Lately Issues with connecting to dynamics CRM 365 online using Plugin Registration, Migration utitlity , package deployer tool etc have been faced by many. Below common issues are faced by people:

1. metadata contains a reference that cannot be resolved at (……)
2. once you login , it does connects to the org but nothing happens. no error.
3. Internal server error.

the quick and easy resolution the above issues is to get the latest versions of all these tools from nuget manager by using powershell or visiting http://xrm.tools/ and not the one which is available under microsoft downloads.

Download tools using PowerShell

1. In your Windows Start menu, type Windows Powershell and open it.
2. Navigate to the folder you want to install the tools to. For example if you want to install them in a devtools folder on your D drive, type cd D:\devtools.
3. Copy and paste the following PowerShell script into the PowerShell window and press Enter.

   $sourceNugetExe = "https://dist.nuget.org/win-x86-commandline/latest/nuget.exe"
   $targetNugetExe = ".\nuget.exe"
   Remove-Item .\Tools -Force -Recurse -ErrorAction Ignore
   Invoke-WebRequest $sourceNugetExe -OutFile $targetNugetExe
   Set-Alias nuget $targetNugetExe -Scope Global -Verbose
   
   ##
   ##Download Plugin Registration Tool
   ##
   ./nuget install Microsoft.CrmSdk.XrmTooling.PluginRegistrationTool -O .\Tools
   md .\Tools\PluginRegistration
   $prtFolder = Get-ChildItem ./Tools | Where-Object {$_.Name -match 'Microsoft.CrmSdk.XrmTooling.PluginRegistrationTool.'}
   move .\Tools\$prtFolder\tools\*.* .\Tools\PluginRegistration
   Remove-Item .\Tools\$prtFolder -Force -Recurse
   
   ##
   ##Download CoreTools
   ##
   ./nuget install Microsoft.CrmSdk.CoreTools -O .\Tools
   md .\Tools\CoreTools
   $coreToolsFolder = Get-ChildItem ./Tools | Where-Object {$_.Name -match 'Microsoft.CrmSdk.CoreTools.'}
   move .\Tools\$coreToolsFolder\content\bin\coretools\*.* .\Tools\CoreTools
   Remove-Item .\Tools\$coreToolsFolder -Force -Recurse
   
   ##
   ##Download Configuration Migration
   ##
   ./nuget install Microsoft.CrmSdk.XrmTooling.ConfigurationMigration.Wpf -O .\Tools
   md .\Tools\ConfigurationMigration
   $configMigFolder = Get-ChildItem ./Tools | Where-Object {$_.Name -match 'Microsoft.CrmSdk.XrmTooling.ConfigurationMigration.Wpf.'}
   move .\Tools\$configMigFolder\tools\*.* .\Tools\ConfigurationMigration
   Remove-Item .\Tools\$configMigFolder -Force -Recurse
   
   ##
   ##Download Package Deployer 
   ##
   ./nuget install Microsoft.CrmSdk.XrmTooling.PackageDeployment.WPF -O .\Tools
   md .\Tools\PackageDeployment
   $pdFolder = Get-ChildItem ./Tools | Where-Object {$_.Name -match 'Microsoft.CrmSdk.XrmTooling.PackageDeployment.Wpf.'}
   move .\Tools\$pdFolder\tools\*.* .\Tools\PackageDeployment
   Remove-Item .\Tools\$pdFolder -Force -Recurse
   
   ##
   ##Remove NuGet.exe
   ##
   Remove-Item nuget.exe

1. You will find the tools in the following folders:

• [Your folder]\Tools\ConfigurationMigration
• [Your folder]\Tools\CoreTools
• [Your folder]\Tools\PackageDeployment
• [Your folder]\Tools\PluginRegistration

i hope this helps!