Fix fd handling in WASIp1 implementation (#327)

`PathResolution.resolve()` returned the input fd unchanged for "." paths, causing fd table entries to alias the same host fd. Closing one invalidated the other, which errored with EBADF.

Multiple related fixes are included to clean up the general situation with FD handling in WASIp1 implementation:

- Fix fd aliasing in `PathResolution.resolve()`: When the path resolves without opening a new fd (e.g. "."), dup via `openat(fd, ".")` so callers always get an independently closeable fd.
- Fix `SplitPath` premature deinit: Use `borrowing func withFields` to keep `SplitPath: ~Copyable` alive during operations that use its parent fd.
- Add `WASIBridgeToHost.runAndClose`: Scoped API that ensures `close()` is called, replacing the previous `deinit`-based cleanup.
- Add `isBorrowed` to `WASIEntry`: Stdio entries are marked as borrowed so `closeAll()` never closes process stdin/stdout/stderr (previously broken when `fd_renumber` moved stdio to different WASI fd positions).
- Fix `directoryEntry(fd:)` error codes: Return `EBADF` for missing fds, `ENOTDIR` for non-directory fds (was `ENOTDIR` for both).

I ran tests locally 10 times in a row and on CI 5 times in a row on this PR, no failures, I think this is sufficient to say that flakiness is resolved.

Resolves #334.

Author: MaxDesiatov

Benchmarks/Benchmarks/MacroPlugin/MacroPlugin.swift

@@ -151,6 +151,7 @@ let benchmarks: @Sendable () -> () = {
             let pluginToHost: FileDescriptor
             let pump: Function
             let expandMessage: String
+            let bridge: WASIBridgeToHost
 
             init(filePath: FilePath, expandMessage: String) throws {
                 let engine = Engine()
@@ -164,16 +165,22 @@ let benchmarks: @Sendable () -> () = {
                   stdout: pluginToHostPipes.writeEnd,
                   stderr: .standardError
                 )
-                var imports = Imports()
-                bridge.link(to: &imports, store: store)
-                let instance = try module.instantiate(store: store, imports: imports)
-                try instance.exports[function: "_start"]!()
-                let pump = instance.exports[function: "swift_wasm_macro_v1_pump"]!
-
-                self.hostToPlugin = hostToPluginPipes.writeEnd
-                self.pluginToHost = pluginToHostPipes.readEnd
-                self.pump = pump
-                self.expandMessage = expandMessage
+                do {
+                    var imports = Imports()
+                    bridge.link(to: &imports, store: store)
+                    let instance = try module.instantiate(store: store, imports: imports)
+                    try instance.exports[function: "_start"]!()
+                    let pump = instance.exports[function: "swift_wasm_macro_v1_pump"]!
+
+                    self.hostToPlugin = hostToPluginPipes.writeEnd
+                    self.pluginToHost = pluginToHostPipes.readEnd
+                    self.pump = pump
+                    self.expandMessage = expandMessage
+                    self.bridge = bridge
+                } catch {
+                    try bridge.close()
+                    throw error
+                }
             }
 
             func writeMessage(_ message: String) throws {
@@ -204,6 +211,10 @@ let benchmarks: @Sendable () -> () = {
                 try pump()
                 _ = try readMessage()
             }
+
+            func close() throws {
+                try bridge.close()
+            }
         }
 
         guard let expandMessage = expandMessages[file] else {
@@ -214,10 +225,12 @@ let benchmarks: @Sendable () -> () = {
             let setup = try Setup(filePath: macrosDir.appending(file), expandMessage: expandMessage)
             try setup.writeMessage(handshakeMessage)
             try setup.tick()
+            try setup.close()
         }
 
         Benchmark("Expand \(file)") { benchmark, setup in
             try setup.tick()
+            try setup.close()
         } setup: { () -> Setup in
             let setup = try Setup(
                 filePath: macrosDir.appending(file),

Benchmarks/Benchmarks/WishYouWereFast/WishYouWereFast.swift

@@ -31,10 +31,12 @@ let benchmarks: @Sendable () -> () = {
                 filePath: FilePath(wishYouWereFast.appendingPathComponent(file).path)
             )
             let wasi = try WASIBridgeToHost(fileSystem: .host().withStdio(stdout: devNull, stderr: devNull))
-            var imports = Imports()
-            wasi.link(to: &imports, store: store)
-            let instance = try module.instantiate(store: store, imports: imports)
-            _ = try wasi.start(instance)
+            _ = try wasi.runAndClose { wasi in
+                var imports = Imports()
+                wasi.link(to: &imports, store: store)
+                let instance = try module.instantiate(store: store, imports: imports)
+                return try wasi.start(instance)
+            }
         }
     }
 }

Examples/Sources/WASI-Hello/Hello.swift

@@ -12,16 +12,17 @@ struct Example {
 
         // Create a WASI instance forwarding to the host environment.
         let wasi = try WASIBridgeToHost()
-        // Create engine and store
-        let engine = Engine()
-        let store = Store(engine: engine)
-        // Instantiate a parsed module importing WASI
-        var imports = Imports()
-        wasi.link(to: &imports, store: store)
-        let instance = try module.instantiate(store: store, imports: imports)
-
-        // Start the WASI command-line application.
-        let exitCode = try wasi.start(instance)
+        // Start the WASI command-line application and close the bridge.
+        let exitCode = try wasi.runAndClose { wasi in
+            // Create engine and store
+            let engine = Engine()
+            let store = Store(engine: engine)
+            // Instantiate a parsed module importing WASI
+            var imports = Imports()
+            wasi.link(to: &imports, store: store)
+            let instance = try module.instantiate(store: store, imports: imports)
+            return try wasi.start(instance)
+        }
         // Exit the Swift program with the WASI exit code.
         exit(Int32(exitCode))
     }

Sources/CLICommands/DebuggerServer.swift

@@ -113,6 +113,7 @@
                     await shutDownStream.first { _ in true }
                     cancellableGroup.cancelAll()
                 }
+                try await debuggerHandler.close()
             }
         }
     }

Sources/CLICommands/Run.swift

@@ -298,12 +298,14 @@ package struct Run: AsyncParsableCommand {
         let wasi = try WASIBridgeToHost(args: [path] + arguments, environment: environment, preopens: preopens)
         let engine = Engine(configuration: deriveRuntimeConfiguration(), interceptor: interceptor)
         let store = Store(engine: engine)
-        var imports = Imports()
-        wasi.link(to: &imports, store: store)
-        let moduleInstance = try module.instantiate(store: store, imports: imports)
         return {
-            let exitCode = try wasi.start(moduleInstance)
-            throw ExitCode(Int32(exitCode))
+            try wasi.runAndClose { wasi in
+                var imports = Imports()
+                wasi.link(to: &imports, store: store)
+                let moduleInstance = try module.instantiate(store: store, imports: imports)
+                let exitCode = try wasi.start(moduleInstance)
+                throw ExitCode(Int32(exitCode))
+            }
         }
     }
 

Sources/WASI/FileSystem.swift

@@ -8,6 +8,9 @@ struct FileAccessMode: OptionSet {
 }
 
 protocol WASIEntry {
+    /// Whether this entry wraps a borrowed file descriptor that should not be
+    /// closed when the WASI instance is torn down (e.g. process stdio).
+    var isBorrowed: Bool { get }
     func attributes() throws -> WASIAbi.Filestat
     func fileType() throws -> WASIAbi.FileType
     func status() throws -> WASIAbi.Fdflags
@@ -21,6 +24,10 @@ protocol WASIEntry {
     func close() throws
 }
 
+extension WASIEntry {
+    var isBorrowed: Bool { false }
+}
+
 protocol WASIFile: WASIEntry {
     func fdStat() throws -> WASIAbi.FdStat
     func setFdStatFlags(_ flags: WASIAbi.Fdflags) throws
@@ -129,6 +136,22 @@ struct FdTable {
             return fd
         }
     }
+
+    /// Closes all owned file descriptors, skipping borrowed ones (e.g. stdio).
+    mutating func closeAll() throws {
+        var firstError: (any Error)?
+        for (_, entry) in map {
+            let wasiEntry = entry.asEntry()
+            guard !wasiEntry.isBorrowed else { continue }
+            do {
+                try wasiEntry.close()
+            } catch {
+                if firstError == nil { firstError = error }
+            }
+        }
+        map = map.filter { $0.value.asEntry().isBorrowed }
+        if let firstError { throw firstError }
+    }
 }
 
 /// Content of a file that can be retrieved from the file system.

Sources/WASI/Platform/Directory.swift

@@ -90,6 +90,7 @@ extension DirEntry: WASIDir, FdWASIEntry {
             symlinkFollow: symlinkFollow, path: path,
             oflags: [], accessMode: .write, fdflags: []
         )
+        defer { try? fd.close() }
         let (access, modification) = try WASIAbi.Timestamp.platformTimeSpec(
             atim: atim, mtim: mtim, fstFlags: fstFlags
         )
@@ -100,10 +101,10 @@ extension DirEntry: WASIDir, FdWASIEntry {
 
     func removeFile(atPath path: String) throws {
         let result = try SandboxPrimitives.openParent(start: fd, path: path)
-        let dir = result.parentFd
-        let basename = result.basename
-        try WASIAbi.Errno.translatingPlatformErrno {
-            try dir.remove(at: FilePath(basename), options: [])
+        try result.withFields { dir, basename in
+            try WASIAbi.Errno.translatingPlatformErrno {
+                try dir.remove(at: FilePath(basename), options: [])
+            }
         }
     }
 
@@ -113,10 +114,10 @@ extension DirEntry: WASIDir, FdWASIEntry {
         #else
             let path = SandboxPrimitives.stripDirSuffix(path)
             let result = try SandboxPrimitives.openParent(start: fd, path: path)
-            let dir = result.parentFd
-            let basename = result.basename
-            try WASIAbi.Errno.translatingPlatformErrno {
-                try dir.remove(at: FilePath(basename), options: .removeDirectory)
+            try result.withFields { dir, basename in
+                try WASIAbi.Errno.translatingPlatformErrno {
+                    try dir.remove(at: FilePath(basename), options: .removeDirectory)
+                }
             }
         #endif
     }
@@ -125,10 +126,10 @@ extension DirEntry: WASIDir, FdWASIEntry {
         let result = try SandboxPrimitives.openParent(
             start: fd, path: destPath
         )
-        let destDir = result.parentFd
-        let destBasename = result.basename
-        try WASIAbi.Errno.translatingPlatformErrno {
-            try destDir.createSymlink(original: FilePath(sourcePath), link: FilePath(destBasename))
+        try result.withFields { destDir, destBasename in
+            try WASIAbi.Errno.translatingPlatformErrno {
+                try destDir.createSymlink(original: FilePath(sourcePath), link: FilePath(destBasename))
+            }
         }
     }
 
@@ -152,24 +153,23 @@ extension DirEntry: WASIDir, FdWASIEntry {
             let sourceResult = try SandboxPrimitives.openParent(
                 start: fd, path: oldPath
             )
-            let sourceDir = sourceResult.parentFd
-            let sourceBasename = sourceResult.basename
             let destResult = try SandboxPrimitives.openParent(
                 start: newDir.fd, path: newPath
             )
-            let destDir = destResult.parentFd
-            let destBasename = destResult.basename
-
-            // Re-append a slash if the original path had one
-            let finalSourceBasename = oldHasTrailingSlash ? sourceBasename + "/" : sourceBasename
-            let finalDestBasename = newHasTrailingSlash ? destBasename + "/" : destBasename
-
-            try WASIAbi.Errno.translatingPlatformErrno {
-                try sourceDir.rename(
-                    at: FilePath(finalSourceBasename),
-                    to: destDir,
-                    at: FilePath(finalDestBasename)
-                )
+            try sourceResult.withFields { sourceDir, sourceBasename in
+                try destResult.withFields { destDir, destBasename in
+                    // Re-append a slash if the original path had one
+                    let finalSourceBasename = oldHasTrailingSlash ? sourceBasename + "/" : sourceBasename
+                    let finalDestBasename = newHasTrailingSlash ? destBasename + "/" : destBasename
+
+                    try WASIAbi.Errno.translatingPlatformErrno {
+                        try sourceDir.rename(
+                            at: FilePath(finalSourceBasename),
+                            to: destDir,
+                            at: FilePath(finalDestBasename)
+                        )
+                    }
+                }
             }
         #endif
     }
@@ -216,10 +216,10 @@ extension DirEntry: WASIDir, FdWASIEntry {
 
     func createDirectory(atPath path: String) throws {
         let result = try SandboxPrimitives.openParent(start: fd, path: path)
-        let dir = result.parentFd
-        let basename = result.basename
-        try WASIAbi.Errno.translatingPlatformErrno {
-            try dir.createDirectory(at: FilePath(basename), permissions: .ownerReadWriteExecute)
+        try result.withFields { dir, basename in
+            try WASIAbi.Errno.translatingPlatformErrno {
+                try dir.createDirectory(at: FilePath(basename), permissions: .ownerReadWriteExecute)
+            }
         }
     }
 
@@ -232,15 +232,15 @@ extension DirEntry: WASIDir, FdWASIEntry {
                 options.insert(.noFollow)
             }
             let result = try SandboxPrimitives.openParent(start: fd, path: path)
-            let dir = result.parentFd
-            let basename = result.basename
-            let attributes = try basename.withCString { cBasename in
-                try WASIAbi.Errno.translatingPlatformErrno {
-                    try dir.attributes(at: cBasename, options: options)
+            return try result.withFields { dir, basename in
+                let attributes = try basename.withCString { cBasename in
+                    try WASIAbi.Errno.translatingPlatformErrno {
+                        try dir.attributes(at: cBasename, options: options)
+                    }
                 }
-            }
 
-            return WASIAbi.Filestat(stat: attributes)
+                return WASIAbi.Filestat(stat: attributes)
+            }
         #endif
     }
 }

Sources/WASI/Platform/File.swift

@@ -106,6 +106,8 @@ struct StdioFileEntry: FdWASIFile {
     let fd: FileDescriptor
     let accessMode: FileAccessMode
 
+    let isBorrowed: Bool = true
+
     func attributes() throws -> WASIAbi.Filestat {
         return WASIAbi.Filestat(
             dev: 0, ino: 0, filetype: .CHARACTER_DEVICE,

Sources/WASI/Platform/SandboxPrimitives/Open.swift

@@ -227,6 +227,15 @@ struct PathResolution {
             case .regular: try regular(component: component)
             }
         }
+
+        // If the path resolved without opening any new fd (e.g. "."),
+        // dup to avoid returning an aliased fd to the caller.
+        if baseFd.rawValue == startFd.rawValue {
+            baseFd = try startFd.open(
+                at: ".", mode, options: options, permissions: permissions
+            )
+        }
+
         resultFd = self.baseFd
         return self.baseFd
     }

Sources/WASI/Platform/SandboxPrimitives/OpenParent.swift

@@ -88,6 +88,10 @@ struct SplitPath: ~Copyable {
     var basename: String
     var isTemporary: Bool
 
+    borrowing func withFields<R>(_ body: (FileDescriptor, String) throws -> R) rethrows -> R {
+        try body(parentFd, basename)
+    }
+
     deinit {
         if isTemporary {
             try? parentFd.close()