Refactor BYO app copy and add overwrite confirmation

Improves the "Copy BYO Apps" functionality by centralizing the `UserAppList.json` update process. The application list is now saved once from the UI before starting the copy, rather than individually within each background task.

Adds a confirmation prompt that warns the user if any application folders already exist in the destination, allowing them to choose whether to overwrite them. The copy logic is updated to remove existing folders before copying to ensure a clean state.

FFUDevelopment/FFUUI.Core/FFUUI.Core.Applications.psm1

@@ -214,9 +214,59 @@ function Invoke-CopyBYOApps {
         [System.Windows.Controls.Button]$Button
     )
         
-    $appsToCopy = $State.Controls.lstApplications.Items | Where-Object { -not [string]::IsNullOrWhiteSpace($_.Source) }
+    $localAppsPath = $State.Controls.txtApplicationPath.Text
-    if (-not $appsToCopy) {
+    $userAppListPath = Join-Path -Path $localAppsPath -ChildPath 'UserAppList.json'
-        [System.Windows.MessageBox]::Show("No applications with a source path specified.", "Copy BYO Apps", "OK", "Information")
+    $listView = $State.Controls.lstApplications
+
+    try {
+        # Ensure items are sorted by current priority before saving
+        # Exclude CopyStatus when saving and ensure Priority is an integer
+        $applications = $listView.Items | Sort-Object Priority | Select-Object @{N = 'Priority'; E = { [int]$_.Priority } }, Name, CommandLine, Arguments, Source
+        $applications | ConvertTo-Json -Depth 5 | Set-Content -Path $userAppListPath -Force -Encoding UTF8
+        WriteLog "Successfully updated UserAppList.json with all applications from the UI."
+    }
+    catch {
+        $errorMessage = "Failed to update UserAppList.json: $_"
+        WriteLog $errorMessage
+        [System.Windows.MessageBox]::Show($errorMessage, "Error", [System.Windows.MessageBoxButton]::OK, [System.Windows.MessageBoxImage]::Error)
+        return
+    }
+
+    $allAppsWithSource = $State.Controls.lstApplications.Items | Where-Object { -not [string]::IsNullOrWhiteSpace($_.Source) }
+    if (-not $allAppsWithSource) {
+        [System.Windows.MessageBox]::Show("UserAppList.json has been updated. No applications with a source path were found to copy.", "Copy BYO Apps", "OK", "Information")
+        return
+    }
+        
+    $win32BasePath = Join-Path -Path $localAppsPath -ChildPath "Win32"
+    
+    $appsToProcess = [System.Collections.Generic.List[object]]::new()
+    $appsThatExist = [System.Collections.Generic.List[string]]::new()
+    $appsToConfirm = [System.Collections.Generic.List[object]]::new()
+
+    foreach ($app in $allAppsWithSource) {
+        $destinationPath = Join-Path -Path $win32BasePath -ChildPath $app.Name
+        if (Test-Path -Path $destinationPath -PathType Container) {
+            $appsThatExist.Add($app.Name)
+            $appsToConfirm.Add($app)
+        }
+        else {
+            $appsToProcess.Add($app)
+        }
+    }
+
+    if ($appsThatExist.Count -gt 0) {
+        $message = "The following application folders already exist in the destination and will be overwritten:`n`n$($appsThatExist -join "`n")`n`nDo you want to proceed with copying and overwriting them?"
+        $result = [System.Windows.MessageBox]::Show($message, "Confirm Overwrite", [System.Windows.MessageBoxButton]::YesNo, [System.Windows.MessageBoxImage]::Warning)
+        
+        if ($result -eq 'Yes') {
+            $appsToProcess.AddRange($appsToConfirm)
+        }
+    }
+
+    if ($appsToProcess.Count -eq 0) {
+        # This message can be suppressed if you prefer no notification when the user clicks "No"
+        # [System.Windows.MessageBox]::Show("No applications selected for copying.", "Copy BYO Apps", "OK", "Information")
         return
     }
         
@@ -225,16 +275,13 @@ function Invoke-CopyBYOApps {
     $State.Controls.pbOverallProgress.Value = 0
     $State.Controls.txtStatus.Text = "Starting BYO app copy..."
         
-    # Define necessary task-specific variables locally
-    $localAppsPath = $State.Controls.txtApplicationPath.Text
-        
     # Create hashtable for task-specific arguments
     $taskArguments = @{
         AppsPath = $localAppsPath
     }
         
     # Select only necessary properties before passing
-    $itemsToProcess = $appsToCopy | Select-Object Priority, Name, CommandLine, Arguments, Source
+    $itemsToProcess = $appsToProcess | Select-Object Priority, Name, CommandLine, Arguments, Source
         
     # Invoke the centralized parallel processing function
     # Pass task type and task-specific arguments
@@ -304,27 +351,18 @@ function Start-CopyBYOApplicationTask {
     $destinationPath = Join-Path -Path $win32BasePath -ChildPath $appName
 
     try {
-        # Check destination
-        if (Test-Path -Path $destinationPath -PathType Container) {
-            $folderSize = (Get-ChildItem -Path $destinationPath -Recurse | Measure-Object -Property Length -Sum -ErrorAction SilentlyContinue).Sum
-            if ($folderSize -gt 1MB) {
-                $status = "Already copied"
-                Invoke-ProgressUpdate -ProgressQueue $ProgressQueue -Identifier $appName -Status $status
-                WriteLog "Skipping copy for $($appName): Destination '$destinationPath' exists and has content."
-                $success = $true
-                return [PSCustomObject]@{ Name = $appName; Status = $status; Success = $success }
-            }
-            else {
-                WriteLog "Destination '$destinationPath' exists but is empty/small. Proceeding with copy."
-            }
-        }
-
         # Ensure base directory exists
         if (-not (Test-Path -Path $win32BasePath -PathType Container)) {
             New-Item -Path $win32BasePath -ItemType Directory -Force | Out-Null
             WriteLog "Created directory: $win32BasePath"
         }
 
+        # If destination exists, remove it to ensure a clean copy and prevent nesting.
+        if (Test-Path -Path $destinationPath -PathType Container) {
+            WriteLog "Removing existing destination folder: $destinationPath"
+            Remove-Item -Path $destinationPath -Recurse -Force -ErrorAction Stop
+        }
+
         # Perform the copy
         $status = "Copying..."
         Invoke-ProgressUpdate -ProgressQueue $ProgressQueue -Identifier $appName -Status $status
@@ -334,60 +372,6 @@ function Start-CopyBYOApplicationTask {
         $success = $true
         WriteLog "Successfully copied '$appName' to '$destinationPath'."
 
-        # ------------------------------------------------------------------
-        # Update (or create) UserAppList.json with the copied application
-        # ------------------------------------------------------------------
-        try {
-            WriteLog "Updating UserAppList.json for '$appName'..."
-            $userAppListPath = Join-Path -Path $AppsPath -ChildPath 'UserAppList.json'
-
-            # Build the new entry
-            $newEntry = [pscustomobject]@{
-                Priority    = [int]$priority
-                Name        = $appName
-                CommandLine = $commandLine
-                Arguments   = $arguments
-                Source      = $sourcePath
-            }
-
-            # Load existing list if present, ensuring it's always an array
-            if (Test-Path -Path $userAppListPath) {
-                try {
-                    # Attempt to load and ensure it's an array
-                    $appList = @(Get-Content -Path $userAppListPath -Raw | ConvertFrom-Json -ErrorAction Stop)
-                }
-                catch {
-                    WriteLog "Warning: Could not parse '$userAppListPath' or it's not a valid JSON array. Initializing as empty array. Error: $($_.Exception.Message)"
-                    $appList = @() # Initialize as empty array on error
-                }
-            }
-            else {
-                $appList = @() # Initialize as empty array if file doesn't exist
-            }
-
-            # Ensure $appList is an array even if ConvertFrom-Json returned $null or a single object somehow
-            if ($null -eq $appList -or $appList -isnot [array]) {
-                # If it was a single object, wrap it in an array. Otherwise, start fresh.
-                $appList = if ($null -ne $appList) { @($appList) } else { @() }
-            }
-
-            # Skip adding if an entry with the same Name already exists
-            if (-not ($appList | Where-Object { $_.Name -eq $newEntry.Name })) {
-                # Now $appList is guaranteed to be an array, so += is safe
-                $appList += $newEntry
-                # Sort by Priority before saving
-                $sortedAppList = $appList | Sort-Object Priority
-                $sortedAppList | ConvertTo-Json -Depth 10 | Set-Content -Path $userAppListPath -Encoding UTF8
-                WriteLog "Added '$($newEntry.Name)' to '$userAppListPath'."
-            }
-            else {
-                WriteLog "'$appName' already exists in '$userAppListPath'."
-            }
-        }
-        catch {
-            WriteLog "Failed to update UserAppList.json for '$appName': $($_.Exception.Message)"
-        }
-
     }
     catch {
         $errorMessage = $_.Exception.Message