diff --git a/lib/virtual-fs/src/empty_fs.rs b/lib/virtual-fs/src/empty_fs.rs
index 04807ef4bad..ce5be69637c 100644
--- a/lib/virtual-fs/src/empty_fs.rs
+++ b/lib/virtual-fs/src/empty_fs.rs
@@ -13,7 +13,14 @@ pub struct EmptyFileSystem {}
 #[allow(unused_variables)]
 impl FileSystem for EmptyFileSystem {
     fn read_dir(&self, path: &Path) -> Result<ReadDir> {
-        Err(FsError::EntryNotFound)
+        // Special-case the root path by returning an empty iterator.
+        // An empty file system should still be readable, just not contain
+        // any entries.
+        if path == Path::new("/") {
+            Ok(ReadDir::new(Vec::new()))
+        } else {
+            Err(FsError::EntryNotFound)
+        }
     }
 
     fn create_dir(&self, path: &Path) -> Result<()> {
@@ -29,7 +36,20 @@ impl FileSystem for EmptyFileSystem {
     }
 
     fn metadata(&self, path: &Path) -> Result<Metadata> {
-        Err(FsError::EntryNotFound)
+        // Special-case the root path by returning an stub value.
+        // An empty file system should still be readable, just not contain
+        // any entries.
+        if path == Path::new("/") {
+            Ok(Metadata {
+                ft: FileType::new_dir(),
+                accessed: 0,
+                created: 0,
+                modified: 0,
+                len: 0,
+            })
+        } else {
+            Err(FsError::EntryNotFound)
+        }
     }
 
     fn symlink_metadata(&self, path: &Path) -> Result<Metadata> {
diff --git a/lib/virtual-fs/src/lib.rs b/lib/virtual-fs/src/lib.rs
index 0775d5f124f..591f086c44c 100644
--- a/lib/virtual-fs/src/lib.rs
+++ b/lib/virtual-fs/src/lib.rs
@@ -665,6 +665,13 @@ pub struct FileType {
 }
 
 impl FileType {
+    pub fn new_dir() -> Self {
+        Self {
+            dir: true,
+            ..Default::default()
+        }
+    }
+
     pub fn is_dir(&self) -> bool {
         self.dir
     }
diff --git a/lib/wasix/src/fs/mod.rs b/lib/wasix/src/fs/mod.rs
index 51e49cc5e7e..1ae2dc0cad0 100644
--- a/lib/wasix/src/fs/mod.rs
+++ b/lib/wasix/src/fs/mod.rs
@@ -363,7 +363,13 @@ async fn merge_filesystems(
     to_check.push_back(PathBuf::from("/"));
 
     while let Some(path) = to_check.pop_front() {
-        let metadata = source.metadata(&path)?;
+        let metadata = match source.metadata(&path) {
+            Ok(m) => m,
+            Err(err) => {
+                tracing::debug!(path=%path.display(), source_fs=?source, ?err, "failed to get metadata for path while merging file systems");
+                return Err(err);
+            }
+        };
 
         if metadata.is_dir() {
             create_dir_all(destination, &path)?;
diff --git a/lib/wasix/src/os/console/mod.rs b/lib/wasix/src/os/console/mod.rs
index 886b44ab2e3..e8129f50cda 100644
--- a/lib/wasix/src/os/console/mod.rs
+++ b/lib/wasix/src/os/console/mod.rs
@@ -222,15 +222,14 @@ impl Console {
             .with_envs(self.env.clone().into_iter())
             .with_args(args)
             .with_capabilities(self.capabilities.clone())
+            .with_stdin(Box::new(self.stdin.clone()))
+            .with_stdout(Box::new(self.stdout.clone()))
+            .with_stderr(Box::new(self.stderr.clone()))
             .prepare_webc_env(prog, &wasi_opts, &pkg, self.runtime.clone(), Some(root_fs))
             // TODO: better error conversion
             .map_err(|err| SpawnError::Other(err.into()))?;
 
-        let env = builder
-            .stdin(Box::new(self.stdin.clone()))
-            .stdout(Box::new(self.stdout.clone()))
-            .stderr(Box::new(self.stderr.clone()))
-            .build()?;
+        let env = builder.build()?;
 
         // Display the welcome message
         if !self.whitelabel && !self.no_welcome {
@@ -365,4 +364,32 @@ mod tests {
 
         assert_eq!(out, "hello VAL1\n");
     }
+
+    /// Regression test to ensure merging of multiple packages works correctly.
+    #[test]
+    fn test_console_python_merge() {
+        std::env::set_var("RUST_LOG", "wasmer_wasix=trace");
+        tracing_subscriber::fmt::init();
+        let tokio_rt = tokio::runtime::Runtime::new().unwrap();
+        let rt_handle = tokio_rt.handle().clone();
+        let _guard = rt_handle.enter();
+
+        let tm = TokioTaskManager::new(tokio_rt);
+        let mut rt = PluggableRuntime::new(Arc::new(tm));
+        rt.set_engine(Some(wasmer::Engine::default()))
+            .set_package_loader(BuiltinPackageLoader::from_env().unwrap());
+
+        let cmd = "wasmer-tests/python-env-dump --help";
+
+        let (mut handle, _proc) = Console::new(cmd, Arc::new(rt)).run().unwrap();
+
+        let code = rt_handle
+            .block_on(async move {
+                let res = handle.wait_finished().await?;
+                Ok::<_, anyhow::Error>(res)
+            })
+            .unwrap();
+
+        assert_eq!(code.raw(), 0);
+    }
 }
diff --git a/lib/wasix/src/state/env.rs b/lib/wasix/src/state/env.rs
index 4b0a8f819f9..bf56e90bb79 100644
--- a/lib/wasix/src/state/env.rs
+++ b/lib/wasix/src/state/env.rs
@@ -869,6 +869,7 @@ impl WasiEnv {
     /// [cmd-atom]: crate::bin_factory::BinaryPackageCommand::atom()
     /// [pkg-fs]: crate::bin_factory::BinaryPackage::webc_fs
     pub fn use_package(&self, pkg: &BinaryPackage) -> Result<(), WasiStateCreationError> {
+        tracing::trace!(packagae=%pkg.package_name, "merging package dependency into wasi environment");
         let root_fs = &self.state.fs.root_fs;
 
         // We first need to copy any files in the package over to the