Fix symlink handling in FUSE and overlay filesystem

The FUSE handlers were using stat() which follows symlinks, causing
symlinks to directories to be incorrectly reported as directories.
This broke operations like `rm -rf` on pnpm's node_modules which uses
symlinks extensively.

Author: penberg

cli/src/fuse.rs

@@ -82,7 +82,7 @@ impl Filesystem for AgentFSFuse {
         };
         let fs = self.fs.clone();
         let (result, path) = self.runtime.block_on(async move {
-            let result = fs.stat(&path).await;
+            let result = fs.lstat(&path).await;
             (result, path)
         });
         match result {
@@ -107,7 +107,7 @@ impl Filesystem for AgentFSFuse {
         };
 
         let fs = self.fs.clone();
-        let result = self.runtime.block_on(async move { fs.stat(&path).await });
+        let result = self.runtime.block_on(async move { fs.lstat(&path).await });
 
         match result {
             Ok(Some(stats)) => reply.attr(&TTL, &fillattr(&stats, self.uid, self.gid)),
@@ -489,7 +489,7 @@ impl Filesystem for AgentFSFuse {
         // Verify target is a directory
         let fs = self.fs.clone();
         let (stat_result, path) = self.runtime.block_on(async move {
-            let result = fs.stat(&path).await;
+            let result = fs.lstat(&path).await;
             (result, path)
         });
 
@@ -620,20 +620,35 @@ impl Filesystem for AgentFSFuse {
         // Get inode before removing so we can uncache
         let fs = self.fs.clone();
         let (stat_result, path) = self.runtime.block_on(async move {
-            let result = fs.stat(&path).await;
+            let result = fs.lstat(&path).await;
             (result, path)
         });
 
-        let ino = stat_result.ok().flatten().map(|s| s.ino as u64);
+        let stats = match &stat_result {
+            Ok(Some(s)) => s,
+            Ok(None) => {
+                reply.error(libc::ENOENT);
+                return;
+            }
+            Err(_) => {
+                reply.error(libc::EIO);
+                return;
+            }
+        };
+
+        if stats.is_directory() {
+            reply.error(libc::EISDIR);
+            return;
+        }
+
+        let ino = stats.ino as u64;
 
         let fs = self.fs.clone();
         let result = self.runtime.block_on(async move { fs.remove(&path).await });
 
         match result {
             Ok(()) => {
-                if let Some(ino) = ino {
-                    self.drop_path(ino);
-                }
+                self.drop_path(ino);
                 reply.ok();
             }
             Err(_) => reply.error(libc::EIO),

cli/tests/all.sh

@@ -6,3 +6,4 @@ DIR="$(dirname "$0")"
 "$DIR/test-syscalls.sh"
 "$DIR/test-run-bash.sh"
 "$DIR/test-mount.sh"
+"$DIR/test-symlinks.sh"

cli/tests/test-symlinks.sh

@@ -0,0 +1,52 @@
+#!/bin/sh
+set -e
+
+echo -n "TEST symlink handling... "
+
+# Create test directory with symlinks on the host (these will be visible in the sandbox)
+TEST_DIR=".agentfs/symlink-test-$$"
+rm -rf "$TEST_DIR"
+mkdir -p "$TEST_DIR/target_dir"
+echo "test content" > "$TEST_DIR/target_dir/file.txt"
+ln -s target_dir "$TEST_DIR/link_to_dir"
+ln -s target_dir/file.txt "$TEST_DIR/link_to_file"
+
+cleanup() {
+    rm -rf "$TEST_DIR"
+}
+trap cleanup EXIT
+
+# Test 1 & 2: Verify symlinks are reported correctly (not as directories)
+output=$(cargo run -- run /bin/bash -c "ls -la $TEST_DIR/" 2>&1 || true)
+
+# The output should contain 'lrwxrwxrwx' for symlinks (not 'drwxr-xr-x' for directory)
+if ! echo "$output" | grep -qE "^lrwx.* link_to_dir"; then
+    echo "FAILED: symlink to directory not reported as symlink"
+    echo "$output"
+    exit 1
+fi
+
+if ! echo "$output" | grep -qE "^lrwx.* link_to_file"; then
+    echo "FAILED: symlink to file not reported as symlink"
+    echo "$output"
+    exit 1
+fi
+
+# Test 3: Verify rm can remove symlink to directory (this was the original bug)
+# Previously this would fail with "Is a directory" because symlinks were misidentified
+output=$(cargo run -- run /bin/bash -c "rm $TEST_DIR/link_to_dir && echo 'symlink removed successfully'" 2>&1 || true)
+
+if ! echo "$output" | grep -q "symlink removed successfully"; then
+    echo "FAILED: could not remove symlink to directory"
+    echo "$output"
+    exit 1
+fi
+
+# Test 4: Verify the target directory still exists on host after removing symlink
+# (The removal was in the delta layer, host should still have it)
+if ! cat "$TEST_DIR/target_dir/file.txt" | grep -q "test content"; then
+    echo "FAILED: target directory should still exist after removing symlink"
+    exit 1
+fi
+
+echo "OK"

sdk/rust/src/filesystem/overlayfs.rs

@@ -543,31 +543,41 @@ impl FileSystem for OverlayFS {
     async fn remove(&self, path: &str) -> Result<()> {
         let normalized = self.normalize_path(path);
 
-        // Check if directory has children in delta - if so, can't remove
-        if let Some(children) = self.delta.readdir(&normalized).await? {
-            if !children.is_empty() {
-                return Err(FsError::NotEmpty.into());
-            }
-        }
+        // Check if path is a symlink - symlinks don't have children, so skip directory checks
+        let is_symlink = if let Some(stats) = self.lstat(&normalized).await? {
+            stats.is_symlink()
+        } else {
+            false
+        };
 
-        // Check for visible children in base (not whiteout-ed)
-        if let Some(base_children) = self.base.readdir(&normalized).await? {
-            for child in base_children {
-                let child_path = format!("{}/{}", normalized, child);
-                if !self.is_whiteout(&child_path).await? {
+        // Only check for children if not a symlink (directories need to be empty)
+        if !is_symlink {
+            // Check if directory has children in delta - if so, can't remove
+            if let Some(children) = self.delta.readdir(&normalized).await? {
+                if !children.is_empty() {
                     return Err(FsError::NotEmpty.into());
                 }
             }
+
+            // Check for visible children in base (not whiteout-ed)
+            if let Some(base_children) = self.base.readdir(&normalized).await? {
+                for child in base_children {
+                    let child_path = format!("{}/{}", normalized, child);
+                    if !self.is_whiteout(&child_path).await? {
+                        return Err(FsError::NotEmpty.into());
+                    }
+                }
+            }
         }
 
         // Try to remove from delta
         let removed_from_delta = self.delta.remove(&normalized).await.is_ok();
 
-        // Check if it exists in base (and not already whiteout)
+        // Check if it exists in base (and not already whiteout) - use lstat to not follow symlinks
         let exists_in_base = if self.is_whiteout(&normalized).await? {
             false
         } else {
-            self.base.stat(&normalized).await?.is_some()
+            self.base.lstat(&normalized).await?.is_some()
         };
 
         // If exists in base, create whiteout