diff --git a/codex-rs/exec-server/src/client.rs b/codex-rs/exec-server/src/client.rs
index 26b3e46e8859..978c502b7d94 100644
--- a/codex-rs/exec-server/src/client.rs
+++ b/codex-rs/exec-server/src/client.rs
@@ -48,8 +48,6 @@ use crate::protocol::FS_CANONICALIZE_METHOD;
 use crate::protocol::FS_COPY_METHOD;
 use crate::protocol::FS_CREATE_DIRECTORY_METHOD;
 use crate::protocol::FS_GET_METADATA_METHOD;
-use crate::protocol::FS_JOIN_METHOD;
-use crate::protocol::FS_PARENT_METHOD;
 use crate::protocol::FS_READ_DIRECTORY_METHOD;
 use crate::protocol::FS_READ_FILE_METHOD;
 use crate::protocol::FS_REMOVE_METHOD;
@@ -62,10 +60,6 @@ use crate::protocol::FsCreateDirectoryParams;
 use crate::protocol::FsCreateDirectoryResponse;
 use crate::protocol::FsGetMetadataParams;
 use crate::protocol::FsGetMetadataResponse;
-use crate::protocol::FsJoinParams;
-use crate::protocol::FsJoinResponse;
-use crate::protocol::FsParentParams;
-use crate::protocol::FsParentResponse;
 use crate::protocol::FsReadDirectoryParams;
 use crate::protocol::FsReadDirectoryResponse;
 use crate::protocol::FsReadFileParams;
@@ -463,17 +457,6 @@ impl ExecServerClient {
         self.call(FS_CANONICALIZE_METHOD, &params).await
     }
 
-    pub async fn fs_join(&self, params: FsJoinParams) -> Result<FsJoinResponse, ExecServerError> {
-        self.call(FS_JOIN_METHOD, &params).await
-    }
-
-    pub async fn fs_parent(
-        &self,
-        params: FsParentParams,
-    ) -> Result<FsParentResponse, ExecServerError> {
-        self.call(FS_PARENT_METHOD, &params).await
-    }
-
     pub async fn fs_read_directory(
         &self,
         params: FsReadDirectoryParams,
diff --git a/codex-rs/exec-server/src/lib.rs b/codex-rs/exec-server/src/lib.rs
index 2d198d921d6b..6c322fd41fbe 100644
--- a/codex-rs/exec-server/src/lib.rs
+++ b/codex-rs/exec-server/src/lib.rs
@@ -71,10 +71,6 @@ pub use protocol::FsCreateDirectoryParams;
 pub use protocol::FsCreateDirectoryResponse;
 pub use protocol::FsGetMetadataParams;
 pub use protocol::FsGetMetadataResponse;
-pub use protocol::FsJoinParams;
-pub use protocol::FsJoinResponse;
-pub use protocol::FsParentParams;
-pub use protocol::FsParentResponse;
 pub use protocol::FsReadDirectoryEntry;
 pub use protocol::FsReadDirectoryParams;
 pub use protocol::FsReadDirectoryResponse;
diff --git a/codex-rs/exec-server/src/protocol.rs b/codex-rs/exec-server/src/protocol.rs
index 49b1f762db99..8b9819b64da2 100644
--- a/codex-rs/exec-server/src/protocol.rs
+++ b/codex-rs/exec-server/src/protocol.rs
@@ -26,8 +26,6 @@ pub const FS_WRITE_FILE_METHOD: &str = "fs/writeFile";
 pub const FS_CREATE_DIRECTORY_METHOD: &str = "fs/createDirectory";
 pub const FS_GET_METADATA_METHOD: &str = "fs/getMetadata";
 pub const FS_CANONICALIZE_METHOD: &str = "fs/canonicalize";
-pub const FS_JOIN_METHOD: &str = "fs/join";
-pub const FS_PARENT_METHOD: &str = "fs/parent";
 pub const FS_READ_DIRECTORY_METHOD: &str = "fs/readDirectory";
 pub const FS_REMOVE_METHOD: &str = "fs/remove";
 pub const FS_COPY_METHOD: &str = "fs/copy";
@@ -263,33 +261,6 @@ pub struct FsCanonicalizeResponse {
     pub path: PathUri,
 }
 
-// TODO(anp): remove fs/join from the protocol.
-#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
-#[serde(rename_all = "camelCase")]
-pub struct FsJoinParams {
-    pub base_path: PathUri,
-    pub path: PathBuf,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
-#[serde(rename_all = "camelCase")]
-pub struct FsJoinResponse {
-    pub path: PathUri,
-}
-
-// TODO(anp): remove fs/parent from the protocol.
-#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
-#[serde(rename_all = "camelCase")]
-pub struct FsParentParams {
-    pub path: PathUri,
-}
-
-#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
-#[serde(rename_all = "camelCase")]
-pub struct FsParentResponse {
-    pub path: Option<PathUri>,
-}
-
 #[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(rename_all = "camelCase")]
 pub struct FsReadDirectoryParams {
diff --git a/codex-rs/exec-server/src/server/file_system_handler.rs b/codex-rs/exec-server/src/server/file_system_handler.rs
index 4ffdc1d9a9bd..1b6281f25be2 100644
--- a/codex-rs/exec-server/src/server/file_system_handler.rs
+++ b/codex-rs/exec-server/src/server/file_system_handler.rs
@@ -3,7 +3,6 @@ use std::io;
 use base64::Engine as _;
 use base64::engine::general_purpose::STANDARD;
 use codex_app_server_protocol::JSONRPCErrorError;
-use codex_utils_path_uri::PathUri;
 
 use crate::CopyOptions;
 use crate::CreateDirectoryOptions;
@@ -20,10 +19,6 @@ use crate::protocol::FsCreateDirectoryParams;
 use crate::protocol::FsCreateDirectoryResponse;
 use crate::protocol::FsGetMetadataParams;
 use crate::protocol::FsGetMetadataResponse;
-use crate::protocol::FsJoinParams;
-use crate::protocol::FsJoinResponse;
-use crate::protocol::FsParentParams;
-use crate::protocol::FsParentResponse;
 use crate::protocol::FsReadDirectoryEntry;
 use crate::protocol::FsReadDirectoryParams;
 use crate::protocol::FsReadDirectoryResponse;
@@ -125,33 +120,6 @@ impl FileSystemHandler {
         Ok(FsCanonicalizeResponse { path })
     }
 
-    pub(crate) async fn join(
-        &self,
-        params: FsJoinParams,
-    ) -> Result<FsJoinResponse, JSONRPCErrorError> {
-        // TODO(anp): remove and migrate callers to PathUri.
-        let base_path = params.base_path.to_abs_path().map_err(map_fs_error)?;
-        let path = base_path.join(params.path);
-        let path = PathUri::from_abs_path(&path).map_err(map_fs_error)?;
-        Ok(FsJoinResponse { path })
-    }
-
-    pub(crate) async fn parent(
-        &self,
-        params: FsParentParams,
-    ) -> Result<FsParentResponse, JSONRPCErrorError> {
-        // TODO(anp): remove and migrate callers to PathUri.
-        let path = params
-            .path
-            .to_abs_path()
-            .map_err(map_fs_error)?
-            .parent()
-            .map(|path| PathUri::from_abs_path(&path))
-            .transpose()
-            .map_err(map_fs_error)?;
-        Ok(FsParentResponse { path })
-    }
-
     pub(crate) async fn read_directory(
         &self,
         params: FsReadDirectoryParams,
@@ -297,68 +265,4 @@ mod tests {
             assert_eq!(response.data_base64, STANDARD.encode("ok"));
         }
     }
-
-    #[tokio::test]
-    async fn protocol_join_and_parent_preserve_native_path_operations() {
-        let temp_dir = tempfile::tempdir().expect("tempdir");
-        let runtime_paths = ExecServerRuntimePaths::new(
-            std::env::current_exe().expect("current exe"),
-            /*codex_linux_sandbox_exe*/ None,
-        )
-        .expect("runtime paths");
-        let handler = FileSystemHandler::new(runtime_paths);
-        let native_base =
-            AbsolutePathBuf::from_absolute_path(temp_dir.path()).expect("absolute tempdir");
-        let base_path = PathUri::from_abs_path(&native_base).expect("path URI");
-
-        let joined = handler
-            .join(FsJoinParams {
-                base_path: base_path.clone(),
-                path: "nested/file.txt".into(),
-            })
-            .await
-            .expect("join path");
-        assert_eq!(
-            joined.path,
-            PathUri::from_abs_path(&native_base.join("nested/file.txt")).expect("joined path URI")
-        );
-
-        let parent = handler
-            .parent(FsParentParams {
-                path: joined.path.clone(),
-            })
-            .await
-            .expect("parent path");
-        assert_eq!(
-            parent.path,
-            native_base
-                .join("nested/file.txt")
-                .parent()
-                .map(|path| PathUri::from_abs_path(&path).expect("parent path URI"))
-        );
-
-        let absolute_path = native_base.join("absolute.txt");
-        let joined = handler
-            .join(FsJoinParams {
-                base_path,
-                path: absolute_path.as_path().to_path_buf(),
-            })
-            .await
-            .expect("join absolute path");
-        assert_eq!(
-            joined.path,
-            PathUri::from_abs_path(&absolute_path).expect("absolute path URI")
-        );
-
-        let native_root = native_base
-            .ancestors()
-            .last()
-            .expect("absolute path should have a root");
-        let root = PathUri::from_abs_path(&native_root).expect("root path URI");
-        let parent = handler
-            .parent(FsParentParams { path: root })
-            .await
-            .expect("root parent");
-        assert_eq!(parent, FsParentResponse { path: None });
-    }
 }
diff --git a/codex-rs/exec-server/src/server/handler.rs b/codex-rs/exec-server/src/server/handler.rs
index 395ce6773050..73e8f22684e6 100644
--- a/codex-rs/exec-server/src/server/handler.rs
+++ b/codex-rs/exec-server/src/server/handler.rs
@@ -25,10 +25,6 @@ use crate::protocol::FsCreateDirectoryParams;
 use crate::protocol::FsCreateDirectoryResponse;
 use crate::protocol::FsGetMetadataParams;
 use crate::protocol::FsGetMetadataResponse;
-use crate::protocol::FsJoinParams;
-use crate::protocol::FsJoinResponse;
-use crate::protocol::FsParentParams;
-use crate::protocol::FsParentResponse;
 use crate::protocol::FsReadDirectoryParams;
 use crate::protocol::FsReadDirectoryResponse;
 use crate::protocol::FsReadFileParams;
@@ -270,22 +266,6 @@ impl ExecServerHandler {
         self.file_system.canonicalize(params).await
     }
 
-    pub(crate) async fn fs_join(
-        &self,
-        params: FsJoinParams,
-    ) -> Result<FsJoinResponse, JSONRPCErrorError> {
-        self.require_initialized_for("filesystem")?;
-        self.file_system.join(params).await
-    }
-
-    pub(crate) async fn fs_parent(
-        &self,
-        params: FsParentParams,
-    ) -> Result<FsParentResponse, JSONRPCErrorError> {
-        self.require_initialized_for("filesystem")?;
-        self.file_system.parent(params).await
-    }
-
     pub(crate) async fn fs_read_directory(
         &self,
         params: FsReadDirectoryParams,
diff --git a/codex-rs/exec-server/src/server/registry.rs b/codex-rs/exec-server/src/server/registry.rs
index 1f652c1c4c3d..4ba7ce865195 100644
--- a/codex-rs/exec-server/src/server/registry.rs
+++ b/codex-rs/exec-server/src/server/registry.rs
@@ -11,8 +11,6 @@ use crate::protocol::FS_CANONICALIZE_METHOD;
 use crate::protocol::FS_COPY_METHOD;
 use crate::protocol::FS_CREATE_DIRECTORY_METHOD;
 use crate::protocol::FS_GET_METADATA_METHOD;
-use crate::protocol::FS_JOIN_METHOD;
-use crate::protocol::FS_PARENT_METHOD;
 use crate::protocol::FS_READ_DIRECTORY_METHOD;
 use crate::protocol::FS_READ_FILE_METHOD;
 use crate::protocol::FS_REMOVE_METHOD;
@@ -21,8 +19,6 @@ use crate::protocol::FsCanonicalizeParams;
 use crate::protocol::FsCopyParams;
 use crate::protocol::FsCreateDirectoryParams;
 use crate::protocol::FsGetMetadataParams;
-use crate::protocol::FsJoinParams;
-use crate::protocol::FsParentParams;
 use crate::protocol::FsReadDirectoryParams;
 use crate::protocol::FsReadFileParams;
 use crate::protocol::FsRemoveParams;
@@ -121,18 +117,6 @@ pub(crate) fn build_router() -> RpcRouter<ExecServerHandler> {
             handler.fs_canonicalize(params).await
         },
     );
-    router.request(
-        FS_JOIN_METHOD,
-        |handler: Arc<ExecServerHandler>, params: FsJoinParams| async move {
-            handler.fs_join(params).await
-        },
-    );
-    router.request(
-        FS_PARENT_METHOD,
-        |handler: Arc<ExecServerHandler>, params: FsParentParams| async move {
-            handler.fs_parent(params).await
-        },
-    );
     router.request(
         FS_READ_DIRECTORY_METHOD,
         |handler: Arc<ExecServerHandler>, params: FsReadDirectoryParams| async move {