cake.Common.Tools.Roundhouse...
Importing namespace Cake.Common.Tools.SignTool...
Importing namespace Cake.Common.Tools.SpecFlow...
Importing namespace Cake.Common.Tools.SpecFlow.StepDefinitionReport...
Importing namespace Cake.Common.Tools.SpecFlow.TestExecutionReport...
Importing namespace Cake.Common.Tools.TextTransform...
Importing namespace Cake.Common.Tools.VSTest...
Importing namespace Cake.Common.Tools.VSWhere...
Importing namespace Cake.Common.Tools.VSWhere.All...
Importing namespace Cake.Common.Tools.VSWhere.Latest...
Importing namespace Cake.Common.Tools.VSWhere.Legacy...
Importing namespace Cake.Common.Tools.VSWhere.Product...
Importing namespace Cake.Common.Tools.WiX...
Importing namespace Cake.Common.Tools.WiX.Heat...
Importing namespace Cake.Common.Tools.XBuild...
Importing namespace Cake.Common.Tools.XUnit...
Importing namespace Cake.Common.Xml...
Importing namespace Cake.Core...
Importing namespace Cake.Core.Diagnostics...
Importing namespace Cake.Core.IO...
Importing namespace Cake.Core.Scripting...
Importing namespace System...
Importing namespace System.Collections.Generic...
Importing namespace System.IO...
Importing namespace System.Linq...
Importing namespace System.Text...
Importing namespace System.Threading.Tasks...
Compiling build script...
```

Reproduce the report with the listed .NET tool-manifest commands and the minimal build.cake script on Windows or an equivalent environment. Trace the automatic bootstrapping and warning output shown in the log, then verify that each warning is emitted only once and that the existing build command still completes as expected.

Written by the indexing model from the issue text.