diff --git a/Source/v2/Meadow.CLI/Commands/Current/App/AppTools.cs b/Source/v2/Meadow.CLI/Commands/Current/App/AppTools.cs
index 59435a9a..8b50d7ba 100644
--- a/Source/v2/Meadow.CLI/Commands/Current/App/AppTools.cs
+++ b/Source/v2/Meadow.CLI/Commands/Current/App/AppTools.cs
@@ -7,8 +7,6 @@ namespace Meadow.CLI.Commands.DeviceManagement;
 
 internal static class AppTools
 {
-    internal const string MeadowRootFolder = "meadow0";
-
     internal static string ValidateAndSanitizeAppPath(string? path)
     {
         path ??= Directory.GetCurrentDirectory();
@@ -124,15 +122,15 @@ internal static string SanitizeMeadowFilename(string fileName)
 
         if (string.IsNullOrWhiteSpace(folder))
         {
-            folder = Path.DirectorySeparatorChar + MeadowRootFolder;
+            folder = Path.DirectorySeparatorChar + AppManager.MeadowRootFolder;
         }
         else
         {
             if (!folder.StartsWith(Path.DirectorySeparatorChar))
             {
-                if (!folder.StartsWith($"{MeadowRootFolder}"))
+                if (!folder.StartsWith($"{AppManager.MeadowRootFolder}"))
                 {
-                    folder = $"{Path.DirectorySeparatorChar}{MeadowRootFolder}{Path.DirectorySeparatorChar}{folder}";
+                    folder = $"{Path.DirectorySeparatorChar}{AppManager.MeadowRootFolder}{Path.DirectorySeparatorChar}{folder}";
                 }
                 else
                 {
diff --git a/Source/v2/Meadow.Cli/Commands/Current/File/FileDeleteCommand.cs b/Source/v2/Meadow.Cli/Commands/Current/File/FileDeleteCommand.cs
index fb789510..bf3da405 100644
--- a/Source/v2/Meadow.Cli/Commands/Current/File/FileDeleteCommand.cs
+++ b/Source/v2/Meadow.Cli/Commands/Current/File/FileDeleteCommand.cs
@@ -76,6 +76,15 @@ protected override async ValueTask ExecuteCommand()
     private async Task DeleteFileRecursive(IMeadowDevice device, string directoryname, MeadowFileInfo fileInfo, CancellationToken cancellationToken)
     {
         var meadowFile = AppTools.SanitizeMeadowFilename(Path.Combine(directoryname, fileInfo.Name));
+
+        foreach (var folder in AppManager.PersistantFolders)
+        {
+            if (meadowFile.StartsWith($"/{AppManager.MeadowRootFolder}/{folder}"))
+            {
+                return;
+            }
+        }
+
         if (fileInfo.IsDirectory)
         {
             // Add a backslash as we're a directory and not a file
diff --git a/Source/v2/Meadow.Cli/Commands/Current/File/FileListCommand.cs b/Source/v2/Meadow.Cli/Commands/Current/File/FileListCommand.cs
index 8061345b..8db5b576 100644
--- a/Source/v2/Meadow.Cli/Commands/Current/File/FileListCommand.cs
+++ b/Source/v2/Meadow.Cli/Commands/Current/File/FileListCommand.cs
@@ -35,7 +35,7 @@ protected override async ValueTask ExecuteCommand()
             Logger?.LogInformation($"Getting file list...");
         }
 
-        var files = await device.GetFileList(Folder ?? $"/{AppTools.MeadowRootFolder}/", Verbose, CancellationToken);
+        var files = await device.GetFileList(Folder ?? $"/{AppManager.MeadowRootFolder}/", Verbose, CancellationToken);
 
         if (files == null || files.Length == 0)
         {
diff --git a/Source/v2/Meadow.Cli/Commands/Current/Firmware/FirmwareWriteCommand.cs b/Source/v2/Meadow.Cli/Commands/Current/Firmware/FirmwareWriteCommand.cs
index b1d436b9..b489e7e5 100644
--- a/Source/v2/Meadow.Cli/Commands/Current/Firmware/FirmwareWriteCommand.cs
+++ b/Source/v2/Meadow.Cli/Commands/Current/Firmware/FirmwareWriteCommand.cs
@@ -223,7 +223,7 @@ protected override async ValueTask ExecuteCommand()
             }
             else
             {
-                await connection!.Device!.WriteFile(osFileWithoutBootloader, $"/{AppTools.MeadowRootFolder}/update/os/{package.OsWithoutBootloader}");
+                await connection!.Device!.WriteFile(osFileWithoutBootloader, $"/{AppManager.MeadowRootFolder}/update/os/{package.OsWithoutBootloader}");
             }
         }
 
@@ -361,7 +361,7 @@ private async Task<IMeadowConnection> FindMeadowConnection(IList<string> portsTo
         }
         else
         {
-            await connection.Device!.WriteFile(runtimePath, $"/{AppTools.MeadowRootFolder}/update/os/{destinationFilename}");
+            await connection.Device!.WriteFile(runtimePath, $"/{AppManager.MeadowRootFolder}/update/os/{destinationFilename}");
         }
 
         return connection;
@@ -403,7 +403,7 @@ private async Task WriteEspFiles(IMeadowConnection? connection, DeviceInfo? devi
         {
             foreach (var file in fileList)
             {
-                await connection!.Device!.WriteFile(file, $"/{AppTools.MeadowRootFolder}/update/os/{Path.GetFileName(file)}");
+                await connection!.Device!.WriteFile(file, $"/{AppManager.MeadowRootFolder}/update/os/{Path.GetFileName(file)}");
                 await Task.Delay(500);
             }
         }
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/DownloadOsCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/DownloadOsCommand.cs
deleted file mode 100644
index 5995118d..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/DownloadOsCommand.cs
+++ /dev/null
@@ -1,16 +0,0 @@
-using CliFx.Attributes;
-using Meadow.Cloud.Client;
-using Meadow.Software;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("download os", Description = "** Deprecated ** Use `firmware download` instead")]
-public class DownloadOsCommand : FirmwareDownloadCommand
-{
-    public DownloadOsCommand(FileManager fileManager, IMeadowCloudClient meadowCloudClient, ILoggerFactory loggerFactory)
-        : base(fileManager, meadowCloudClient, loggerFactory)
-    {
-        Logger.LogWarning($"Deprecated command - use `firmware download` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/FlashOsCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/FlashOsCommand.cs
deleted file mode 100644
index 00fad646..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/FlashOsCommand.cs
+++ /dev/null
@@ -1,20 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("flash os", Description = "** Deprecated ** Use `firmware write` instead")]
-public class FlashOsCommand : BaseDeviceCommand<FlashOsCommand>
-{
-    public FlashOsCommand(
-            MeadowConnectionManager connectionManager,
-            ILoggerFactory loggerFactory)
-        : base(connectionManager, loggerFactory)
-    {
-    }
-
-    protected override ValueTask ExecuteCommand()
-    {
-        throw new CommandException($"Deprecated command. Use `firmware write` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/InstallDfuCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/InstallDfuCommand.cs
deleted file mode 100644
index a28bb0c3..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/InstallDfuCommand.cs
+++ /dev/null
@@ -1,14 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("install dfu", Description = "** Deprecated ** Use `dfu install` instead")]
-public class InstallDfuCommand : DfuInstallCommand
-{
-    public InstallDfuCommand(ISettingsManager settingsManager, ILoggerFactory loggerFactory)
-        : base(settingsManager, loggerFactory, "0.11")
-    {
-        Logger?.LogWarning($"Deprecated command - use `dfu install` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/ListPortsCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/ListPortsCommand.cs
deleted file mode 100644
index d99402d2..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/ListPortsCommand.cs
+++ /dev/null
@@ -1,19 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("list ports", Description = "** Deprecated ** Use `port list` instead")]
-public class ListPortsCommand : PortListCommand
-{
-    public ListPortsCommand(ISettingsManager settingsManager, ILoggerFactory loggerFactory)
-        : base(loggerFactory)
-    {
-        Logger?.LogWarning($"Deprecated command - use `port list` instead");
-    }
-
-    protected override ValueTask ExecuteCommand()
-    {
-        return base.ExecuteCommand();
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/MonoDisableCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/MonoDisableCommand.cs
deleted file mode 100644
index 8d9e63bf..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/MonoDisableCommand.cs
+++ /dev/null
@@ -1,14 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("mono disable", Description = "** Deprecated ** Use `runtime disable` instead")]
-public class MonoDisableCommand : RuntimeDisableCommand
-{
-    public MonoDisableCommand(MeadowConnectionManager connectionManager, ILoggerFactory loggerFactory)
-        : base(connectionManager, loggerFactory)
-    {
-        Logger?.LogWarning($"Deprecated command - use `runtime disable` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/MonoEnableCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/MonoEnableCommand.cs
deleted file mode 100644
index d19bafe9..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/MonoEnableCommand.cs
+++ /dev/null
@@ -1,14 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("mono enable", Description = "** Deprecated ** Use `runtime enable` instead")]
-public class MonoEnableCommand : RuntimeEnableCommand
-{
-    public MonoEnableCommand(MeadowConnectionManager connectionManager, ILoggerFactory loggerFactory)
-        : base(connectionManager, loggerFactory)
-    {
-        Logger?.LogWarning($"Deprecated command - use `runtime enable` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/MonoStateCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/MonoStateCommand.cs
deleted file mode 100644
index 4fd2a7d3..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/MonoStateCommand.cs
+++ /dev/null
@@ -1,14 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("mono state", Description = "** Deprecated ** Use `runtime state` instead")]
-public class MonoStateCommand : RuntimeStateCommand
-{
-    public MonoStateCommand(MeadowConnectionManager connectionManager, ILoggerFactory loggerFactory)
-        : base(connectionManager, loggerFactory)
-    {
-        Logger?.LogWarning($"Deprecated command - use `runtime state` instead");
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Commands/Legacy/UsePortCommand.cs b/Source/v2/Meadow.Cli/Commands/Legacy/UsePortCommand.cs
deleted file mode 100644
index c46db0fa..00000000
--- a/Source/v2/Meadow.Cli/Commands/Legacy/UsePortCommand.cs
+++ /dev/null
@@ -1,28 +0,0 @@
-using CliFx.Attributes;
-using Microsoft.Extensions.Logging;
-
-namespace Meadow.CLI.Commands.DeviceManagement;
-
-[Command("use port", Description = "** Deprecated ** Use `port select` (if connecting via serial port) or `config route` (if connecting via IP) instead")]
-public class UsePortCommand : BaseCommand<UsePortCommand>
-{
-    private readonly ISettingsManager _settingsManager;
-
-    [CommandParameter(0, Name = "Port", IsRequired = true)]
-    public string Port { get; set; } = default!;
-
-    public UsePortCommand(ILoggerFactory loggerFactory, ISettingsManager settingsManager)
-        : base(loggerFactory)
-    {
-        Logger?.LogWarning($"Deprecated command -use `config route` instead");
-        _settingsManager = settingsManager;
-    }
-
-    protected override ValueTask ExecuteCommand()
-    {
-        _settingsManager.SaveSetting("route", Port);
-        Logger?.LogInformation($"Using {Port}");
-
-        return ValueTask.CompletedTask;
-    }
-}
\ No newline at end of file
diff --git a/Source/v2/Meadow.Cli/Meadow.CLI.csproj b/Source/v2/Meadow.Cli/Meadow.CLI.csproj
index 3624b1bf..ce3c5ca7 100644
--- a/Source/v2/Meadow.Cli/Meadow.CLI.csproj
+++ b/Source/v2/Meadow.Cli/Meadow.CLI.csproj
@@ -10,7 +10,7 @@
     <Authors>Wilderness Labs, Inc</Authors>
     <Company>Wilderness Labs, Inc</Company>
     <GeneratePackageOnBuild>true</GeneratePackageOnBuild>
-    <PackageVersion>2.0.54.0</PackageVersion>
+    <PackageVersion>2.0.55.0</PackageVersion>
     <Platforms>AnyCPU</Platforms>
     <PackageProjectUrl>http://developer.wildernesslabs.co/Meadow/Meadow.CLI/</PackageProjectUrl>
     <RepositoryUrl>https://github.com/WildernessLabs/Meadow.CLI</RepositoryUrl>
diff --git a/Source/v2/Meadow.Cli/Properties/AssemblyInfo.cs b/Source/v2/Meadow.Cli/Properties/AssemblyInfo.cs
index fe1b57c9..be708e11 100644
--- a/Source/v2/Meadow.Cli/Properties/AssemblyInfo.cs
+++ b/Source/v2/Meadow.Cli/Properties/AssemblyInfo.cs
@@ -6,5 +6,5 @@ namespace Meadow.CLI;
 
 public static class Constants
 {
-    public const string CLI_VERSION = "2.0.54.0";
+    public const string CLI_VERSION = "2.0.55.0";
 }
\ No newline at end of file
diff --git a/Source/v2/Meadow.Tooling.Core/App/AppManager.cs b/Source/v2/Meadow.Tooling.Core/App/AppManager.cs
index a08b74b0..8a6722f3 100644
--- a/Source/v2/Meadow.Tooling.Core/App/AppManager.cs
+++ b/Source/v2/Meadow.Tooling.Core/App/AppManager.cs
@@ -14,13 +14,14 @@ namespace Meadow.CLI;
 
 public static class AppManager
 {
-    static readonly string MeadowRootFolder = "meadow0";
+    public static readonly string MeadowRootFolder = "meadow0";
 
-    static readonly string[] PersistantFolders = new string[]
+    public static readonly string[] PersistantFolders = new string[]
     {
         "Data",
         "Documents",
         "update-store",
+        "system",
     };
 
     private static bool MatchingDllExists(string file)
@@ -132,8 +133,13 @@ public static async Task DeployApplication(
         // delete those files
         foreach (var file in removeFiles)
         {
+            if (PersistantFolders.Contains(file.Path))
+            {
+                continue;
+            }
+
             logger?.LogInformation($"Deleting '{file}'");
-            var folder = string.IsNullOrEmpty(file.Path) ? $"/{MeadowRootFolder}/" : $"{file.Path}";
+            var folder = string.IsNullOrEmpty(file.Path) ? $"/{MeadowRootFolder}/" : $"/{MeadowRootFolder}/{file.Path}/";
 
             await connection.DeleteFile($"{folder}{file.Name}", cancellationToken);
         }