diff --git a/Runtimes/NET/BepisLoader/BepisLoader.cs b/Runtimes/NET/BepisLoader/BepisLoader.cs
index 9e83cbb1..a243b9d7 100644
--- a/Runtimes/NET/BepisLoader/BepisLoader.cs
+++ b/Runtimes/NET/BepisLoader/BepisLoader.cs
@@ -1,4 +1,3 @@
-using System.Diagnostics;
 using System.Reflection;
 using System.Runtime.InteropServices;
 using System.Runtime.Loader;
@@ -11,10 +10,11 @@ public class BepisLoader
     internal static AssemblyLoadContext alc = null!;
     static void Main(string[] args)
     {
+        resoDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
 #if DEBUG
-        File.WriteAllText("BepisLoader.log", "BepisLoader started\n");
+        logPath = Path.Combine(resoDir, "BepisLoader.log");
+        File.WriteAllText(logPath, "BepisLoader started\n");
 #endif
-        resoDir = Directory.GetCurrentDirectory();
 
         alc = new BepisLoadContext();
 
@@ -31,20 +31,6 @@ static void Main(string[] args)
 
         var asm = alc.LoadFromAssemblyPath(Path.Combine(bepinPath, "core", "BepInEx.NET.CoreCLR.dll"));
 
-        // Check if we're launching from outside the game directory
-        var exePath = Process.GetCurrentProcess().MainModule?.FileName;
-        if (exePath != null)
-        {
-            var exeDir = Path.GetDirectoryName(exePath);
-            if (exeDir != resoDir)
-            {
-                // Change working directory to the game directory for direct launches
-                Log($"Changing working directory from {resoDir} to {exeDir}");
-                Directory.SetCurrentDirectory(exeDir);
-                resoDir = exeDir;
-            }
-        }
-
         var resoDllPath = Path.Combine(resoDir, "Renderite.Host.dll");
         if (!File.Exists(resoDllPath)) resoDllPath = Path.Combine(resoDir, "Resonite.dll");
 
@@ -54,18 +40,19 @@ static void Main(string[] args)
 
         // Find and load Resonite
         var resoAsm = AppDomain.CurrentDomain.GetAssemblies().FirstOrDefault(x => x.GetName().Name == "Renderite.Host");
-        if (resoAsm == null && File.Exists(resoDllPath))
-        {
-            resoAsm = alc.LoadFromAssemblyPath(resoDllPath);
-        }
+
         try
         {
+            if (resoAsm == null)
+            {
+                resoAsm = alc.LoadFromAssemblyPath(resoDllPath);
+            }
             var result = resoAsm.EntryPoint!.Invoke(null, [args]);
             if (result is Task task) task.Wait();
         }
         catch (Exception e)
         {
-            File.WriteAllLines("BepisCrash.log", [DateTime.Now.ToString("yyyy-MM-dd HH:mm:ss") + " - Resonite crashed", e.ToString()]);
+            File.WriteAllLines(Path.Combine(resoDir, "BepisCrash.log"), [DateTime.Now.ToString("yyyy-MM-dd HH:mm:ss") + " - Resonite crashed", e.ToString()]);
         }
     }
 
@@ -167,6 +154,7 @@ private static string GetUnmanagedLibraryName(string name)
     }
 
 #if DEBUG
+    private static string logPath;
     private static object _lock = new object();
 #endif
     public static void Log(string message)
@@ -174,7 +162,7 @@ public static void Log(string message)
 #if DEBUG
         lock (_lock)
         {
-            File.AppendAllLines("BepisLoader.log", [message]);
+            File.AppendAllLines(logPath, [message]);
         }
 #endif
     }
diff --git a/build/Program.cs b/build/Program.cs
index 9dfad98a..21f51bcb 100644
--- a/build/Program.cs
+++ b/build/Program.cs
@@ -4,6 +4,7 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using System.Runtime.Versioning;
 using System.Text;
 using Cake.Common;
 using Cake.Common.IO;
@@ -573,10 +574,74 @@ public override void Run(BuildContext ctx)
     }
 }
 
+[TaskName("FixThunderstoreLinuxPermissions")]
+[IsDependentOn(typeof(BuildThunderstorePackageTask))]
+[SupportedOSPlatform("linux")]
+public sealed class FixThunderstoreLinuxPermissionsTask : FrostingTask<BuildContext>
+{
+    public override bool ShouldRun(BuildContext ctx) =>
+        ctx.Distributions.Any(d => d.Runtime == "BepisLoader") &&
+        System.Runtime.InteropServices.RuntimeInformation.IsOSPlatform(System.Runtime.InteropServices.OSPlatform.Linux);
+
+    [SupportedOSPlatform("linux")]
+    public override void Run(BuildContext ctx)
+    {
+        ctx.Log.Information("Fixing Linux permissions in Thunderstore package...");
+
+        var thunderstorePackageDir = ctx.DistributionDirectory.Combine("thunderstore-package");
+        var packageFiles = ctx.GetFiles(thunderstorePackageDir.Combine("*.zip").FullPath);
+
+        foreach (var packageFile in packageFiles)
+        {
+            ctx.Log.Information($"Fixing Linux permissions in {packageFile.GetFilename()}...");
+
+            var tempDir = ctx.DistributionDirectory.Combine("temp-thunderstore-fix");
+            if (ctx.DirectoryExists(tempDir))
+            {
+                ctx.CleanDirectory(tempDir);
+            }
+            else
+            {
+                ctx.CreateDirectory(tempDir);
+            }
+
+            System.IO.Compression.ZipFile.ExtractToDirectory(packageFile.FullPath, tempDir.FullPath);
+
+            var executablePermissions = System.IO.UnixFileMode.UserExecute |
+                                       System.IO.UnixFileMode.GroupExecute |
+                                       System.IO.UnixFileMode.OtherExecute;
+
+            var executableFiles = new[] { "LinuxBootstrap.sh" };
+
+            foreach (var fileName in executableFiles)
+            {
+                var filePath = tempDir.CombineWithFilePath($"BepInExPack/{fileName}");
+                if (ctx.FileExists(filePath))
+                {
+                    var fileInfo = new System.IO.FileInfo(filePath.FullPath);
+                    var originalMode = fileInfo.UnixFileMode;
+                    ctx.Log.Information($"Original permissions for {fileName}: {Convert.ToString((int)originalMode, 8).PadLeft(3, '0')} ({originalMode})");
+
+                    fileInfo.UnixFileMode |= executablePermissions;
+
+                    var newMode = fileInfo.UnixFileMode;
+                    ctx.Log.Information($"New permissions for {fileName}: {Convert.ToString((int)newMode, 8).PadLeft(3, '0')} ({newMode})");
+                }
+            }
+
+            ctx.DeleteFile(packageFile);
+
+            System.IO.Compression.ZipFile.CreateFromDirectory(tempDir.FullPath, packageFile.FullPath);
+
+            ctx.Log.Information($"Fixed Linux permissions in {packageFile.GetFilename()}");
+        }
+    }
+}
+
 [TaskName("Publish")]
 [IsDependentOn(typeof(MakeDistTask))]
 [IsDependentOn(typeof(PushNuGetTask))]
-[IsDependentOn(typeof(BuildThunderstorePackageTask))]
+[IsDependentOn(typeof(FixThunderstoreLinuxPermissionsTask))]
 public sealed class PublishTask : FrostingTask<BuildContext>
 {
     public override void Run(BuildContext ctx)
@@ -587,9 +652,9 @@ public override void Run(BuildContext ctx)
         {
             var targetZipName = $"BepInEx-{dist.Target}-{ctx.BuildPackageVersion}.zip";
             ctx.Log.Information($"Packing {targetZipName}");
-            ctx.Zip(ctx.DistributionDirectory.Combine(dist.Target),
-                    ctx.DistributionDirectory
-                       .CombineWithFilePath(targetZipName));
+            // https://github.com/cake-build/cake/issues/2592
+            System.IO.Compression.ZipFile.CreateFromDirectory(ctx.DistributionDirectory.Combine(dist.Target).FullPath,
+                    ctx.DistributionDirectory.CombineWithFilePath(targetZipName).FullPath);
         }