fix: Prevent invalid file system merging errors

This commit changes the EmptyFileSystem read_dir() implementation to
always return an empty iterator when trying to read the root path "/".

This is done because some code paths expect the root to always be
readable.

This also makes sense theoretically, because an empty file system should
still be readable, just not contain any files.

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> {

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
     }

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)?;

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 {

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