diff --git a/azure-pipelines/e2e_projects/overlays-bad-paths/vcpkg-configuration.json b/azure-pipelines/e2e_projects/overlays-bad-paths/vcpkg-configuration.json
index ca49482b31..827dc498e6 100644
--- a/azure-pipelines/e2e_projects/overlays-bad-paths/vcpkg-configuration.json
+++ b/azure-pipelines/e2e_projects/overlays-bad-paths/vcpkg-configuration.json
@@ -1,4 +1,4 @@
 {
-  "overlay-ports": [ "./azure-pipelines/e2e_projects/overlays-project-with-config/config-overlays" ],
+  "overlay-ports": [ "./azure-pipelines/e2e_projects/overlays-project-with-config/config-overlays/nonexistent" ],
   "overlay-triplets": [ 123 ]
 }
diff --git a/azure-pipelines/end-to-end-tests-dir/overlays.ps1 b/azure-pipelines/end-to-end-tests-dir/overlays.ps1
index f91bf42d11..9d5bf445c1 100644
--- a/azure-pipelines/end-to-end-tests-dir/overlays.ps1
+++ b/azure-pipelines/end-to-end-tests-dir/overlays.ps1
@@ -1,9 +1,13 @@
 . $PSScriptRoot/../end-to-end-tests-prelude.ps1
 
 # Tests a simple project with overlay ports and triplets configured on a vcpkg-configuration.json file
-$e2eProjects = "$PSScriptRoot/../e2e_projects"
+Copy-Item -Recurse -LiteralPath @(
+    "$PSScriptRoot/../e2e_projects/overlays-project-with-config",
+    "$PSScriptRoot/../e2e_projects/overlays-project-config-embedded",
+    "$PSScriptRoot/../e2e_projects/overlays-bad-paths"
+    ) $TestingRoot
 
-$manifestRoot = "$e2eProjects/overlays-project-with-config"
+$manifestRoot = "$TestingRoot/overlays-project-with-config"
 $env:VCPKG_OVERLAY_PORTS = "$manifestRoot/env-overlays"
 
 Run-Vcpkg install --x-manifest-root=$manifestRoot `
@@ -13,7 +17,7 @@ Run-Vcpkg install --x-manifest-root=$manifestRoot `
 Throw-IfFailed
 
 # Tests overlays configured in env and cli on a project with configuration embedded on the manifest file
-$manifestRoot = "$e2eProjects/overlays-project-config-embedded"
+$manifestRoot = "$TestingRoot/overlays-project-config-embedded"
 $env:VCPKG_OVERLAY_PORTS = "$manifestRoot/env-overlays"
 Run-Vcpkg install --x-manifest-root=$manifestRoot `
     --overlay-ports=$manifestRoot/cli-overlays `
@@ -22,7 +26,7 @@ Run-Vcpkg install --x-manifest-root=$manifestRoot `
 Throw-IfFailed
 
 # Config with bad paths
-$manifestRoot = "$e2eProjects/overlays-bad-paths"
+$manifestRoot = "$TestingRoot/overlays-bad-paths"
 $env:VCPKG_OVERLAY_PORTS = "$manifestRoot/env_overlays"
 Run-Vcpkg install --x-manifest-root=$manifestRoot `
     --overlay-triplets=$manifestRoot/my-triplets `
@@ -30,7 +34,7 @@ Run-Vcpkg install --x-manifest-root=$manifestRoot `
 Throw-IfNotFailed
 
 # Test overlay_triplet paths remain relative to the manifest root after x-update-baseline
-$manifestRoot = "$e2eProjects/overlays-project-with-config"
+$manifestRoot = "$TestingRoot/overlays-project-with-config"
 $configurationBefore = Get-Content "$manifestRoot/vcpkg-configuration.json" | ConvertFrom-Json
 Run-Vcpkg x-update-baseline --x-manifest-root=$manifestRoot
 $configurationAfter = Get-Content "$manifestRoot/vcpkg-configuration.json" | ConvertFrom-Json
diff --git a/azure-pipelines/end-to-end-tests-dir/patterns.ps1 b/azure-pipelines/end-to-end-tests-dir/patterns.ps1
index 8cc837ee29..b34948cce7 100644
--- a/azure-pipelines/end-to-end-tests-dir/patterns.ps1
+++ b/azure-pipelines/end-to-end-tests-dir/patterns.ps1
@@ -1,84 +1,94 @@
 . $PSScriptRoot/../end-to-end-tests-prelude.ps1
 
-### <Initialize registry>
-# Creates a git registry to run the e2e tests on
-$e2eProjects = "$PSScriptRoot/../e2e_projects"
-$manifestRoot = "$e2eProjects/registries-package-patterns"
-$e2eRegistryPath = "$PSScriptRoot/../e2e_registry".Replace('\', '\\')
-Push-Location $e2eRegistryPath
 try
 {
-	Write-Host "Initializing test registry"
-	if (Test-Path "$e2eRegistryPath/.git")
-	{
-		Remove-Item -Recurse -Force "$e2eRegistryPath/.git"
-	}
-	
+    Copy-Item -Recurse -LiteralPath @(
+        "$PSScriptRoot/../e2e_projects/registries-package-patterns",
+        "$PSScriptRoot/../e2e_registry"
+        ) $WorkingRoot
 
-	$gitConfig = @(
-		'-c', 'user.name=Nobody',
-		'-c', 'user.email=nobody@example.com',
-		'-c', 'core.autocrlf=false'
-	)
+    $manifestRoot = "$WorkingRoot/registries-package-patterns"
+    $e2eRegistryPath = "$WorkingRoot/e2e_registry".Replace('\', '\\')
+    Push-Location $e2eRegistryPath
+    ### <Initialize registry>
+    # Creates a git registry to run the e2e tests on
+    try
+    {
+        Write-Host "Initializing test registry"
+        if (Test-Path "$e2eRegistryPath/.git")
+        {
+            Remove-Item -Recurse -Force "$e2eRegistryPath/.git"
+        }
+        
 
-	git @gitConfig init . | Out-Null
-	Throw-IfFailed
-	git @gitConfig add -A | Out-Null
-	Throw-IfFailed
-	git @gitConfig commit -m "initial commit" | Out-Null
-	Throw-IfFailed
-	$e2eRegistryBaseline = git rev-parse HEAD
-	Throw-IfFailed
-}
-finally 
-{
-	Pop-Location
-}
-### </Initialize Registry>
+        $gitConfig = @(
+            '-c', 'user.name=Nobody',
+            '-c', 'user.email=nobody@example.com',
+            '-c', 'core.autocrlf=false'
+        )
 
-$commonArgs += @("--x-manifest-root=$manifestRoot")
+        git @gitConfig init . | Out-Null
+        Throw-IfFailed
+        git @gitConfig add -A | Out-Null
+        Throw-IfFailed
+        git @gitConfig commit -m "initial commit" | Out-Null
+        Throw-IfFailed
+        $e2eRegistryBaseline = git rev-parse HEAD
+        Throw-IfFailed
+    }
+    finally 
+    {
+        Pop-Location
+    }
+    ### </Initialize Registry>
 
-# [patterns] No patterns (no default)
-Write-Host "[patterns] No patterns (no default)"
-$inFile = "$manifestRoot/no-patterns.json.in"
-(Get-Content -Path "$inFile").Replace("`$E2ERegistryPath", $e2eRegistryPath).Replace("`$E2ERegistryBaseline", $e2eRegistryBaseline) `
-| Out-File "$manifestRoot/vcpkg.json"
+    function Update-VcpkgJson {
+        param($PreReplacementName)
+        $content = Get-Content -LiteralPath "$manifestRoot/$PreReplacementName"
+        $content = $content.Replace('$E2ERegistryPath', $e2eRegistryPath)
+        $content = $content.Replace('$E2ERegistryBaseline', $e2eRegistryBaseline)
+        Set-Content -LiteralPath "$manifestRoot/vcpkg.json" -Value $content
+    }
 
-Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
-Throw-IfFailed
-Refresh-TestRoot
+    $commonArgs += @("--x-manifest-root=$manifestRoot")
 
-# [patterns] Patterns only (no default)
-Write-Host "[patterns] Patterns only (no default)"
-$inFile = "$manifestRoot/only-patterns.json.in"
-(Get-Content -Path "$inFile").Replace("`$E2ERegistryPath", $e2eRegistryPath).Replace("`$E2ERegistryBaseline", $e2eRegistryBaseline) `
-| Out-File "$manifestRoot/vcpkg.json"
+    # [patterns] No patterns (no default)
+    Write-Host "[patterns] No patterns (no default)"
+    Update-VcpkgJson 'no-patterns.json.in'
+    Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
+    Throw-IfFailed
+    Refresh-TestRoot
 
-Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
-Throw-IfFailed
-Refresh-TestRoot
+    # [patterns] Patterns only (no default)
+    Write-Host "[patterns] Patterns only (no default)"
+    Update-VcpkgJson 'only-patterns.json.in'
+    Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
+    Throw-IfFailed
+    Refresh-TestRoot
 
-# [patterns] Patterns with default
-Write-Host "[patterns] Patterns with default"
-$inFile = "$manifestRoot/with-default.json.in"
-(Get-Content -Path "$inFile").Replace("`$E2ERegistryPath", $e2eRegistryPath).Replace("`$E2ERegistryBaseline", $e2eRegistryBaseline) `
-| Out-File "$manifestRoot/vcpkg.json"
+    # [patterns] Patterns with default
+    Write-Host "[patterns] Patterns with default"
+    Update-VcpkgJson 'with-default.json.in'
+    Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
+    Throw-IfFailed
+    Refresh-TestRoot
 
-Run-Vcpkg -EndToEndTestSilent @commonArgs install | Out-Null
-Throw-IfFailed
-Refresh-TestRoot
-
-# [patterns] Repeated patterns
-Write-Host "[patterns] Repeated patterns"
-$inFile = "$manifestRoot/with-redeclaration.json.in"
-(Get-Content -Path "$inFile").Replace("`$E2ERegistryPath", $e2eRegistryPath).Replace("`$E2ERegistryBaseline", $e2eRegistryBaseline) `
-| Out-File "$manifestRoot/vcpkg.json"
-
-$out = Run-VcpkgAndCaptureOutput -EndToEndTestSilent @commonArgs install
-Throw-IfFailed
-if ($out -notmatch "redeclarations will be ignored")
+    # [patterns] Repeated patterns
+    Write-Host "[patterns] Repeated patterns"
+    Update-VcpkgJson 'with-redeclaration.json.in'
+    $out = Run-VcpkgAndCaptureOutput -EndToEndTestSilent @commonArgs install
+    Throw-IfFailed
+    if ($out -notmatch "redeclarations will be ignored")
+    {
+        $out
+        throw "Expected warning about redeclaration"
+    }
+    Refresh-TestRoot
+}
+finally
 {
-	$out
-	throw "Expected warning about redeclaration"
+    Remove-Item -Recurse -Force -LiteralPath @(
+        "$WorkingRoot/registries-package-patterns",
+        "$WorkingRoot/e2e_registry"
+        ) -ErrorAction SilentlyContinue
 }
-Refresh-TestRoot
\ No newline at end of file