diff --git a/azure-pipelines/end-to-end-tests-dir/create.ps1 b/azure-pipelines/end-to-end-tests-dir/create.ps1
index 61bd564777..7c270b2b98 100644
--- a/azure-pipelines/end-to-end-tests-dir/create.ps1
+++ b/azure-pipelines/end-to-end-tests-dir/create.ps1
@@ -3,8 +3,13 @@
 # Test vcpkg create
 $Script:CurrentTest = "create zlib"
 Write-Host $Script:CurrentTest
-Run-Vcpkg --x-builtin-ports-root=$TestingRoot/ports create zlib https://github.com/madler/zlib/archive/v1.2.11.tar.gz zlib-1.2.11.tar.gz
+$RegistryRoot = Join-Path $TestingRoot 'registry_for_create'
+& $GitExe init $RegistryRoot
+Throw-IfFailed
+Run-Vcpkg x-init-registry $RegistryRoot
+Throw-IfFailed
+Run-Vcpkg --x-registry-root=$RegistryRoot create zlib https://github.com/madler/zlib/archive/v1.2.11.tar.gz zlib-1.2.11.tar.gz
 Throw-IfFailed
 
-Require-FileExists "$TestingRoot/ports/zlib/portfile.cmake"
-Require-FileExists "$TestingRoot/ports/zlib/vcpkg.json"
+Require-FileExists "$RegistryRoot/ports/zlib/portfile.cmake"
+Require-FileExists "$RegistryRoot/ports/zlib/vcpkg.json"
diff --git a/azure-pipelines/end-to-end-tests-dir/registries.ps1 b/azure-pipelines/end-to-end-tests-dir/registries.ps1
index 0a1f39e35c..77b479ed12 100644
--- a/azure-pipelines/end-to-end-tests-dir/registries.ps1
+++ b/azure-pipelines/end-to-end-tests-dir/registries.ps1
@@ -1,6 +1,6 @@
 . "$PSScriptRoot/../end-to-end-tests-prelude.ps1"
 
-$builtinRegistryArgs = $commonArgs + @("--x-builtin-registry-versions-dir=$PSScriptRoot/../e2e_ports/versions")
+$builtinRegistryArgs = $commonArgs
 
 Run-Vcpkg install @builtinRegistryArgs 'vcpkg-internal-e2e-test-port'
 Throw-IfNotFailed
diff --git a/azure-pipelines/end-to-end-tests-dir/versions.ps1 b/azure-pipelines/end-to-end-tests-dir/versions.ps1
index 7475638b67..0ccc4b70a8 100644
--- a/azure-pipelines/end-to-end-tests-dir/versions.ps1
+++ b/azure-pipelines/end-to-end-tests-dir/versions.ps1
@@ -2,18 +2,34 @@
 
 $versionFilesPath = "$PSScriptRoot/../e2e_ports/version-files"
 
+# create custom registry for testing
+$RegistryRootComplete = Join-Path $TestingRoot 'registry_for_versions_complete'
+& $GitExe init $RegistryRootComplete
+Throw-IfFailed
+$RegistryRootIncomplete = Join-Path $TestingRoot 'registry_for_versions_incomplete'
+& $GitExe init $RegistryRootIncomplete
+Throw-IfFailed
+
 # Test verify versions
-mkdir $VersionFilesRoot | Out-Null
-Copy-Item -Recurse "$versionFilesPath/versions_incomplete" $VersionFilesRoot
+Copy-Item -Recurse "$versionFilesPath/versions" "$RegistryRootComplete/versions"
+Copy-Item -Recurse "$versionFilesPath/ports" "$RegistryRootComplete/ports"
+& $GitExe -C "$RegistryRootComplete" add -A 
+Throw-IfFailed
+& $GitExe -C "$RegistryRootComplete" commit -m "add files"
+Throw-IfFailed
+Copy-Item -Recurse "$versionFilesPath/versions_incomplete" "$RegistryRootIncomplete/versions"
+Copy-Item -Recurse "$versionFilesPath/ports_incomplete" "$RegistryRootIncomplete/ports"
+& $GitExe -C "$RegistryRootIncomplete" add -A
+Throw-IfFailed
+& $GitExe -C "$RegistryRootIncomplete" commit -m "add files"
+Throw-IfFailed
 $portsRedirectArgsOK = @(
     "--feature-flags=versions",
-    "--x-builtin-ports-root=$versionFilesPath/ports",
-    "--x-builtin-registry-versions-dir=$versionFilesPath/versions"
+    "--x-registry-root=$RegistryRootComplete"
 )
 $portsRedirectArgsIncomplete = @(
     "--feature-flags=versions",
-    "--x-builtin-ports-root=$versionFilesPath/ports_incomplete",
-    "--x-builtin-registry-versions-dir=$VersionFilesRoot/versions_incomplete"
+    "--x-registry-root=$RegistryRootIncomplete"
 )
 $CurrentTest = "x-verify-ci-versions (All files OK)"
 Write-Host $CurrentTest
@@ -78,23 +94,20 @@ foreach ($opt_registries in @("",",registries"))
     Remove-Item -Recurse $buildtreesRoot/versioning -ErrorAction SilentlyContinue
     Run-Vcpkg @commonArgs "--feature-flags=versions$opt_registries" install `
         "--dry-run" `
-        "--x-manifest-root=$versionFilesPath/without-default-baseline-2" `
-        "--x-builtin-registry-versions-dir=$versionFilesPath/default-baseline-2/versions"
+        "--x-manifest-root=$versionFilesPath/without-default-baseline-2"
     Throw-IfFailed
     Require-FileNotExists $buildtreesRoot/versioning
 
     $CurrentTest = "default baseline 2"
     Run-Vcpkg @commonArgs "--feature-flags=versions$opt_registries" install `
         "--dry-run" `
-        "--x-manifest-root=$versionFilesPath/default-baseline-2" `
-        "--x-builtin-registry-versions-dir=$versionFilesPath/default-baseline-2/versions"
+        "--x-manifest-root=$versionFilesPath/default-baseline-2"
     Throw-IfFailed
     Require-FileExists $buildtreesRoot/versioning
 
     $CurrentTest = "using version features fails without flag"
     Run-Vcpkg @commonArgs "--feature-flags=-versions$opt_registries" install `
         "--dry-run" `
-        "--x-manifest-root=$versionFilesPath/default-baseline-2" `
-        "--x-builtin-registry-versions-dir=$versionFilesPath/default-baseline-2/versions"
+        "--x-manifest-root=$versionFilesPath/default-baseline-2"
     Throw-IfNotFailed
 }
diff --git a/azure-pipelines/end-to-end-tests-prelude.ps1 b/azure-pipelines/end-to-end-tests-prelude.ps1
index ca9f98a0d9..8501027339 100644
--- a/azure-pipelines/end-to-end-tests-prelude.ps1
+++ b/azure-pipelines/end-to-end-tests-prelude.ps1
@@ -17,6 +17,14 @@ $commonArgs = @(
 )
 $Script:CurrentTest = 'unassigned'
 $env:X_VCPKG_REGISTRIES_CACHE = Join-Path $TestingRoot 'registries'
+if ($IsWindows)
+{
+    $GitExe = 'git.exe'
+}
+else
+{
+    $GitExe = 'git'
+}
 
 function Refresh-TestRoot {
     Remove-Item -Recurse -Force $TestingRoot -ErrorAction SilentlyContinue