diff --git a/Makefile b/Makefile
index 28d9b8219..9b864ed19 100644
--- a/Makefile
+++ b/Makefile
@@ -25,7 +25,7 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py cwltool/cwlprov/*.py tests/*.py tests/cwl-conformance/*.py) setup.py
-DEVPKGS=diff_cover pylint pep257 pydocstyle 'tox<4' tox-pyenv auto-walrus \
+DEVPKGS=diff_cover pylint pep257 pydocstyle 'tox>4' auto-walrus \
 	isort wheel autoflake pyupgrade bandit -rlint-requirements.txt\
 	-rtest-requirements.txt -rmypy-requirements.txt -rdocs/requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
diff --git a/cwltool/builder.py b/cwltool/builder.py
index cf6d6d5ac..5c615a3ec 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -9,6 +9,7 @@
 
 from cwl_utils import expression
 from cwl_utils.file_formats import check_format
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, CWLOutputType
 from mypy_extensions import mypyc_attr
 from rdflib import Graph
 from ruamel.yaml.comments import CommentedMap
@@ -26,8 +27,6 @@
 from .stdfsaccess import StdFsAccess
 from .utils import (
     CONTENT_LIMIT,
-    CWLObjectType,
-    CWLOutputType,
     HasReqsHints,
     LoadListingType,
     aslist,
@@ -95,7 +94,7 @@ class Builder(HasReqsHints):
     def __init__(
         self,
         job: CWLObjectType,
-        files: list[CWLObjectType],
+        files: MutableSequence[CWLFileType | CWLDirectoryType],
         bindings: list[CWLObjectType],
         schemaDefs: MutableMapping[str, CWLObjectType],
         names: Names,
@@ -166,7 +165,7 @@ def build_job_script(self, commands: list[str]) -> str | None:
             return self.job_script_provider.build_job_script(self, commands)
         return None
 
-    def _capture_files(self, f: CWLObjectType) -> CWLObjectType:
+    def _capture_files(self, f: CWLFileType | CWLDirectoryType) -> CWLFileType | CWLDirectoryType:
         self.files.append(f)
         return f
 
@@ -356,13 +355,13 @@ def bind_input(
                     )
                 binding = {}
 
-            def _capture_files(f: CWLObjectType) -> CWLObjectType:
+            def _capture_files(f: CWLFileType | CWLDirectoryType) -> CWLFileType | CWLDirectoryType:
                 self.files.append(f)
                 return f
 
             if schema["type"] == "org.w3id.cwl.cwl.File":
-                datum = cast(CWLObjectType, datum)
-                self.files.append(datum)
+                file_datum = cast(CWLFileType, datum)
+                self.files.append(file_datum)
 
                 loadContents_sourceline: (
                     None | MutableMapping[str, str | list[int]] | CWLObjectType
@@ -380,14 +379,16 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                         debug,
                     ):
                         try:
-                            with self.fs_access.open(cast(str, datum["location"]), "rb") as f2:
-                                datum["contents"] = content_limit_respected_read(f2)
+                            with self.fs_access.open(file_datum["location"], "rb") as f2:
+                                file_datum["contents"] = content_limit_respected_read(f2)
                         except Exception as e:
-                            raise Exception("Reading {}\n{}".format(datum["location"], e)) from e
+                            raise Exception(
+                                "Reading {}\n{}".format(file_datum["location"], e)
+                            ) from e
 
                 if "secondaryFiles" in schema:
-                    if "secondaryFiles" not in datum:
-                        datum["secondaryFiles"] = []
+                    if "secondaryFiles" not in file_datum:
+                        file_datum["secondaryFiles"] = []
                         sf_schema = aslist(schema["secondaryFiles"])
                     elif not discover_secondaryFiles:
                         sf_schema = []  # trust the inputs
@@ -396,7 +397,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
 
                     for num, sf_entry in enumerate(sf_schema):
                         if "required" in sf_entry and sf_entry["required"] is not None:
-                            required_result = self.do_eval(sf_entry["required"], context=datum)
+                            required_result = self.do_eval(sf_entry["required"], context=file_datum)
                             if not (isinstance(required_result, bool) or required_result is None):
                                 if sf_schema == schema["secondaryFiles"]:
                                     sf_item: Any = sf_schema[num]
@@ -418,7 +419,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                         if "$(" in sf_entry["pattern"] or "${" in sf_entry["pattern"]:
                             sfpath = self.do_eval(sf_entry["pattern"], context=datum)
                         else:
-                            sfpath = substitute(cast(str, datum["basename"]), sf_entry["pattern"])
+                            sfpath = substitute(file_datum["basename"], sf_entry["pattern"])
 
                         for sfname in aslist(sfpath):
                             if not sfname:
@@ -426,7 +427,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                             found = False
 
                             if isinstance(sfname, str):
-                                d_location = cast(str, datum["location"])
+                                d_location = file_datum["location"]
                                 if "/" in d_location:
                                     sf_location = (
                                         d_location[0 : d_location.rindex("/") + 1] + sfname
@@ -435,6 +436,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                                     sf_location = d_location + sfname
                                 sfbasename = sfname
                             elif isinstance(sfname, MutableMapping):
+                                sfname = cast(CWLFileType | CWLDirectoryType, sfname)
                                 sf_location = sfname["location"]
                                 sfbasename = sfname["basename"]
                             else:
@@ -447,10 +449,7 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                                     f"{type(sfname)!r} from {sf_entry['pattern']!r}."
                                 )
 
-                            for d in cast(
-                                MutableSequence[MutableMapping[str, str]],
-                                datum["secondaryFiles"],
-                            ):
+                            for d in file_datum["secondaryFiles"]:
                                 if not d.get("basename"):
                                     d["basename"] = d["location"][d["location"].rindex("/") + 1 :]
                                 if d["basename"] == sfbasename:
@@ -459,8 +458,8 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                             if not found:
 
                                 def addsf(
-                                    files: MutableSequence[CWLObjectType],
-                                    newsf: CWLObjectType,
+                                    files: MutableSequence[CWLFileType | CWLDirectoryType],
+                                    newsf: CWLFileType | CWLDirectoryType,
                                 ) -> None:
                                     for f in files:
                                         if f["location"] == newsf["location"]:
@@ -470,23 +469,19 @@ def addsf(
 
                                 if isinstance(sfname, MutableMapping):
                                     addsf(
-                                        cast(
-                                            MutableSequence[CWLObjectType],
-                                            datum["secondaryFiles"],
-                                        ),
-                                        sfname,
+                                        file_datum["secondaryFiles"],
+                                        cast(CWLFileType | CWLDirectoryType, sfname),
                                     )
                                 elif discover_secondaryFiles and self.fs_access.exists(sf_location):
                                     addsf(
-                                        cast(
-                                            MutableSequence[CWLObjectType],
-                                            datum["secondaryFiles"],
+                                        file_datum["secondaryFiles"],
+                                        CWLFileType(
+                                            **{
+                                                "location": sf_location,
+                                                "basename": sfname,
+                                                "class": "File",
+                                            }
                                         ),
-                                        {
-                                            "location": sf_location,
-                                            "basename": sfname,
-                                            "class": "File",
-                                        },
                                     )
                                 elif sf_required:
                                     raise SourceLine(
@@ -496,12 +491,10 @@ def addsf(
                                         debug,
                                     ).makeError(
                                         "Missing required secondary file '%s' from file object: %s"
-                                        % (sfname, json_dumps(datum, indent=4))
+                                        % (sfname, json_dumps(file_datum, indent=4))
                                     )
 
-                    normalizeFilesDirs(
-                        cast(MutableSequence[CWLObjectType], datum["secondaryFiles"])
-                    )
+                    normalizeFilesDirs(file_datum["secondaryFiles"])
 
                 if "format" in schema:
                     eval_format: Any = self.do_eval(schema["format"])
@@ -546,7 +539,7 @@ def addsf(
                         )
                     try:
                         check_format(
-                            datum,
+                            file_datum,
                             evaluated_format,
                             self.formatgraph,
                         )
@@ -557,21 +550,21 @@ def addsf(
                         ) from ve
 
                 visit_class(
-                    datum.get("secondaryFiles", []),
+                    file_datum.get("secondaryFiles", []),
                     ("File", "Directory"),
                     self._capture_files,
                 )
 
             if schema["type"] == "org.w3id.cwl.cwl.Directory":
-                datum = cast(CWLObjectType, datum)
+                dir_datum = cast(CWLDirectoryType, datum)
                 ll = schema.get("loadListing") or self.loadListing
                 if ll and ll != "no_listing":
                     get_listing(
                         self.fs_access,
-                        datum,
+                        dir_datum,
                         (ll == "deep_listing"),
                     )
-                self.files.append(datum)
+                self.files.append(dir_datum)
 
             if schema["type"] == "Any":
                 visit_class(datum, ("File", "Directory"), self._capture_files)
@@ -596,9 +589,7 @@ def tostr(self, value: MutableMapping[str, str] | Any) -> str:
         match value:
             case {"class": "File" | "Directory" as class_name, **rest}:
                 if "path" not in rest:
-                    raise WorkflowException(
-                        '{} object missing "path": {}'.format(class_name, value)
-                    )
+                    raise WorkflowException(f'{class_name} object missing "path": {value}')
                 return str(rest["path"])
             case ScalarFloat():
                 rep = RoundTripRepresenter()
diff --git a/cwltool/checker.py b/cwltool/checker.py
index d81642e1d..c30a0d0b5 100644
--- a/cwltool/checker.py
+++ b/cwltool/checker.py
@@ -3,6 +3,7 @@
 from collections.abc import Iterator, MutableMapping, MutableSequence, Sized
 from typing import Any, Literal, NamedTuple, Optional, Union, cast
 
+from cwl_utils.types import CWLObjectType, CWLOutputType, SinkType
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import SourceLine, bullets, strip_dup_lineno
 from schema_salad.utils import json_dumps
@@ -10,7 +11,7 @@
 from .errors import WorkflowException
 from .loghandler import _logger
 from .process import shortname
-from .utils import CWLObjectType, CWLOutputType, SinkType, aslist
+from .utils import aslist
 
 
 def _get_type(tp: Any) -> Any:
@@ -21,8 +22,8 @@ def _get_type(tp: Any) -> Any:
 
 
 def check_types(
-    srctype: SinkType,
-    sinktype: SinkType,
+    srctype: SinkType | None,
+    sinktype: SinkType | None,
     linkMerge: str | None,
     valueFrom: str | None,
 ) -> Literal["pass"] | Literal["warning"] | Literal["exception"]:
@@ -55,7 +56,7 @@ def check_types(
             raise WorkflowException(f"Unrecognized linkMerge enum {linkMerge!r}")
 
 
-def merge_flatten_type(src: SinkType) -> CWLOutputType:
+def merge_flatten_type(src: SinkType | None) -> CWLOutputType | None:
     """Return the merge flattened type of the source type."""
     match src:
         case MutableSequence():
@@ -66,7 +67,9 @@ def merge_flatten_type(src: SinkType) -> CWLOutputType:
             return {"items": src, "type": "array"}
 
 
-def can_assign_src_to_sink(src: SinkType, sink: SinkType | None, strict: bool = False) -> bool:
+def can_assign_src_to_sink(
+    src: SinkType | None, sink: SinkType | None, strict: bool = False
+) -> bool:
     """
     Check for identical type specifications, ignoring extra keys like inputBinding.
 
@@ -84,8 +87,8 @@ def can_assign_src_to_sink(src: SinkType, sink: SinkType | None, strict: bool =
             return False
         if src["type"] == "array" and sink["type"] == "array":
             return can_assign_src_to_sink(
-                cast(MutableSequence[CWLOutputType], src["items"]),
-                cast(MutableSequence[CWLOutputType], sink["items"]),
+                cast(MutableSequence[CWLOutputType | None], src["items"]),
+                cast(MutableSequence[CWLOutputType | None], sink["items"]),
                 strict,
             )
         if src["type"] == "record" and sink["type"] == "record":
diff --git a/cwltool/command_line_tool.py b/cwltool/command_line_tool.py
index a9d5e57e2..499601979 100644
--- a/cwltool/command_line_tool.py
+++ b/cwltool/command_line_tool.py
@@ -14,7 +14,6 @@
 import urllib.parse
 from collections.abc import (
     Generator,
-    Iterable,
     Mapping,
     MutableMapping,
     MutableSequence,
@@ -22,8 +21,17 @@
 from enum import Enum
 from functools import cmp_to_key, partial
 from re import Pattern
-from typing import TYPE_CHECKING, Any, Optional, TextIO, Union, cast
+from typing import Any, Optional, TYPE_CHECKING, TextIO, Union, cast
 
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_directory,
+    is_file,
+    is_file_or_directory,
+)
 from mypy_extensions import mypyc_attr
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import RecordSchema
@@ -33,12 +41,7 @@
 from schema_salad.utils import json_dumps
 from schema_salad.validate import validate_ex
 
-from .builder import (
-    INPUT_OBJ_VOCAB,
-    Builder,
-    content_limit_respected_read_bytes,
-    substitute,
-)
+from .builder import Builder, INPUT_OBJ_VOCAB, content_limit_respected_read_bytes, substitute
 from .context import LoadingContext, RuntimeContext, getdefault
 from .docker import DockerCommandLineJob, PodmanCommandLineJob
 from .errors import UnsupportedRequirement, WorkflowException
@@ -60,9 +63,6 @@
 from .udocker import UDockerCommandLineJob
 from .update import ORDERED_VERSIONS, ORIGINAL_CWLVERSION
 from .utils import (
-    CWLObjectType,
-    CWLOutputType,
-    DirectoryType,
     JobsGeneratorType,
     OutputCallbackType,
     adjustDirObjs,
@@ -178,18 +178,7 @@ def run(
         try:
             normalizeFilesDirs(self.builder.job)
             ev = self.builder.do_eval(self.script)
-            normalizeFilesDirs(
-                cast(
-                    Optional[
-                        Union[
-                            MutableSequence[MutableMapping[str, Any]],
-                            MutableMapping[str, Any],
-                            DirectoryType,
-                        ]
-                    ],
-                    ev,
-                )
-            )
+            normalizeFilesDirs(ev)
             if self.output_callback:
                 self.output_callback(cast(Optional[CWLObjectType], ev), "success")
         except WorkflowException as err:
@@ -239,7 +228,9 @@ def remove_path(f: CWLObjectType) -> None:
         del f["path"]
 
 
-def revmap_file(builder: Builder, outdir: str, f: CWLObjectType) -> CWLObjectType | None:
+def revmap_file(
+    builder: Builder, outdir: str, f: CWLFileType | CWLDirectoryType
+) -> CWLFileType | CWLDirectoryType:
     """
     Remap a file from internal path to external path.
 
@@ -258,18 +249,18 @@ def revmap_file(builder: Builder, outdir: str, f: CWLObjectType) -> CWLObjectTyp
     # quoted any further.
 
     if "location" in f and "path" not in f:
-        location = cast(str, f["location"])
+        location = f["location"]
         if location.startswith("file://"):
             f["path"] = uri_file_path(location)
         else:
-            f["location"] = builder.fs_access.join(outdir, cast(str, f["location"]))
+            f["location"] = builder.fs_access.join(outdir, f["location"])
             return f
 
-    if "dirname" in f:
+    if is_file(f) and "dirname" in f:
         del f["dirname"]
 
     if "path" in f:
-        path = builder.fs_access.join(builder.outdir, cast(str, f["path"]))
+        path = builder.fs_access.join(builder.outdir, f["path"])
         uripath = file_uri(path)
         del f["path"]
 
@@ -379,9 +370,9 @@ def check_valid_locations(fs_access: StdFsAccess, ob: CWLObjectType) -> None:
     location = cast(str, ob["location"])
     if location.startswith("_:"):
         pass
-    if ob["class"] == "File" and not fs_access.isfile(location):
+    if is_file(ob) and not fs_access.isfile(location):
         raise ValidationException("Does not exist or is not a File: '%s'" % location)
-    if ob["class"] == "Directory" and not fs_access.isdir(location):
+    if is_directory(ob) and not fs_access.isdir(location):
         raise ValidationException("Does not exist or is not a Directory: '%s'" % location)
 
 
@@ -449,7 +440,7 @@ def make_job_runner(self, runtimeContext: RuntimeContext) -> type[JobBase]:
 
     @staticmethod
     def make_path_mapper(
-        reffiles: list[CWLObjectType],
+        reffiles: MutableSequence[CWLFileType | CWLDirectoryType],
         stagedir: str,
         runtimeContext: RuntimeContext,
         separateDirs: bool,
@@ -596,10 +587,7 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
 
                         filelist = True
                         for e in entry:
-                            if not isinstance(e, MutableMapping) or e.get("class") not in (
-                                "File",
-                                "Directory",
-                            ):
+                            if not is_file_or_directory(e):
                                 filelist = False
                                 break
 
@@ -619,11 +607,8 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                     et: CWLObjectType = {}
                     writable = t.get("writable", False)
                     et["writable"] = writable
-                    if isinstance(entry, Mapping) and entry.get("class") in (
-                        "File",
-                        "Directory",
-                    ):
-                        if writable and "secondaryFiles" in entry:
+                    if is_file_or_directory(entry):
+                        if writable and is_file(entry) and "secondaryFiles" in entry:
                             secFiles = cast(MutableSequence[CWLObjectType], entry["secondaryFiles"])
                             for sf in secFiles:
                                 sf["writable"] = writable
@@ -704,7 +689,7 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                     )
                 )
 
-            if t2["entry"].get("class") not in ("File", "Directory"):
+            if not is_file_or_directory(t2["entry"]):
                 raise SourceLine(initialWorkdir, "listing", WorkflowException, debug).makeError(
                     "Entry at index %s of listing is not a File or Directory object, was %s"
                     % (i, t2)
@@ -718,10 +703,10 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                 t2entry["writable"] = t2copy.get("writable")
                 t2["entry"] = t2entry
 
-            ls[i] = t2["entry"]
+            ls[i] = cast(CWLObjectType, t2["entry"])
 
         for i, t3 in enumerate(ls):
-            if t3.get("class") not in ("File", "Directory"):
+            if not is_file_or_directory(t3):
                 # Check that every item is a File or Directory object now
                 raise SourceLine(initialWorkdir, "listing", WorkflowException, debug).makeError(
                     f"Entry at index {i} of listing is not a Dirent, File or "
@@ -729,7 +714,7 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                 )
             if "basename" not in t3:
                 continue
-            basename = os.path.normpath(cast(str, t3["basename"]))
+            basename = os.path.normpath(t3["basename"])
             t3["basename"] = basename
             if basename.startswith("../"):
                 raise SourceLine(initialWorkdir, "listing", WorkflowException, debug).makeError(
@@ -761,18 +746,19 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
             return  # Only testing
 
         with SourceLine(initialWorkdir, "listing", WorkflowException, debug):
-            j.generatefiles["listing"] = ls
+            j.generatefiles["listing"] = cast(MutableSequence[CWLFileType | CWLDirectoryType], ls)
             for entry in ls:
                 if "basename" in entry:
                     basename = cast(str, entry["basename"])
+                    entry["basename"] = os.path.basename(basename)
                     dirname = os.path.join(builder.outdir, os.path.dirname(basename))
                     entry["dirname"] = dirname
-                    entry["basename"] = os.path.basename(basename)
-                    if "secondaryFiles" in entry:
-                        for sec_file in cast(
-                            MutableSequence[CWLObjectType], entry["secondaryFiles"]
-                        ):
-                            sec_file["dirname"] = dirname
+                    if is_file(entry):
+                        if "secondaryFiles" in entry:
+                            for sec_file in cast(
+                                MutableSequence[CWLObjectType], entry["secondaryFiles"]
+                            ):
+                                sec_file["dirname"] = dirname
                 normalizeFilesDirs(entry)
                 self.updatePathmap(
                     cast(Optional[str], entry.get("dirname")) or builder.outdir,
@@ -780,7 +766,7 @@ def _initialworkdir(self, j: JobBase | None, builder: Builder) -> None:
                     entry,
                 )
 
-                if "listing" in entry:
+                if is_directory(entry) and "listing" in entry:
 
                     def remove_dirname(d: CWLObjectType) -> None:
                         if "dirname" in d:
@@ -857,10 +843,11 @@ def calc_checksum(location: str) -> str | None:
                     if (
                         "location" in e
                         and e["location"] == location
+                        and is_file(e)
                         and "checksum" in e
                         and e["checksum"] != "sha1$hash"
                     ):
-                        return cast(str, e["checksum"])
+                        return e["checksum"]
                 return None
 
             def remove_prefix(s: str, prefix: str) -> str:
@@ -1019,7 +1006,7 @@ def update_status_output_callback(
                     )
                 j.stdin = stdin_eval
                 if j.stdin:
-                    reffiles.append({"class": "File", "path": j.stdin})
+                    reffiles.append(CWLFileType(**{"class": "File", "path": j.stdin}))
 
         if self.tool.get("stderr"):
             with SourceLine(self.tool, "stderr", ValidationException, debug):
@@ -1299,7 +1286,7 @@ def collect_output(
         fs_access: StdFsAccess,
         compute_checksum: bool = True,
     ) -> CWLOutputType | None:
-        r: list[CWLOutputType] = []
+        r: MutableSequence[CWLFileType | CWLDirectoryType] = []
         empty_and_optional = False
         debug = _logger.isEnabledFor(logging.DEBUG)
         result: CWLOutputType | None = None
@@ -1347,9 +1334,9 @@ def collect_output(
                                 key=cmp_to_key(locale.strcoll),
                             )
                             r.extend(
-                                cast(
-                                    Iterable[CWLOutputType],
-                                    [
+                                [
+                                    cast(
+                                        CWLFileType | CWLDirectoryType,
                                         {
                                             "location": g,
                                             "path": fs_access.join(
@@ -1360,16 +1347,16 @@ def collect_output(
                                             "nameroot": os.path.splitext(decoded_basename)[0],
                                             "nameext": os.path.splitext(decoded_basename)[1],
                                             "class": "File" if fs_access.isfile(g) else "Directory",
-                                        }
-                                        for g, decoded_basename in zip(
+                                        },
+                                    )
+                                    for g, decoded_basename in zip(
+                                        sorted_glob_result,
+                                        map(
+                                            lambda x: os.path.basename(urllib.parse.unquote(x)),
                                             sorted_glob_result,
-                                            map(
-                                                lambda x: os.path.basename(urllib.parse.unquote(x)),
-                                                sorted_glob_result,
-                                            ),
-                                        )
-                                    ],
-                                )
+                                        ),
+                                    )
+                                ]
                             )
                         except OSError as e:
                             _logger.warning(str(e), exc_info=builder.debug)
@@ -1377,28 +1364,28 @@ def collect_output(
                             _logger.error("Unexpected error from fs_access", exc_info=True)
                             raise
 
-                for files in cast(list[dict[str, Optional[CWLOutputType]]], r):
+                for files in r:
                     rfile = files.copy()
                     revmap(rfile)
-                    if files["class"] == "Directory":
+                    if is_directory(files):
                         ll = binding.get("loadListing") or builder.loadListing
                         if ll and ll != "no_listing":
                             get_listing(fs_access, files, (ll == "deep_listing"))
                     else:
                         if binding.get("loadContents"):
-                            with fs_access.open(cast(str, rfile["location"]), "rb") as f:
+                            with fs_access.open(rfile["location"], "rb") as f:
                                 files["contents"] = str(
                                     content_limit_respected_read_bytes(f), "utf-8"
                                 )
                         if compute_checksum:
-                            with fs_access.open(cast(str, rfile["location"]), "rb") as f:
+                            with fs_access.open(rfile["location"], "rb") as f:
                                 checksum = hashlib.sha1()  # nosec
                                 contents = f.read(1024 * 1024)
                                 while contents != b"":
                                     checksum.update(contents)
                                     contents = f.read(1024 * 1024)
                                 files["checksum"] = "sha1$%s" % checksum.hexdigest()
-                        files["size"] = fs_access.size(cast(str, rfile["location"]))
+                        files["size"] = fs_access.size(rfile["location"])
 
             optional = False
             single = False
diff --git a/cwltool/context.py b/cwltool/context.py
index 4e106ac48..44129b40f 100644
--- a/cwltool/context.py
+++ b/cwltool/context.py
@@ -8,6 +8,7 @@
 from collections.abc import Callable, Iterable
 from typing import IO, TYPE_CHECKING, Any, Literal, Optional, TextIO, Union
 
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro.schema import Names
 from schema_salad.ref_resolver import Loader
@@ -16,7 +17,7 @@
 from .mpi import MpiConfig
 from .pathmapper import PathMapper
 from .stdfsaccess import StdFsAccess
-from .utils import DEFAULT_TMP_PREFIX, CWLObjectType, HasReqsHints, ResolverType
+from .utils import DEFAULT_TMP_PREFIX, HasReqsHints, ResolverType
 
 if TYPE_CHECKING:
     from _typeshed import SupportsWrite
diff --git a/cwltool/cuda.py b/cwltool/cuda.py
index 86dcb3cdd..ec3635373 100644
--- a/cwltool/cuda.py
+++ b/cwltool/cuda.py
@@ -3,8 +3,9 @@
 import subprocess  # nosec
 import xml.dom.minidom  # nosec
 
+from cwl_utils.types import CWLObjectType
+
 from .loghandler import _logger
-from .utils import CWLObjectType
 
 
 def cuda_version_and_device_count() -> tuple[str, int]:
diff --git a/cwltool/cwlprov/provenance_profile.py b/cwltool/cwlprov/provenance_profile.py
index c0aa5ec5b..6658bd54c 100644
--- a/cwltool/cwlprov/provenance_profile.py
+++ b/cwltool/cwlprov/provenance_profile.py
@@ -6,8 +6,15 @@
 from collections.abc import MutableMapping, MutableSequence, Sequence
 from io import BytesIO
 from pathlib import PurePath, PurePosixPath
-from typing import TYPE_CHECKING, Any, cast
-
+from typing import TYPE_CHECKING, Any, TypedDict, cast
+
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    is_directory,
+    is_file,
+)
 from prov.identifier import Identifier, QualifiedName
 from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity
 from schema_salad.sourceline import SourceLine
@@ -17,7 +24,7 @@
 from ..loghandler import _logger
 from ..process import Process, shortname
 from ..stdfsaccess import StdFsAccess
-from ..utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring
+from ..utils import JobsType, get_listing, posix_path, versionstring
 from ..workflow_job import WorkflowJob
 from .provenance_constants import (
     ACCOUNT_UUID,
@@ -40,6 +47,16 @@
 if TYPE_CHECKING:
     from .ro import ResearchObject
 
+CWLArtifact = TypedDict("CWLArtifact", {"@id": str})
+
+
+class _CWLDirectoryArtifact(CWLArtifact, CWLDirectoryType):
+    pass
+
+
+class _CWLFileArtifact(CWLArtifact, CWLFileType):
+    pass
+
 
 def copy_job_order(job: Process | JobsType, job_order_object: CWLObjectType) -> CWLObjectType:
     """Create copy of job object for provenance."""
@@ -243,15 +260,15 @@ def record_process_end(
         self.generate_output_prov(outputs, process_run_id, process_name)
         self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when)
 
-    def declare_file(self, value: CWLObjectType) -> tuple[ProvEntity, ProvEntity, str]:
+    def declare_file(self, value: _CWLFileArtifact) -> tuple[ProvEntity, ProvEntity, str]:
         """Construct a FileEntity for the given CWL File object."""
-        if value["class"] != "File":
+        if not is_file(value):
             raise ValueError("Must have class:File: %s" % value)
         # Need to determine file hash aka RO filename
         entity: ProvEntity | None = None
         checksum = None
         if "checksum" in value:
-            csum = cast(str, value["checksum"])
+            csum = value["checksum"]
             (method, checksum) = csum.split("$", 1)
             if method == SHA1 and self.research_object.has_data_file(checksum):
                 entity = self.document.entity("data:" + checksum)
@@ -269,7 +286,7 @@ def declare_file(self, value: CWLObjectType) -> tuple[ProvEntity, ProvEntity, st
 
         if not entity and "contents" in value:
             # Anonymous file, add content as string
-            entity, checksum = self.declare_string(cast(str, value["contents"]))
+            entity, checksum = self.declare_string(value["contents"])
 
         # By here one of them should have worked!
         if not entity or not checksum:
@@ -279,7 +296,7 @@ def declare_file(self, value: CWLObjectType) -> tuple[ProvEntity, ProvEntity, st
         # secondaryFiles. Note that multiple uses of a file might thus record
         # different names for the same entity, so we'll
         # make/track a specialized entity by UUID
-        file_id = cast(str, value.setdefault("@id", uuid.uuid4().urn))
+        file_id = value.setdefault("@id", uuid.uuid4().urn)
         # A specialized entity that has just these names
         file_entity = self.document.entity(
             file_id,
@@ -287,20 +304,20 @@ def declare_file(self, value: CWLObjectType) -> tuple[ProvEntity, ProvEntity, st
         )
 
         if "basename" in value:
-            file_entity.add_attributes({CWLPROV["basename"]: cast(str, value["basename"])})
+            file_entity.add_attributes({CWLPROV["basename"]: value["basename"]})
         if "nameroot" in value:
-            file_entity.add_attributes({CWLPROV["nameroot"]: cast(str, value["nameroot"])})
+            file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]})
         if "nameext" in value:
-            file_entity.add_attributes({CWLPROV["nameext"]: cast(str, value["nameext"])})
+            file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]})
         self.document.specializationOf(file_entity, entity)
 
         # Check for secondaries
-        for sec in cast(MutableSequence[CWLObjectType], value.get("secondaryFiles", [])):
+        for sec in value.get("secondaryFiles", []):
             # TODO: Record these in a specializationOf entity with UUID?
-            if sec["class"] == "File":
-                (sec_entity, _, _) = self.declare_file(sec)
-            elif sec["class"] == "Directory":
-                sec_entity = self.declare_directory(sec)
+            if is_file(sec):
+                (sec_entity, _, _) = self.declare_file(cast(_CWLFileArtifact, sec))
+            elif is_directory(sec):
+                sec_entity = self.declare_directory(cast(_CWLDirectoryArtifact, sec))
             else:
                 raise ValueError(f"Got unexpected secondaryFiles value: {sec}")
             # We don't know how/when/where the secondary file was generated,
@@ -315,14 +332,14 @@ def declare_file(self, value: CWLObjectType) -> tuple[ProvEntity, ProvEntity, st
 
         return file_entity, entity, checksum
 
-    def declare_directory(self, value: CWLObjectType) -> ProvEntity:
+    def declare_directory(self, value: _CWLDirectoryArtifact) -> ProvEntity:
         """Register any nested files/directories."""
         # FIXME: Calculate a hash-like identifier for directory
         # so we get same value if it's the same filenames/hashes
         # in a different location.
         # For now, mint a new UUID to identify this directory, but
         # attempt to keep it inside the value dictionary
-        dir_id = cast(str, value.setdefault("@id", uuid.uuid4().urn))
+        dir_id = value.setdefault("@id", uuid.uuid4().urn)
 
         # New annotation file to keep the ORE Folder listing
         ore_doc_fn = dir_id.replace("urn:uuid:", "directory-") + ".ttl"
@@ -339,7 +356,7 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity:
         )
 
         if "basename" in value:
-            coll.add_attributes({CWLPROV["basename"]: cast(str, value["basename"])})
+            coll.add_attributes({CWLPROV["basename"]: value["basename"]})
 
         # ORE description of ro:Folder, saved separately
         coll_b = dir_bundle.entity(
@@ -475,11 +492,11 @@ def declare_artefact(self, value: Any) -> ProvEntity:
 
             # Base case - we found a File we need to update
             case {"class": "File"}:
-                entity = self.declare_file(value)[0]
+                entity = self.declare_file(cast(_CWLFileArtifact, value))[0]
                 value["@id"] = entity.identifier.uri
                 return entity
             case {"class": "Directory"}:
-                entity = self.declare_directory(value)
+                entity = self.declare_directory(cast(_CWLDirectoryArtifact, value))
                 value["@id"] = entity.identifier.uri
                 return entity
             case {**rest}:
diff --git a/cwltool/cwlprov/ro.py b/cwltool/cwlprov/ro.py
index 28b7c86df..392b183f5 100644
--- a/cwltool/cwlprov/ro.py
+++ b/cwltool/cwlprov/ro.py
@@ -13,18 +13,20 @@
 from typing import IO, TYPE_CHECKING, Any, Optional, cast
 
 import prov.model as provM
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_directory,
+    is_file,
+    is_file_or_directory,
+)
 from prov.model import ProvDocument
 
 from ..loghandler import _logger
 from ..stdfsaccess import StdFsAccess
-from ..utils import (
-    CWLObjectType,
-    CWLOutputType,
-    create_tmp_dir,
-    local_path,
-    posix_path,
-    versionstring,
-)
+from ..utils import create_tmp_dir, local_path, posix_path, versionstring
 from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy
 from .provenance_constants import (
     ACCOUNT_UUID,
@@ -495,7 +497,7 @@ def _authored_by(self) -> AuthoredBy | None:
             return authored_by
         return None
 
-    def generate_snapshot(self, prov_dep: CWLObjectType) -> None:
+    def generate_snapshot(self, prov_dep: CWLFileType | CWLDirectoryType) -> None:
         """Copy all of the CWL files to the snapshot/ directory."""
         self.self_check()
         for key, value in prov_dep.items():
@@ -521,8 +523,8 @@ def generate_snapshot(self, prov_dep: CWLObjectType) -> None:
                     except PermissionError:
                         pass  # FIXME: avoids duplicate snapshotting; need better solution
             elif key in ("secondaryFiles", "listing"):
-                for files in cast(MutableSequence[CWLObjectType], value):
-                    if isinstance(files, MutableMapping):
+                for files in cast(MutableSequence[CWLFileType | CWLDirectoryType], value):
+                    if is_file_or_directory(files):
                         self.generate_snapshot(files)
             else:
                 pass
@@ -635,17 +637,17 @@ def _add_to_bagit(self, rel_path: str, **checksums: str) -> None:
 
     def _relativise_files(
         self,
-        structure: CWLObjectType | CWLOutputType | MutableSequence[CWLObjectType],
+        structure: CWLObjectType | CWLOutputType | MutableSequence[CWLObjectType] | None,
     ) -> None:
         """Save any file objects into the RO and update the local paths."""
         # Base case - we found a File we need to update
         _logger.debug("[provenance] Relativising: %s", structure)
 
         if isinstance(structure, MutableMapping):
-            if structure.get("class") == "File":
+            if is_file(structure):
                 relative_path: str | PurePosixPath | None = None
                 if "checksum" in structure:
-                    raw_checksum = cast(str, structure["checksum"])
+                    raw_checksum = structure["checksum"]
                     alg, checksum = raw_checksum.split("$")
                     if alg != SHA1:
                         raise TypeError(
@@ -659,7 +661,7 @@ def _relativise_files(
                     # Register in RO; but why was this not picked
                     # up by used_artefacts?
                     _logger.info("[provenance] Adding to RO %s", structure["location"])
-                    with self.fsaccess.open(cast(str, structure["location"]), "rb") as fp:
+                    with self.fsaccess.open(structure["location"], "rb") as fp:
                         relative_path = self.add_data_file(fp)
                         checksum = PurePosixPath(relative_path).name
                         structure["checksum"] = f"{SHA1}${checksum}"
@@ -668,14 +670,14 @@ def _relativise_files(
                 if "path" in structure:
                     del structure["path"]
 
-            if structure.get("class") == "Directory":
+            if is_directory(structure):
                 # TODO: Generate anonymous Directory with a "listing"
                 # pointing to the hashed files
                 del structure["location"]
 
             for val in structure.values():
                 try:
-                    self._relativise_files(val)
+                    self._relativise_files(cast(CWLOutputType, val))
                 except OSError:
                     pass
             return
diff --git a/cwltool/cwlprov/writablebagfile.py b/cwltool/cwlprov/writablebagfile.py
index ecd6463d6..f0f7fb323 100644
--- a/cwltool/cwlprov/writablebagfile.py
+++ b/cwltool/cwlprov/writablebagfile.py
@@ -14,10 +14,11 @@
 from pathlib import Path, PurePosixPath
 from typing import Any, BinaryIO, cast
 
+from cwl_utils.types import CWLObjectType
 from schema_salad.utils import json_dumps
 
 from ..loghandler import _logger
-from ..utils import CWLObjectType, local_path, posix_path
+from ..utils import local_path, posix_path
 from .provenance_constants import (
     CWLPROV,
     CWLPROV_VERSION,
diff --git a/cwltool/docker.py b/cwltool/docker.py
index 69fecc830..b26ac78c2 100644
--- a/cwltool/docker.py
+++ b/cwltool/docker.py
@@ -9,11 +9,12 @@
 import subprocess  # nosec
 import sys
 import threading
-from collections.abc import Callable, MutableMapping
+from collections.abc import Callable, MutableMapping, MutableSequence
 from io import StringIO  # pylint: disable=redefined-builtin
 from typing import Optional, cast
 
 import requests
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType
 
 from .builder import Builder
 from .context import RuntimeContext
@@ -22,7 +23,7 @@
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper
-from .utils import CWLObjectType, create_tmp_dir, ensure_writable
+from .utils import create_tmp_dir, ensure_writable
 
 _IMAGES: set[str] = set()
 _IMAGES_LOCK = threading.Lock()
@@ -84,7 +85,9 @@ def __init__(
         self,
         builder: Builder,
         joborder: CWLObjectType,
-        make_path_mapper: Callable[[list[CWLObjectType], str, RuntimeContext, bool], PathMapper],
+        make_path_mapper: Callable[
+            [MutableSequence[CWLFileType | CWLDirectoryType], str, RuntimeContext, bool], PathMapper
+        ],
         requirements: list[CWLObjectType],
         hints: list[CWLObjectType],
         name: str,
@@ -446,7 +449,9 @@ def __init__(
         self,
         builder: Builder,
         joborder: CWLObjectType,
-        make_path_mapper: Callable[[list[CWLObjectType], str, RuntimeContext, bool], PathMapper],
+        make_path_mapper: Callable[
+            [MutableSequence[CWLFileType | CWLDirectoryType], str, RuntimeContext, bool], PathMapper
+        ],
         requirements: list[CWLObjectType],
         hints: list[CWLObjectType],
         name: str,
diff --git a/cwltool/executors.py b/cwltool/executors.py
index 491078e83..8bcdfa519 100644
--- a/cwltool/executors.py
+++ b/cwltool/executors.py
@@ -13,6 +13,7 @@
 from typing import Optional, cast
 
 import psutil
+from cwl_utils.types import CWLObjectType
 from mypy_extensions import mypyc_attr
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import SourceLine
@@ -27,7 +28,7 @@
 from .process import Process, cleanIntermediate, relocateOutputs
 from .task_queue import TaskQueue
 from .update import ORIGINAL_CWLVERSION
-from .utils import CWLObjectType, JobsType
+from .utils import JobsType
 from .workflow import Workflow
 from .workflow_job import WorkflowJob, WorkflowJobStep
 
diff --git a/cwltool/factory.py b/cwltool/factory.py
index fc00eb061..aee4abb6f 100644
--- a/cwltool/factory.py
+++ b/cwltool/factory.py
@@ -1,12 +1,13 @@
 import os
 from typing import Any
 
+from cwl_utils.types import CWLObjectType
+
 from . import load_tool
 from .context import LoadingContext, RuntimeContext
 from .errors import WorkflowException
 from .executors import JobExecutor, SingleJobExecutor
 from .process import Process
-from .utils import CWLObjectType
 
 
 class WorkflowStatus(Exception):
diff --git a/cwltool/job.py b/cwltool/job.py
index 4f49c95fe..9def5fddd 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -21,6 +21,7 @@
 from typing import IO, TYPE_CHECKING, Optional, TextIO, Union, cast
 
 import psutil
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, CWLOutputType
 from prov.model import PROV
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dump, json_dumps
@@ -35,9 +36,6 @@
 from .process import stage_files
 from .secrets import SecretStore
 from .utils import (
-    CWLObjectType,
-    CWLOutputType,
-    DirectoryType,
     HasReqsHints,
     OutputCallbackType,
     bytes2str_in_dicts,
@@ -108,7 +106,9 @@ def __init__(
         self,
         builder: Builder,
         joborder: CWLObjectType,
-        make_path_mapper: Callable[[list[CWLObjectType], str, RuntimeContext, bool], PathMapper],
+        make_path_mapper: Callable[
+            [MutableSequence[CWLFileType | CWLDirectoryType], str, RuntimeContext, bool], PathMapper
+        ],
         requirements: list[CWLObjectType],
         hints: list[CWLObjectType],
         name: str,
@@ -138,11 +138,13 @@ def __init__(
         self.tmpdir = ""
 
         self.environment: MutableMapping[str, str] = {}
-        self.generatefiles: DirectoryType = {
-            "class": "Directory",
-            "listing": [],
-            "basename": "",
-        }
+        self.generatefiles = CWLDirectoryType(
+            **{
+                "class": "Directory",
+                "listing": [],
+                "basename": "",
+            }
+        )
         self.stagedir: str | None = None
         self.inplace_update = False
         self.prov_obj: ProvenanceProfile | None = None
@@ -160,6 +162,7 @@ def run(
         self,
         runtimeContext: RuntimeContext,
         tmpdir_lock: Union[threading.Lock, None] = None,
+        # use `threading.Lock | None` when we drop support for Python 3.12
     ) -> None:
         pass
 
diff --git a/cwltool/load_tool.py b/cwltool/load_tool.py
index 853c203be..4c34094c6 100644
--- a/cwltool/load_tool.py
+++ b/cwltool/load_tool.py
@@ -12,6 +12,7 @@
 from typing import Any, Union, cast
 
 from cwl_utils.parser import cwl_v1_2, cwl_v1_2_utils
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.fetcher import Fetcher
@@ -32,7 +33,7 @@
 from .loghandler import _logger
 from .process import Process, get_schema, shortname
 from .update import ALLUPDATES
-from .utils import CWLObjectType, ResolverType, visit_class
+from .utils import ResolverType, visit_class
 
 docloaderctx: ContextType = {
     "cwl": "https://w3id.org/cwl/cwl#",
diff --git a/cwltool/main.py b/cwltool/main.py
index b8d74ded0..582066b05 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -23,6 +23,13 @@
 import coloredlogs
 import requests
 import ruamel.yaml
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_file,
+)
 from rich_argparse import RichHelpFormatter
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from ruamel.yaml.main import YAML
@@ -89,8 +96,6 @@
 from .update import ALLUPDATES, UPDATES
 from .utils import (
     DEFAULT_TMP_PREFIX,
-    CWLObjectType,
-    CWLOutputType,
     HasReqsHints,
     adjustDirObjs,
     normalizeFilesDirs,
@@ -245,8 +250,8 @@ def generate_example_input(
             for field in cast(list[CWLObjectType], fields):
                 value, f_comment = generate_example_input(field["type"], None)
                 example.insert(0, shortname(cast(str, field["name"])), value, f_comment)
-        case {"type": str(inp_type), "default": default}:
-            example = default
+        case {"type": str(inp_type), "default": default_value}:
+            example = default_value
             comment = f"default value of type {inp_type!r}"
         case {"type": str(inp_type)}:
             example = defaults.get(inp_type, str(inptype))
@@ -298,7 +303,7 @@ def realize_input_schema(
             if isinstance(entry["type"], Mapping):
                 entry["type"] = cast(
                     CWLOutputType,
-                    realize_input_schema([entry["type"]], schema_defs),
+                    realize_input_schema([cast(CWLObjectType, entry["type"])], schema_defs),
                 )
             if entry["type"] == "array":
                 items = entry["items"] if not isinstance(entry["items"], str) else [entry["items"]]
@@ -565,14 +570,14 @@ def prov_deps(
     document_loader: Loader,
     uri: str,
     basedir: str | None = None,
-) -> CWLObjectType:
+) -> CWLFileType:
     deps = find_deps(obj, document_loader, uri, basedir=basedir)
 
-    def remove_non_cwl(deps: CWLObjectType) -> None:
-        if "secondaryFiles" in deps:
-            sec_files = cast(list[CWLObjectType], deps["secondaryFiles"])
+    def remove_non_cwl(deps: CWLFileType | CWLDirectoryType) -> None:
+        if is_file(deps) and "secondaryFiles" in deps:
+            sec_files = deps["secondaryFiles"]
             for index, entry in enumerate(sec_files):
-                if not ("format" in entry and entry["format"] == CWL_IANA):
+                if not (is_file(entry) and "format" in entry and entry["format"] == CWL_IANA):
                     del sec_files[index]
                 else:
                     remove_non_cwl(entry)
@@ -587,13 +592,15 @@ def find_deps(
     uri: str,
     basedir: str | None = None,
     nestdirs: bool = True,
-) -> CWLObjectType:
+) -> CWLFileType:
     """Find the dependencies of the CWL document."""
-    deps: CWLObjectType = {
-        "class": "File",
-        "location": uri,
-        "format": CWL_IANA,
-    }
+    deps = CWLFileType(
+        **{
+            "class": "File",
+            "location": uri,
+            "format": CWL_IANA,
+        }
+    )
 
     def loadref(base: str, uri: str) -> CommentedMap | CommentedSeq | str | None:
         return document_loader.fetch(document_loader.fetcher.urljoin(base, uri))
@@ -607,7 +614,7 @@ def loadref(base: str, uri: str) -> CommentedMap | CommentedSeq | str | None:
         nestdirs=nestdirs,
     )
     if sfs is not None:
-        deps["secondaryFiles"] = cast(MutableSequence[CWLOutputType], mergedirs(sfs))
+        deps["secondaryFiles"] = mergedirs(sfs)
 
     return deps
 
diff --git a/cwltool/mutation.py b/cwltool/mutation.py
index 622807ec6..b3da0a004 100644
--- a/cwltool/mutation.py
+++ b/cwltool/mutation.py
@@ -2,8 +2,9 @@
 
 from typing import NamedTuple, cast
 
+from cwl_utils.types import CWLObjectType
+
 from .errors import WorkflowException
-from .utils import CWLObjectType
 
 
 class _MutationState(NamedTuple):
diff --git a/cwltool/pack.py b/cwltool/pack.py
index 8c250c51b..968e8364c 100644
--- a/cwltool/pack.py
+++ b/cwltool/pack.py
@@ -5,6 +5,7 @@
 from collections.abc import Callable, MutableMapping, MutableSequence
 from typing import Any, Optional, Union, cast
 
+from cwl_utils.types import CWLObjectType, CWLOutputType
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import Loader, SubLoader
 from schema_salad.utils import ResolveType
@@ -13,7 +14,6 @@
 from .load_tool import fetch_document, resolve_and_validate_document
 from .process import shortname, uniquename
 from .update import ORDERED_VERSIONS, ORIGINAL_CWLVERSION, update
-from .utils import CWLObjectType, CWLOutputType
 
 LoadRefType = Callable[[Optional[str], str], ResolveType]
 
@@ -79,7 +79,7 @@ def replace_refs(d: Any, rewrite: dict[str, str], stem: str, newstem: str) -> No
 
 
 def import_embed(
-    d: MutableSequence[CWLObjectType] | CWLObjectType | CWLOutputType,
+    d: MutableSequence[CWLObjectType] | CWLObjectType | CWLOutputType | None,
     seen: set[str],
 ) -> None:
     if isinstance(d, MutableSequence):
diff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py
index 0cf5f7086..9e25d6c0f 100644
--- a/cwltool/pathmapper.py
+++ b/cwltool/pathmapper.py
@@ -3,9 +3,10 @@
 import stat
 import urllib
 import uuid
-from collections.abc import ItemsView, Iterable, Iterator, KeysView
+from collections.abc import ItemsView, Iterable, Iterator, KeysView, MutableSequence
 from typing import NamedTuple, Optional, cast
 
+from cwl_utils.types import CWLDirectoryType, CWLFileType, is_directory
 from mypy_extensions import mypyc_attr
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import uri_file_path
@@ -13,7 +14,7 @@
 
 from .loghandler import _logger
 from .stdfsaccess import abspath
-from .utils import CWLObjectType, dedup, downloadHttpFile
+from .utils import dedup, downloadHttpFile
 
 
 class MapperEnt(NamedTuple):
@@ -75,7 +76,7 @@ class PathMapper:
 
     def __init__(
         self,
-        referenced_files: list[CWLObjectType],
+        referenced_files: MutableSequence[CWLFileType | CWLDirectoryType],
         basedir: str,
         stagedir: str,
         separateDirs: bool = True,
@@ -88,7 +89,7 @@ def __init__(
 
     def visitlisting(
         self,
-        listing: list[CWLObjectType],
+        listing: MutableSequence[CWLFileType | CWLDirectoryType],
         stagedir: str,
         basedir: str,
         copy: bool = False,
@@ -105,7 +106,7 @@ def visitlisting(
 
     def visit(
         self,
-        obj: CWLObjectType,
+        obj: CWLFileType | CWLDirectoryType,
         stagedir: str,
         basedir: str,
         copy: bool = False,
@@ -116,10 +117,10 @@ def visit(
         stagedir = cast(Optional[str], obj.get("dirname")) or stagedir
         tgt = os.path.join(
             stagedir,
-            cast(str, obj["basename"]),
+            obj["basename"],
         )
-        if obj["class"] == "Directory":
-            location = cast(str, obj["location"])
+        if is_directory(obj):
+            location = obj["location"]
             if location.startswith("file://"):
                 resolved = uri_file_path(location)
             else:
@@ -130,18 +131,18 @@ def visit(
             if location.startswith("file://"):
                 staged = False
             self.visitlisting(
-                cast(list[CWLObjectType], obj.get("listing", [])),
+                obj.get("listing", []),
                 tgt,
                 basedir,
                 copy=copy,
                 staged=staged,
             )
-        elif obj["class"] == "File":
-            path = cast(str, obj["location"])
+        else:
+            path = obj["location"]
             ab = abspath(path, basedir)
             if "contents" in obj and path.startswith("_:"):
                 self._pathmap[path] = MapperEnt(
-                    cast(str, obj["contents"]),
+                    obj["contents"],
                     tgt,
                     "CreateWritableFile" if copy else "CreateFile",
                     staged,
@@ -172,14 +173,16 @@ def visit(
                         deref, tgt, "WritableFile" if copy else "File", staged
                     )
             self.visitlisting(
-                cast(list[CWLObjectType], obj.get("secondaryFiles", [])),
+                obj.get("secondaryFiles", []),
                 stagedir,
                 basedir,
                 copy=copy,
                 staged=staged,
             )
 
-    def setup(self, referenced_files: list[CWLObjectType], basedir: str) -> None:
+    def setup(
+        self, referenced_files: MutableSequence[CWLFileType | CWLDirectoryType], basedir: str
+    ) -> None:
         """
         For each file, set the target to its own directory.
 
diff --git a/cwltool/process.py b/cwltool/process.py
index 75069b859..4f11b8a24 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -19,6 +19,7 @@
     Iterator,
     MutableMapping,
     MutableSequence,
+    Sequence,
     Sized,
 )
 from importlib.resources import files
@@ -26,6 +27,15 @@
 from typing import TYPE_CHECKING, Any, Optional, Union, cast
 
 from cwl_utils import expression
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_directory,
+    is_file,
+    is_file_or_directory,
+)
 from mypy_extensions import mypyc_attr
 from rdflib import Graph
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
@@ -52,8 +62,6 @@
 from .stdfsaccess import StdFsAccess
 from .update import INTERNAL_VERSION, ORDERED_VERSIONS, ORIGINAL_CWLVERSION
 from .utils import (
-    CWLObjectType,
-    CWLOutputType,
     HasReqsHints,
     JobsGeneratorType,
     LoadListingType,
@@ -309,9 +317,9 @@ def relocateOutputs(
 
     def _collectDirEntries(
         obj: CWLObjectType | MutableSequence[CWLObjectType] | None,
-    ) -> Iterator[CWLObjectType]:
+    ) -> Iterator[CWLFileType | CWLDirectoryType]:
         if isinstance(obj, dict):
-            if obj.get("class") in ("File", "Directory"):
+            if is_file_or_directory(obj):
                 yield obj
             else:
                 for sub_obj in obj.values():
@@ -447,7 +455,9 @@ def avroize_type(
                 cast(MutableSequence[CWLOutputType], items), name_prefix
             )
         case {"type": f_type}:
-            cast(CWLObjectType, field_type)["type"] = avroize_type(f_type, name_prefix)
+            cast(CWLObjectType, field_type)["type"] = avroize_type(
+                cast(CWLObjectType, f_type), name_prefix
+            )
         case "File":
             return "org.w3id.cwl.cwl.File"
         case "Directory":
@@ -477,7 +487,7 @@ def get_overrides(overrides: MutableSequence[CWLObjectType], toolid: str) -> CWL
 
 
 def var_spool_cwl_detector(
-    obj: CWLOutputType,
+    obj: CWLOutputType | None,
     item: Any | None = None,
     obj_key: Any | None = None,
 ) -> bool:
@@ -811,7 +821,7 @@ def inc(d: list[int]) -> None:
         except (ValidationException, WorkflowException) as err:
             raise WorkflowException("Invalid job input record:\n" + str(err)) from err
 
-        files: list[CWLObjectType] = []
+        files: MutableSequence[CWLFileType | CWLDirectoryType] = []
         bindings = CommentedSeq()
         outdir = ""
         tmpdir = ""
@@ -1127,9 +1137,10 @@ def uniquename(stem: str, names: set[str] | None = None) -> str:
     return u
 
 
-def nestdir(base: str, deps: CWLObjectType) -> CWLObjectType:
+def nestdir(base: str, deps: CWLFileType | CWLDirectoryType) -> CWLFileType | CWLDirectoryType:
+    """Add intermediate directory objects to preserve the  relative layout."""
     dirname = os.path.dirname(base) + "/"
-    subid = cast(str, deps["location"])
+    subid = deps["location"]
     if subid.startswith(dirname):
         s2 = subid[len(dirname) :]
         sp = s2.split("/")
@@ -1137,22 +1148,24 @@ def nestdir(base: str, deps: CWLObjectType) -> CWLObjectType:
         while sp:
             loc = dirname + "/".join(sp)
             nx = sp.pop()
-            deps = {
-                "class": "Directory",
-                "basename": nx,
-                "listing": [deps],
-                "location": loc,
-            }
+            deps = CWLDirectoryType(
+                **{
+                    "class": "Directory",
+                    "basename": nx,
+                    "listing": [deps],
+                    "location": loc,
+                }
+            )
     return deps
 
 
 def mergedirs(
-    listing: MutableSequence[CWLObjectType],
-) -> MutableSequence[CWLObjectType]:
-    r: list[CWLObjectType] = []
-    ents: dict[str, CWLObjectType] = {}
+    listing: MutableSequence[CWLFileType | CWLDirectoryType],
+) -> MutableSequence[CWLFileType | CWLDirectoryType]:
+    r: list[CWLFileType | CWLDirectoryType] = []
+    ents: dict[str, CWLFileType | CWLDirectoryType] = {}
     for e in listing:
-        basename = cast(str, e["basename"])
+        basename = e["basename"]
         if basename not in ents:
             ents[basename] = e
         elif e["location"] != ents[basename]["location"]:
@@ -1160,19 +1173,16 @@ def mergedirs(
                 "Conflicting basename in listing or secondaryFiles, '%s' used by both '%s' and '%s'"
                 % (basename, e["location"], ents[basename]["location"])
             )
-        elif e["class"] == "Directory":
+        elif is_directory(e):
             if e.get("listing"):
                 # name already in entries
                 # merge it into the existing listing
-                cast(list[CWLObjectType], ents[basename].setdefault("listing", [])).extend(
-                    cast(list[CWLObjectType], e["listing"])
+                cast(CWLDirectoryType, ents[basename]).setdefault("listing", []).extend(
+                    e["listing"]
                 )
     for e in ents.values():
-        if e["class"] == "Directory" and "listing" in e:
-            e["listing"] = cast(
-                MutableSequence[CWLOutputType],
-                mergedirs(cast(list[CWLObjectType], e["listing"])),
-            )
+        if is_directory(e) and "listing" in e:
+            e["listing"] = mergedirs(e["listing"])
     r.extend(ents.values())
     return r
 
@@ -1182,13 +1192,18 @@ def mergedirs(
 
 def scandeps(
     base: str,
-    doc: CWLObjectType | MutableSequence[CWLObjectType],
+    doc: (
+        CWLFileType
+        | CWLDirectoryType
+        | CWLObjectType
+        | Sequence[CWLFileType | CWLDirectoryType | CWLObjectType]
+    ),
     reffields: set[str],
     urlfields: set[str],
     loadref: Callable[[str, str], CommentedMap | CommentedSeq | str | None],
     urljoin: Callable[[str, str], str] = urllib.parse.urljoin,
     nestdirs: bool = True,
-) -> MutableSequence[CWLObjectType]:
+) -> MutableSequence[CWLFileType | CWLDirectoryType]:
     """
     Search for external files references in a CWL document or input object.
 
@@ -1208,72 +1223,74 @@ def scandeps(
       produce the same relative file system locations.
     :returns: A list of File or Directory dependencies
     """
-    r: MutableSequence[CWLObjectType] = []
+    r: MutableSequence[CWLFileType | CWLDirectoryType] = []
     if isinstance(doc, MutableMapping):
         if "id" in doc:
             if cast(str, doc["id"]).startswith("file://"):
                 df, _ = urllib.parse.urldefrag(cast(str, doc["id"]))
                 if base != df:
-                    r.append({"class": "File", "location": df, "format": CWL_IANA})
+                    r.append(CWLFileType(**{"class": "File", "location": df, "format": CWL_IANA}))
                     base = df
 
-        if doc.get("class") in ("File", "Directory") and "location" in urlfields:
-            u = cast(Optional[str], doc.get("location", doc.get("path")))
+        if is_file_or_directory(doc) and "location" in urlfields:
+            u = doc.get("location", doc.get("path"))
             if u and not u.startswith("_:"):
-                deps: CWLObjectType = {
-                    "class": doc["class"],
-                    "location": urljoin(base, u),
-                }
+                deps: CWLFileType | CWLDirectoryType
+                if is_file(doc):
+                    deps = CWLFileType(
+                        **{
+                            "class": "File",
+                        }
+                    )
+                    if "secondaryFiles" in doc:
+                        deps["secondaryFiles"] = scandeps(
+                            base,
+                            doc["secondaryFiles"],
+                            reffields,
+                            urlfields,
+                            loadref,
+                            urljoin=urljoin,
+                            nestdirs=nestdirs,
+                        )
+                else:
+                    deps = CWLDirectoryType(
+                        **{
+                            "class": "Directory",
+                        }
+                    )
+                    if "listing" in doc:
+                        deps["listing"] = doc["listing"]
+                deps["location"] = urljoin(base, u)
                 if "basename" in doc:
                     deps["basename"] = doc["basename"]
-                match doc:
-                    case {"class": "Directory", "listing": listing}:
-                        deps["listing"] = listing
-                    case {"class": "File", "secondaryFiles": sec_files}:
-                        deps["secondaryFiles"] = cast(
-                            CWLOutputType,
-                            scandeps(
-                                base,
-                                cast(
-                                    Union[CWLObjectType, MutableSequence[CWLObjectType]],
-                                    sec_files,
-                                ),
-                                reffields,
-                                urlfields,
-                                loadref,
-                                urljoin=urljoin,
-                                nestdirs=nestdirs,
-                            ),
-                        )
                 if nestdirs:
                     deps = nestdir(base, deps)
                 r.append(deps)
             else:
-                match doc:
-                    case {"class": "Directory", "listing": listing}:
-                        r.extend(
-                            scandeps(
-                                base,
-                                cast(MutableSequence[CWLObjectType], listing),
-                                reffields,
-                                urlfields,
-                                loadref,
-                                urljoin=urljoin,
-                                nestdirs=nestdirs,
-                            )
+                if is_directory(doc) and "listing" in doc:
+                    r.extend(
+                        scandeps(
+                            base,
+                            doc["listing"],
+                            reffields,
+                            urlfields,
+                            loadref,
+                            urljoin=urljoin,
+                            nestdirs=nestdirs,
                         )
-                    case {"class": "File", "secondaryFiles": sec_files}:
-                        r.extend(
-                            scandeps(
-                                base,
-                                cast(MutableSequence[CWLObjectType], sec_files),
-                                reffields,
-                                urlfields,
-                                loadref,
-                                urljoin=urljoin,
-                                nestdirs=nestdirs,
-                            )
+                    )
+                elif is_file(doc) and "secondaryFiles" in doc:
+                    r.extend(
+                        scandeps(
+                            base,
+                            doc["secondaryFiles"],
+                            reffields,
+                            urlfields,
+                            loadref,
+                            urljoin=urljoin,
+                            nestdirs=nestdirs,
                         )
+                    )
 
         for k, v in doc.items():
             if k in reffields:
@@ -1300,11 +1317,13 @@ def scandeps(
                             Union[MutableSequence[CWLObjectType], CWLObjectType],
                             loadref(base, u2),
                         )
-                        deps2: CWLObjectType = {
-                            "class": "File",
-                            "location": subid,
-                            "format": CWL_IANA,
-                        }
+                        deps2 = CWLFileType(
+                            **{
+                                "class": "File",
+                                "location": subid,
+                                "format": CWL_IANA,
+                            }
+                        )
                         sf = scandeps(
                             subid,
                             sub,
@@ -1315,19 +1334,18 @@ def scandeps(
                             nestdirs=nestdirs,
                         )
                         if sf:
-                            deps2["secondaryFiles"] = cast(
-                                MutableSequence[CWLOutputType], mergedirs(sf)
-                            )
+                            deps2["secondaryFiles"] = mergedirs(sf)
                         if nestdirs:
-                            deps2 = nestdir(base, deps2)
-                        r.append(deps2)
+                            r.append(nestdir(base, deps2))
+                        else:
+                            r.append(deps2)
             elif k in urlfields and k != "location":
                 for u3 in aslist(v):
-                    deps = {"class": "File", "location": urljoin(base, u3)}
+                    deps = CWLFileType(**{"class": "File", "location": urljoin(base, u3)})
                     if nestdirs:
                         deps = nestdir(base, deps)
                     r.append(deps)
-            elif doc.get("class") in ("File", "Directory") and k in (
+            elif is_file_or_directory(doc) and k in (
                 "listing",
                 "secondaryFiles",
             ):
diff --git a/cwltool/procgenerator.py b/cwltool/procgenerator.py
index eb7eca076..1dd963b06 100644
--- a/cwltool/procgenerator.py
+++ b/cwltool/procgenerator.py
@@ -1,6 +1,7 @@
 import copy
 from typing import cast
 
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.exceptions import ValidationException
 from schema_salad.sourceline import indent
@@ -10,7 +11,7 @@
 from .load_tool import load_tool
 from .loghandler import _logger
 from .process import Process, shortname
-from .utils import CWLObjectType, JobsGeneratorType, OutputCallbackType
+from .utils import JobsGeneratorType, OutputCallbackType
 
 
 class ProcessGeneratorJob:
diff --git a/cwltool/secrets.py b/cwltool/secrets.py
index 6a39231e4..4fea75994 100644
--- a/cwltool/secrets.py
+++ b/cwltool/secrets.py
@@ -3,7 +3,7 @@
 import uuid
 from collections.abc import MutableMapping, MutableSequence
 
-from .utils import CWLObjectType, CWLOutputType
+from cwl_utils.types import CWLObjectType, CWLOutputType
 
 
 class SecretStore:
diff --git a/cwltool/singularity.py b/cwltool/singularity.py
index 5551882b8..75ebb769d 100644
--- a/cwltool/singularity.py
+++ b/cwltool/singularity.py
@@ -9,10 +9,11 @@
 import shutil
 import sys
 import threading
-from collections.abc import Callable, MutableMapping
+from collections.abc import Callable, MutableMapping, MutableSequence
 from subprocess import check_call, check_output  # nosec
 from typing import cast
 
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType
 from packaging.version import Version
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
@@ -28,7 +29,7 @@
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper
 from .singularity_utils import singularity_supports_userns
-from .utils import CWLObjectType, create_tmp_dir, ensure_non_writable, ensure_writable
+from .utils import create_tmp_dir, ensure_non_writable, ensure_writable
 
 # Cached version number of singularity
 # This is a list containing major and minor versions as integer.
@@ -169,7 +170,9 @@ def __init__(
         self,
         builder: Builder,
         joborder: CWLObjectType,
-        make_path_mapper: Callable[[list[CWLObjectType], str, RuntimeContext, bool], PathMapper],
+        make_path_mapper: Callable[
+            [MutableSequence[CWLFileType | CWLDirectoryType], str, RuntimeContext, bool], PathMapper
+        ],
         requirements: list[CWLObjectType],
         hints: list[CWLObjectType],
         name: str,
diff --git a/cwltool/subgraph.py b/cwltool/subgraph.py
index 8bad72a47..5378ec3ad 100644
--- a/cwltool/subgraph.py
+++ b/cwltool/subgraph.py
@@ -2,11 +2,12 @@
 from collections.abc import Mapping, MutableMapping, MutableSequence
 from typing import Any, NamedTuple, Union, cast
 
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 from .context import LoadingContext
 from .load_tool import load_tool, make_tool
-from .utils import CWLObjectType, aslist
+from .utils import aslist
 from .workflow import Workflow, WorkflowStep
 
 
diff --git a/cwltool/update.py b/cwltool/update.py
index 91a63f496..48b9484c9 100644
--- a/cwltool/update.py
+++ b/cwltool/update.py
@@ -3,13 +3,14 @@
 from functools import partial
 from typing import cast
 
+from cwl_utils.types import CWLObjectType, CWLOutputType
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader
 from schema_salad.sourceline import SourceLine
 
 from .loghandler import _logger
-from .utils import CWLObjectType, CWLOutputType, aslist, visit_class, visit_field
+from .utils import aslist, visit_class, visit_field
 
 
 def v1_2to1_3dev1(doc: CommentedMap, loader: Loader, baseuri: str) -> tuple[CommentedMap, str]:
@@ -124,7 +125,7 @@ def rewrite_requirements(t: CWLObjectType) -> None:
                 rewrite_requirements(s)
 
     def update_secondaryFiles(
-        t: CWLOutputType, top: bool = False
+        t: CWLOutputType | None, top: bool = False
     ) -> MutableSequence[MutableMapping[str, str]] | MutableMapping[str, str]:
         if isinstance(t, CommentedSeq):
             new_seq = copy.deepcopy(t)
diff --git a/cwltool/utils.py b/cwltool/utils.py
index 2975f0199..f3702192c 100644
--- a/cwltool/utils.py
+++ b/cwltool/utils.py
@@ -2,6 +2,15 @@
 
 import collections
 
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_directory,
+    is_file,
+)
+
 try:
     import fcntl
 except ImportError:
@@ -25,6 +34,7 @@
     Iterable,
     MutableMapping,
     MutableSequence,
+    Sequence,
 )
 from datetime import datetime
 from email.utils import parsedate_to_datetime
@@ -41,9 +51,7 @@
     NamedTuple,
     Optional,
     TypeAlias,
-    TypedDict,
     Union,
-    cast,
 )
 
 import requests
@@ -68,16 +76,6 @@
 
 processes_to_kill: Deque["subprocess.Popen[str]"] = collections.deque()
 
-CWLOutputType: TypeAlias = Union[
-    None,
-    bool,
-    str,
-    int,
-    float,
-    MutableSequence["CWLOutputType"],
-    MutableMapping[str, "CWLOutputType"],
-]
-CWLObjectType: TypeAlias = MutableMapping[str, Optional[CWLOutputType]]
 """Typical raw dictionary found in lightly parsed CWL."""
 
 JobsType: TypeAlias = Union[
@@ -89,10 +87,6 @@
 DestinationsType: TypeAlias = MutableMapping[str, Optional[CWLOutputType]]
 ScatterDestinationsType: TypeAlias = MutableMapping[str, list[Optional[CWLOutputType]]]
 ScatterOutputCallbackType: TypeAlias = Callable[[Optional[ScatterDestinationsType], str], None]
-SinkType: TypeAlias = Union[CWLOutputType, CWLObjectType]
-DirectoryType = TypedDict(
-    "DirectoryType", {"class": str, "listing": list[CWLObjectType], "basename": str}
-)
 JSONType: TypeAlias = Union[dict[str, "JSONType"], list["JSONType"], str, int, float, bool, None]
 
 
@@ -254,15 +248,18 @@ def adjustDirObjs(rec: Any, op: Union[Callable[..., Any], "partial[Any]"]) -> No
     visit_class(rec, ("Directory",), op)
 
 
-def dedup(listing: list[CWLObjectType]) -> list[CWLObjectType]:
+def dedup(
+    listing: MutableSequence[CWLFileType | CWLDirectoryType],
+) -> MutableSequence[CWLFileType | CWLDirectoryType]:
+    """Remove duplicate entries from a CWL Directory 'listing'."""
     marksub = set()
 
     def mark(d: dict[str, str]) -> None:
         marksub.add(d["location"])
 
     for entry in listing:
-        if entry["class"] == "Directory":
-            for e in cast(list[CWLObjectType], entry.get("listing", [])):
+        if is_directory(entry):
+            for e in entry.get("listing", []):
                 adjustFileObjs(e, mark)
                 adjustDirObjs(e, mark)
 
@@ -271,37 +268,41 @@ def mark(d: dict[str, str]) -> None:
     for r in listing:
         if r["location"] not in marksub and r["location"] not in markdup:
             dd.append(r)
-            markdup.add(cast(str, r["location"]))
+            markdup.add(r["location"])
 
     return dd
 
 
-def get_listing(fs_access: "StdFsAccess", rec: CWLObjectType, recursive: bool = True) -> None:
+def get_listing(
+    fs_access: "StdFsAccess", rec: CWLObjectType | CWLDirectoryType, recursive: bool = True
+) -> None:
     """Expand, recursively, any 'listing' fields in a Directory."""
-    if rec.get("class") != "Directory":
-        finddirs: list[CWLObjectType] = []
+    if not is_directory(rec):
+        finddirs: list[CWLDirectoryType] = []
         visit_class(rec, ("Directory",), finddirs.append)
         for f in finddirs:
             get_listing(fs_access, f, recursive=recursive)
         return
     if "listing" in rec:
         return
-    listing: list[CWLOutputType] = []
-    loc = cast(str, rec["location"])
+    listing: MutableSequence[CWLFileType | CWLDirectoryType] = []
+    loc = rec["location"]
     for ld in fs_access.listdir(loc):
         parse = urllib.parse.urlparse(ld)
         bn = os.path.basename(urllib.request.url2pathname(parse.path))
         if fs_access.isdir(ld):
-            ent: MutableMapping[str, Any] = {
-                "class": "Directory",
-                "location": ld,
-                "basename": bn,
-            }
+            ent = CWLDirectoryType(
+                **{
+                    "class": "Directory",
+                    "location": ld,
+                    "basename": bn,
+                }
+            )
             if recursive:
                 get_listing(fs_access, ent, recursive)
             listing.append(ent)
         else:
-            listing.append({"class": "File", "location": ld, "basename": bn})
+            listing.append(CWLFileType(**{"class": "File", "location": ld, "basename": bn}))
     rec["listing"] = listing
 
 
@@ -401,17 +402,24 @@ def ensure_non_writable(path: str) -> None:
 
 
 def normalizeFilesDirs(
-    job: None | (
-        MutableSequence[MutableMapping[str, Any]] | MutableMapping[str, Any] | DirectoryType
-    ),
+    job: Sequence[CWLObjectType | CWLOutputType | None] | CWLObjectType | CWLOutputType | None,
 ) -> None:
-    def addLocation(d: dict[str, Any]) -> None:
+    """
+    Add missing `location`s and `basename`s to CWL File and Directory objects.
+
+    :raises ValidationException: if anonymous objects are missing required fields,
+                                 or if the location ends in '/' but the object isn't
+                                 a directory
+
+    """
+
+    def addLocation(d: CWLFileType | CWLDirectoryType) -> None:
         if "location" not in d:
-            if d["class"] == "File" and ("contents" not in d):
+            if is_file(d) and ("contents" not in d):
                 raise ValidationException(
                     "Anonymous file object must have 'contents' and 'basename' fields."
                 )
-            if d["class"] == "Directory" and ("listing" not in d or "basename" not in d):
+            if is_directory(d) and ("listing" not in d or "basename" not in d):
                 raise ValidationException(
                     "Anonymous directory object must have 'listing' and 'basename' fields."
                 )
@@ -423,7 +431,7 @@ def addLocation(d: dict[str, Any]) -> None:
         path = parse.path
         # strip trailing slash
         if path.endswith("/"):
-            if d["class"] != "Directory":
+            if not is_directory(d):
                 raise ValidationException(
                     "location '%s' ends with '/' but is not a Directory" % d["location"]
                 )
@@ -445,7 +453,7 @@ def addLocation(d: dict[str, Any]) -> None:
             else:
                 d["basename"] = str(os.path.basename(urllib.request.url2pathname(path)))
 
-        if d["class"] == "File":
+        if is_file(d):
             nr, ne = os.path.splitext(d["basename"])
             if d.get("nameroot") != nr:
                 d["nameroot"] = str(nr)
diff --git a/cwltool/workflow.py b/cwltool/workflow.py
index fe34c75ce..6a66b3ef2 100644
--- a/cwltool/workflow.py
+++ b/cwltool/workflow.py
@@ -7,6 +7,7 @@
 from typing import cast
 from uuid import UUID
 
+from cwl_utils.types import CWLObjectType
 from mypy_extensions import mypyc_attr
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.exceptions import ValidationException
@@ -21,13 +22,7 @@
 from .load_tool import load_tool
 from .loghandler import _logger
 from .process import Process, get_overrides, shortname
-from .utils import (
-    CWLObjectType,
-    JobsGeneratorType,
-    OutputCallbackType,
-    StepType,
-    aslist,
-)
+from .utils import JobsGeneratorType, OutputCallbackType, StepType, aslist
 from .workflow_job import WorkflowJob
 
 
diff --git a/cwltool/workflow_job.py b/cwltool/workflow_job.py
index 6e1527c20..c1a3f7d2d 100644
--- a/cwltool/workflow_job.py
+++ b/cwltool/workflow_job.py
@@ -7,6 +7,7 @@
 from typing import TYPE_CHECKING, Optional, Union, cast
 
 from cwl_utils import expression
+from cwl_utils.types import CWLObjectType, CWLOutputType, SinkType
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 
@@ -18,14 +19,11 @@
 from .process import shortname, uniquename
 from .stdfsaccess import StdFsAccess
 from .utils import (
-    CWLObjectType,
-    CWLOutputType,
     JobsGeneratorType,
     OutputCallbackType,
     ParametersType,
     ScatterDestinationsType,
     ScatterOutputCallbackType,
-    SinkType,
     WorkflowStateItem,
     adjustDirObjs,
     aslist,
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index e2dd3606d..c6c3bb105 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,6 +1,5 @@
 mypy==1.19.1  # also update pyproject.toml
 ruamel.yaml>=0.16.0,<0.19
-cwl-utils>=0.32
 cwltest
 types-requests
 types-setuptools
diff --git a/pyproject.toml b/pyproject.toml
index 57b89aa93..81d17192c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ requires = [
     "types-psutil>=7.1.3.20251210",
     "ruamel.yaml>=0.16.0,<0.19",
     "schema-salad>=8.9,<9",
-    "cwl-utils>=0.32",
+    "cwl-utils @ git+https://github.com/common-workflow-language/cwl-utils.git@refs/pull/393/head",
     "toml",
     "argcomplete>=1.12.0",
     "rich-argparse",
diff --git a/requirements.txt b/requirements.txt
index 6dcb90bb9..0ccb07436 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,7 +9,7 @@ coloredlogs
 pydot>=1.4.1
 argcomplete>=1.12.0
 pyparsing!=3.0.2  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
-cwl-utils>=0.32
+cwl-utils @ git+https://github.com/common-workflow-language/cwl-utils.git@refs/pull/393/head
 spython>=0.3.0
 rich-argparse
 typing-extensions>=4.1.0
diff --git a/setup.py b/setup.py
index e473c36fe..ba3c2c8d0 100644
--- a/setup.py
+++ b/setup.py
@@ -159,7 +159,7 @@ def _find_package_data(base: str, globs: list[str], root: str = "cwltool") -> li
         "pydot >= 1.4.1",
         "argcomplete >= 1.12.0",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
-        "cwl-utils >= 0.32",
+        "cwl-utils @ git+https://github.com/common-workflow-language/cwl-utils.git@refs/pull/393/head",
         "spython >= 0.3.0",
         "rich-argparse",
         "typing-extensions >= 4.1.0",
diff --git a/tests/test_context.py b/tests/test_context.py
index 505dfd635..b417180c4 100644
--- a/tests/test_context.py
+++ b/tests/test_context.py
@@ -6,9 +6,10 @@
 from pathlib import Path
 from typing import cast
 
+from cwl_utils.types import CWLObjectType
+
 from cwltool.context import RuntimeContext
 from cwltool.factory import Factory
-from cwltool.utils import CWLObjectType
 from cwltool.workflow_job import WorkflowJobStep
 
 from .util import get_data, needs_docker
diff --git a/tests/test_cuda.py b/tests/test_cuda.py
index 93b1c7a47..391d3fa65 100644
--- a/tests/test_cuda.py
+++ b/tests/test_cuda.py
@@ -2,6 +2,7 @@
 from unittest.mock import MagicMock
 
 import pytest
+from cwl_utils.types import CWLObjectType
 from schema_salad.avro import schema
 
 from cwltool.builder import Builder
@@ -15,7 +16,6 @@
 from cwltool.process import use_custom_schema
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION
-from cwltool.utils import CWLObjectType
 
 from .util import get_data, needs_docker, needs_singularity_3_or_newer
 
diff --git a/tests/test_examples.py b/tests/test_examples.py
index f371f45ae..329bb6d47 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -7,6 +7,7 @@
 import subprocess
 import sys
 import urllib.parse
+from collections.abc import MutableMapping, MutableSequence
 from io import StringIO
 from pathlib import Path
 from typing import Any, cast
@@ -16,6 +17,13 @@
 import pytest
 from cwl_utils.errors import JavascriptException
 from cwl_utils.sandboxjs import param_re
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    CWLParameterContext,
+)
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 
@@ -29,37 +37,37 @@
 from cwltool.errors import WorkflowException
 from cwltool.main import main
 from cwltool.process import CWL_IANA
-from cwltool.utils import CWLObjectType, dedup
+from cwltool.utils import dedup
 
 from .util import get_data, get_main_output, needs_docker, working_directory
 
 sys.argv = [""]
 
 expression_match = [
-    ("(foo)", True),
-    ("(foo.bar)", True),
-    ("(foo['bar'])", True),
-    ('(foo["bar"])', True),
-    ("(foo.bar.baz)", True),
-    ("(foo['bar'].baz)", True),
-    ("(foo['bar']['baz'])", True),
-    ("(foo['b\\'ar']['baz'])", True),
-    ("(foo['b ar']['baz'])", True),
-    ("(foo_bar)", True),
-    ('(foo.["bar"])', False),
-    ('(.foo["bar"])', False),
-    ('(foo ["bar"])', False),
-    ('( foo["bar"])', False),
-    ("(foo[bar].baz)", False),
-    ("(foo['bar\"].baz)", False),
-    ("(foo['bar].baz)", False),
-    ("{foo}", False),
-    ("(foo.bar", False),
-    ("foo.bar)", False),
-    ("foo.b ar)", False),
-    ("foo.b'ar)", False),
-    ("(foo+bar", False),
-    ("(foo bar", False),
+    ("(inputs)", True),
+    ("(inputs.bar)", True),
+    ("(inputs['bar'])", True),
+    ('(inputs["bar"])', True),
+    ("(inputs.bar.baz)", True),
+    ("(inputs['bar'].baz)", True),
+    ("(inputs['bar']['baz'])", True),
+    ("(inputs['b\\'ar']['baz'])", True),
+    ("(inputs['b ar']['baz'])", True),
+    ("(inputs_bar)", True),
+    ('(inputs.["bar"])', False),
+    ('(.inputs["bar"])', False),
+    ('(inputs ["bar"])', False),
+    ('( inputs["bar"])', False),
+    ("(inputs[bar].baz)", False),
+    ("(inputs['bar\"].baz)", False),
+    ("(inputs['bar].baz)", False),
+    ("{inputs}", False),
+    ("(inputs.bar", False),
+    ("inputs.bar)", False),
+    ("inputs.b ar)", False),
+    ("inputs.b'ar)", False),
+    ("(inputs+bar", False),
+    ("(inputs bar", False),
 ]
 
 
@@ -69,54 +77,66 @@ def test_expression_match(expression: str, expected: bool) -> None:
     assert (match is not None) == expected
 
 
-interpolate_input: dict[str, Any] = {
-    "foo": {
+interpolate_input = CWLParameterContext(
+    inputs={
         "bar": {"baz": "zab1"},
         "b ar": {"baz": 2},
         "b'ar": {"baz": True},
         'b"ar': {"baz": None},
     },
-    "lst": ["A", "B"],
-}
+    self=["A", "B"],
+)
 
 interpolate_parameters = [
-    ("$(foo)", interpolate_input["foo"]),
-    ("$(foo.bar)", interpolate_input["foo"]["bar"]),
-    ("$(foo['bar'])", interpolate_input["foo"]["bar"]),
-    ('$(foo["bar"])', interpolate_input["foo"]["bar"]),
-    ("$(foo.bar.baz)", interpolate_input["foo"]["bar"]["baz"]),
-    ("$(foo['bar'].baz)", interpolate_input["foo"]["bar"]["baz"]),
-    ("$(foo['bar'][\"baz\"])", interpolate_input["foo"]["bar"]["baz"]),
-    ("$(foo.bar['baz'])", interpolate_input["foo"]["bar"]["baz"]),
-    ("$(foo['b\\'ar'].baz)", True),
-    ('$(foo["b\'ar"].baz)', True),
-    ("$(foo['b\\\"ar'].baz)", None),
-    ("$(lst[0])", "A"),
-    ("$(lst[1])", "B"),
-    ("$(lst.length)", 2),
-    ("$(lst['length'])", 2),
-    ("-$(foo.bar)", """-{"baz": "zab1"}"""),
-    ("-$(foo['bar'])", """-{"baz": "zab1"}"""),
-    ('-$(foo["bar"])', """-{"baz": "zab1"}"""),
-    ("-$(foo.bar.baz)", "-zab1"),
-    ("-$(foo['bar'].baz)", "-zab1"),
-    ("-$(foo['bar'][\"baz\"])", "-zab1"),
-    ("-$(foo.bar['baz'])", "-zab1"),
-    ("-$(foo['b ar'].baz)", "-2"),
-    ("-$(foo['b\\'ar'].baz)", "-true"),
-    ('-$(foo["b\\\'ar"].baz)', "-true"),
-    ("-$(foo['b\\\"ar'].baz)", "-null"),
-    ("$(foo.bar) $(foo.bar)", """{"baz": "zab1"} {"baz": "zab1"}"""),
-    ("$(foo['bar']) $(foo['bar'])", """{"baz": "zab1"} {"baz": "zab1"}"""),
-    ('$(foo["bar"]) $(foo["bar"])', """{"baz": "zab1"} {"baz": "zab1"}"""),
-    ("$(foo.bar.baz) $(foo.bar.baz)", "zab1 zab1"),
-    ("$(foo['bar'].baz) $(foo['bar'].baz)", "zab1 zab1"),
-    ("$(foo['bar'][\"baz\"]) $(foo['bar'][\"baz\"])", "zab1 zab1"),
-    ("$(foo.bar['baz']) $(foo.bar['baz'])", "zab1 zab1"),
-    ("$(foo['b ar'].baz) $(foo['b ar'].baz)", "2 2"),
-    ("$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)", "true true"),
-    ('$(foo["b\\\'ar"].baz) $(foo["b\\\'ar"].baz)', "true true"),
-    ("$(foo['b\\\"ar'].baz) $(foo['b\\\"ar'].baz)", "null null"),
+    ("$(inputs)", interpolate_input["inputs"]),
+    ("$(inputs.bar)", interpolate_input["inputs"]["bar"]),
+    ("$(inputs['bar'])", interpolate_input["inputs"]["bar"]),
+    ('$(inputs["bar"])', interpolate_input["inputs"]["bar"]),
+    (
+        "$(inputs.bar.baz)",
+        cast(MutableMapping[str, CWLOutputType], interpolate_input["inputs"]["bar"])["baz"],
+    ),
+    (
+        "$(inputs['bar'].baz)",
+        cast(MutableMapping[str, CWLOutputType], interpolate_input["inputs"]["bar"])["baz"],
+    ),
+    (
+        "$(inputs['bar'][\"baz\"])",
+        cast(MutableMapping[str, CWLOutputType], interpolate_input["inputs"]["bar"])["baz"],
+    ),
+    (
+        "$(inputs.bar['baz'])",
+        cast(MutableMapping[str, CWLOutputType], interpolate_input["inputs"]["bar"])["baz"],
+    ),
+    ("$(inputs['b\\'ar'].baz)", True),
+    ('$(inputs["b\'ar"].baz)', True),
+    ("$(inputs['b\\\"ar'].baz)", None),
+    ("$(self[0])", "A"),
+    ("$(self[1])", "B"),
+    ("$(self.length)", 2),
+    ("$(self['length'])", 2),
+    ("-$(inputs.bar)", """-{"baz": "zab1"}"""),
+    ("-$(inputs['bar'])", """-{"baz": "zab1"}"""),
+    ('-$(inputs["bar"])', """-{"baz": "zab1"}"""),
+    ("-$(inputs.bar.baz)", "-zab1"),
+    ("-$(inputs['bar'].baz)", "-zab1"),
+    ("-$(inputs['bar'][\"baz\"])", "-zab1"),
+    ("-$(inputs.bar['baz'])", "-zab1"),
+    ("-$(inputs['b ar'].baz)", "-2"),
+    ("-$(inputs['b\\'ar'].baz)", "-true"),
+    ('-$(inputs["b\\\'ar"].baz)', "-true"),
+    ("-$(inputs['b\\\"ar'].baz)", "-null"),
+    ("$(inputs.bar) $(inputs.bar)", """{"baz": "zab1"} {"baz": "zab1"}"""),
+    ("$(inputs['bar']) $(inputs['bar'])", """{"baz": "zab1"} {"baz": "zab1"}"""),
+    ('$(inputs["bar"]) $(inputs["bar"])', """{"baz": "zab1"} {"baz": "zab1"}"""),
+    ("$(inputs.bar.baz) $(inputs.bar.baz)", "zab1 zab1"),
+    ("$(inputs['bar'].baz) $(inputs['bar'].baz)", "zab1 zab1"),
+    ("$(inputs['bar'][\"baz\"]) $(inputs['bar'][\"baz\"])", "zab1 zab1"),
+    ("$(inputs.bar['baz']) $(inputs.bar['baz'])", "zab1 zab1"),
+    ("$(inputs['b ar'].baz) $(inputs['b ar'].baz)", "2 2"),
+    ("$(inputs['b\\'ar'].baz) $(inputs['b\\'ar'].baz)", "true true"),
+    ('$(inputs["b\\\'ar"].baz) $(inputs["b\\\'ar"].baz)', "true true"),
+    ("$(inputs['b\\\"ar'].baz) $(inputs['b\\\"ar'].baz)", "null null"),
 ]
 
 
@@ -127,31 +147,31 @@ def test_expression_interpolate(pattern: str, expected: Any) -> None:
 
 parameter_to_expressions = [
     (
-        "-$(foo)",
+        "-$(inputs)",
         r"""-{"bar":{"baz":"zab1"},"b ar":{"baz":2},"b'ar":{"baz":true},"b\"ar":{"baz":null}}""",
     ),
-    ("-$(foo.bar)", """-{"baz":"zab1"}"""),
-    ("-$(foo['bar'])", """-{"baz":"zab1"}"""),
-    ('-$(foo["bar"])', """-{"baz":"zab1"}"""),
-    ("-$(foo.bar.baz)", "-zab1"),
-    ("-$(foo['bar'].baz)", "-zab1"),
-    ("-$(foo['bar'][\"baz\"])", "-zab1"),
-    ("-$(foo.bar['baz'])", "-zab1"),
-    ("-$(foo['b ar'].baz)", "-2"),
-    ("-$(foo['b\\'ar'].baz)", "-true"),
-    ('-$(foo["b\\\'ar"].baz)', "-true"),
-    ("-$(foo['b\\\"ar'].baz)", "-null"),
-    ("$(foo.bar) $(foo.bar)", """{"baz":"zab1"} {"baz":"zab1"}"""),
-    ("$(foo['bar']) $(foo['bar'])", """{"baz":"zab1"} {"baz":"zab1"}"""),
-    ('$(foo["bar"]) $(foo["bar"])', """{"baz":"zab1"} {"baz":"zab1"}"""),
-    ("$(foo.bar.baz) $(foo.bar.baz)", "zab1 zab1"),
-    ("$(foo['bar'].baz) $(foo['bar'].baz)", "zab1 zab1"),
-    ("$(foo['bar'][\"baz\"]) $(foo['bar'][\"baz\"])", "zab1 zab1"),
-    ("$(foo.bar['baz']) $(foo.bar['baz'])", "zab1 zab1"),
-    ("$(foo['b ar'].baz) $(foo['b ar'].baz)", "2 2"),
-    ("$(foo['b\\'ar'].baz) $(foo['b\\'ar'].baz)", "true true"),
-    ('$(foo["b\\\'ar"].baz) $(foo["b\\\'ar"].baz)', "true true"),
-    ("$(foo['b\\\"ar'].baz) $(foo['b\\\"ar'].baz)", "null null"),
+    ("-$(inputs.bar)", """-{"baz":"zab1"}"""),
+    ("-$(inputs['bar'])", """-{"baz":"zab1"}"""),
+    ('-$(inputs["bar"])', """-{"baz":"zab1"}"""),
+    ("-$(inputs.bar.baz)", "-zab1"),
+    ("-$(inputs['bar'].baz)", "-zab1"),
+    ("-$(inputs['bar'][\"baz\"])", "-zab1"),
+    ("-$(inputs.bar['baz'])", "-zab1"),
+    ("-$(inputs['b ar'].baz)", "-2"),
+    ("-$(inputs['b\\'ar'].baz)", "-true"),
+    ('-$(inputs["b\\\'ar"].baz)', "-true"),
+    ("-$(inputs['b\\\"ar'].baz)", "-null"),
+    ("$(inputs.bar) $(inputs.bar)", """{"baz":"zab1"} {"baz":"zab1"}"""),
+    ("$(inputs['bar']) $(inputs['bar'])", """{"baz":"zab1"} {"baz":"zab1"}"""),
+    ('$(inputs["bar"]) $(inputs["bar"])', """{"baz":"zab1"} {"baz":"zab1"}"""),
+    ("$(inputs.bar.baz) $(inputs.bar.baz)", "zab1 zab1"),
+    ("$(inputs['bar'].baz) $(inputs['bar'].baz)", "zab1 zab1"),
+    ("$(inputs['bar'][\"baz\"]) $(inputs['bar'][\"baz\"])", "zab1 zab1"),
+    ("$(inputs.bar['baz']) $(inputs.bar['baz'])", "zab1 zab1"),
+    ("$(inputs['b ar'].baz) $(inputs['b ar'].baz)", "2 2"),
+    ("$(inputs['b\\'ar'].baz) $(inputs['b\\'ar'].baz)", "true true"),
+    ('$(inputs["b\\\'ar"].baz) $(inputs["b\\\'ar"].baz)', "true true"),
+    ("$(inputs['b\\\"ar'].baz) $(inputs['b\\\"ar'].baz)", "null null"),
 ]
 
 
@@ -173,22 +193,22 @@ def test_parameter_to_expression(pattern: str, expected: Any) -> None:
 
 
 param_to_expr_interpolate_escapebehavior = (
-    ("\\$(foo.bar.baz)", "$(foo.bar.baz)", 1),
-    ("\\\\$(foo.bar.baz)", "\\zab1", 1),
-    ("\\\\\\$(foo.bar.baz)", "\\$(foo.bar.baz)", 1),
-    ("\\\\\\\\$(foo.bar.baz)", "\\\\zab1", 1),
-    ("\\$foo", "$foo", 1),
-    ("\\foo", "foo", 1),
+    ("\\$(inputs.bar.baz)", "$(inputs.bar.baz)", 1),
+    ("\\\\$(inputs.bar.baz)", "\\zab1", 1),
+    ("\\\\\\$(inputs.bar.baz)", "\\$(inputs.bar.baz)", 1),
+    ("\\\\\\\\$(inputs.bar.baz)", "\\\\zab1", 1),
+    ("\\$inputs", "$inputs", 1),
+    ("\\inputs", "inputs", 1),
     ("\\x", "x", 1),
     ("\\\\x", "\\x", 1),
     ("\\\\\\x", "\\x", 1),
     ("\\\\\\\\x", "\\\\x", 1),
-    ("\\$(foo.bar.baz)", "$(foo.bar.baz)", 2),
-    ("\\\\$(foo.bar.baz)", "\\zab1", 2),
-    ("\\\\\\$(foo.bar.baz)", "\\$(foo.bar.baz)", 2),
-    ("\\\\\\\\$(foo.bar.baz)", "\\\\zab1", 2),
-    ("\\$foo", "\\$foo", 2),
-    ("\\foo", "\\foo", 2),
+    ("\\$(inputs.bar.baz)", "$(inputs.bar.baz)", 2),
+    ("\\\\$(inputs.bar.baz)", "\\zab1", 2),
+    ("\\\\\\$(inputs.bar.baz)", "\\$(inputs.bar.baz)", 2),
+    ("\\\\\\\\$(inputs.bar.baz)", "\\\\zab1", 2),
+    ("\\$inputs", "\\$inputs", 2),
+    ("\\inputs", "\\inputs", 2),
     ("\\x", "\\x", 2),
     ("\\\\x", "\\x", 2),
     ("\\\\\\x", "\\\\x", 2),
@@ -218,32 +238,32 @@ def test_parameter_to_expression_interpolate_escapebehavior(
 
 
 interpolate_bad_parameters = [
-    ("$(fooz)"),
-    ("$(foo.barz)"),
-    ("$(foo['barz'])"),
-    ('$(foo["barz"])'),
-    ("$(foo.bar.bazz)"),
-    ("$(foo['bar'].bazz)"),
-    ("$(foo['bar'][\"bazz\"])"),
-    ("$(foo.bar['bazz'])"),
-    ("$(foo['b\\'ar'].bazz)"),
-    ('$(foo["b\'ar"].bazz)'),
-    ("$(foo['b\\\"ar'].bazz)"),
-    ("$(lst[O])"),  # not "0" the number, but the letter O
-    ("$(lst[2])"),
-    ("$(lst.lengthz)"),
-    ("$(lst['lengthz'])"),
-    ("-$(foo.barz)"),
-    ("-$(foo['barz'])"),
-    ('-$(foo["barz"])'),
-    ("-$(foo.bar.bazz)"),
-    ("-$(foo['bar'].bazz)"),
-    ("-$(foo['bar'][\"bazz\"])"),
-    ("-$(foo.bar['bazz'])"),
-    ("-$(foo['b ar'].bazz)"),
-    ("-$(foo['b\\'ar'].bazz)"),
-    ('-$(foo["b\\\'ar"].bazz)'),
-    ("-$(foo['b\\\"ar'].bazz)"),
+    ("$(inputsz)"),
+    ("$(inputs.barz)"),
+    ("$(inputs['barz'])"),
+    ('$(inputs["barz"])'),
+    ("$(inputs.bar.bazz)"),
+    ("$(inputs['bar'].bazz)"),
+    ("$(inputs['bar'][\"bazz\"])"),
+    ("$(inputs.bar['bazz'])"),
+    ("$(inputs['b\\'ar'].bazz)"),
+    ('$(inputs["b\'ar"].bazz)'),
+    ("$(inputs['b\\\"ar'].bazz)"),
+    ("$(self[O])"),  # not "0" the number, but the letter O
+    ("$(self[2])"),
+    ("$(self.lengthz)"),
+    ("$(self['lengthz'])"),
+    ("-$(inputs.barz)"),
+    ("-$(inputs['barz'])"),
+    ('-$(inputs["barz"])'),
+    ("-$(inputs.bar.bazz)"),
+    ("-$(inputs['bar'].bazz)"),
+    ("-$(inputs['bar'][\"bazz\"])"),
+    ("-$(inputs.bar['bazz'])"),
+    ("-$(inputs['b ar'].bazz)"),
+    ("-$(inputs['b\\'ar'].bazz)"),
+    ('-$(inputs["b\\\'ar"].bazz)'),
+    ("-$(inputs['b\\\"ar'].bazz)"),
 ]
 
 
@@ -254,22 +274,22 @@ def test_expression_interpolate_failures(pattern: str) -> None:
 
 
 interpolate_escapebehavior = (
-    ("\\$(foo.bar.baz)", "$(foo.bar.baz)", 1),
-    ("\\\\$(foo.bar.baz)", "\\zab1", 1),
-    ("\\\\\\$(foo.bar.baz)", "\\$(foo.bar.baz)", 1),
-    ("\\\\\\\\$(foo.bar.baz)", "\\\\zab1", 1),
-    ("\\$foo", "$foo", 1),
-    ("\\foo", "foo", 1),
+    ("\\$(inputs.bar.baz)", "$(inputs.bar.baz)", 1),
+    ("\\\\$(inputs.bar.baz)", "\\zab1", 1),
+    ("\\\\\\$(inputs.bar.baz)", "\\$(inputs.bar.baz)", 1),
+    ("\\\\\\\\$(inputs.bar.baz)", "\\\\zab1", 1),
+    ("\\$inputs", "$inputs", 1),
+    ("\\inputs", "inputs", 1),
     ("\\x", "x", 1),
     ("\\\\x", "\\x", 1),
     ("\\\\\\x", "\\x", 1),
     ("\\\\\\\\x", "\\\\x", 1),
-    ("\\$(foo.bar.baz)", "$(foo.bar.baz)", 2),
-    ("\\\\$(foo.bar.baz)", "\\zab1", 2),
-    ("\\\\\\$(foo.bar.baz)", "\\$(foo.bar.baz)", 2),
-    ("\\\\\\\\$(foo.bar.baz)", "\\\\zab1", 2),
-    ("\\$foo", "\\$foo", 2),
-    ("\\foo", "\\foo", 2),
+    ("\\$(inputs.bar.baz)", "$(inputs.bar.baz)", 2),
+    ("\\\\$(inputs.bar.baz)", "\\zab1", 2),
+    ("\\\\\\$(inputs.bar.baz)", "\\$(inputs.bar.baz)", 2),
+    ("\\\\\\\\$(inputs.bar.baz)", "\\\\zab1", 2),
+    ("\\$inputs", "\\$inputs", 2),
+    ("\\inputs", "\\inputs", 2),
     ("\\x", "\\x", 2),
     ("\\\\x", "\\x", 2),
     ("\\\\\\x", "\\\\x", 2),
@@ -576,24 +596,28 @@ def test_scandeps_defaults_with_secondaryfiles() -> None:
 
 
 def test_dedupe() -> None:
-    not_deduped: list[CWLObjectType] = [
-        {"class": "File", "location": "file:///example/a"},
-        {"class": "File", "location": "file:///example/a"},
-        {"class": "File", "location": "file:///example/d"},
-        {
-            "class": "Directory",
-            "location": "file:///example/c",
-            "listing": [{"class": "File", "location": "file:///example/d"}],
-        },
+    not_deduped: MutableSequence[CWLFileType | CWLDirectoryType] = [
+        CWLFileType(**{"class": "File", "location": "file:///example/a"}),
+        CWLFileType(**{"class": "File", "location": "file:///example/a"}),
+        CWLFileType(**{"class": "File", "location": "file:///example/d"}),
+        CWLDirectoryType(
+            **{
+                "class": "Directory",
+                "location": "file:///example/c",
+                "listing": [{"class": "File", "location": "file:///example/d"}],
+            }
+        ),
     ]
 
     expected = [
-        {"class": "File", "location": "file:///example/a"},
-        {
-            "class": "Directory",
-            "location": "file:///example/c",
-            "listing": [{"class": "File", "location": "file:///example/d"}],
-        },
+        CWLFileType(**{"class": "File", "location": "file:///example/a"}),
+        CWLDirectoryType(
+            **{
+                "class": "Directory",
+                "location": "file:///example/c",
+                "listing": [{"class": "File", "location": "file:///example/d"}],
+            }
+        ),
     ]
 
     assert dedup(not_deduped) == expected
diff --git a/tests/test_http_input.py b/tests/test_http_input.py
index e80260ff9..d98e8a368 100644
--- a/tests/test_http_input.py
+++ b/tests/test_http_input.py
@@ -1,24 +1,27 @@
 import os
+from collections.abc import MutableSequence
 from datetime import datetime
 from pathlib import Path
 
+from cwl_utils.types import CWLDirectoryType, CWLFileType
 from pytest_httpserver import HTTPServer
 
 from cwltool.pathmapper import PathMapper
-from cwltool.utils import CWLObjectType
 
 
 def test_http_path_mapping(tmp_path: Path) -> None:
     input_file_path = (
         "https://raw.githubusercontent.com/common-workflow-language/cwltool/main/tests/2.fasta"
     )
-    base_file: list[CWLObjectType] = [
-        {
-            "class": "File",
-            "location": "https://raw.githubusercontent.com/common-workflow-language/"
-            "cwltool/main/tests/2.fasta",
-            "basename": "chr20.fa",
-        }
+    base_file: MutableSequence[CWLFileType | CWLDirectoryType] = [
+        CWLFileType(
+            **{
+                "class": "File",
+                "location": "https://raw.githubusercontent.com/common-workflow-language/"
+                "cwltool/main/tests/2.fasta",
+                "basename": "chr20.fa",
+            }
+        )
     ]
     pathmap = PathMapper(base_file, os.getcwd(), str(tmp_path))._pathmap
 
@@ -54,12 +57,14 @@ def test_modification_date(tmp_path: Path) -> None:
         )
         location = httpserver.url_for(f"/{remote_file_name}")
 
-        base_file: list[CWLObjectType] = [
-            {
-                "class": "File",
-                "location": location,
-                "basename": remote_file_name,
-            }
+        base_file: MutableSequence[CWLFileType | CWLDirectoryType] = [
+            CWLFileType(
+                **{
+                    "class": "File",
+                    "location": location,
+                    "basename": remote_file_name,
+                }
+            )
         ]
 
         date_now = datetime.now()
diff --git a/tests/test_js_sandbox.py b/tests/test_js_sandbox.py
index 2c5df6339..a7144a8f0 100644
--- a/tests/test_js_sandbox.py
+++ b/tests/test_js_sandbox.py
@@ -9,6 +9,7 @@
 
 import pytest
 from cwl_utils import sandboxjs
+from cwl_utils.types import CWLFileType
 
 from cwltool.factory import Factory
 from cwltool.loghandler import _logger, configure_logging
@@ -41,7 +42,7 @@ def test_value_from_two_concatenated_expressions() -> None:
     js_engine.localdata = threading.local()  # type: ignore[attr-defined]
     factory = Factory()
     echo = factory.make(get_data("tests/wf/vf-concat.cwl"))
-    file = {"class": "File", "location": get_data("tests/wf/whale.txt")}
+    file = CWLFileType(**{"class": "File", "location": get_data("tests/wf/whale.txt")})
 
     assert echo(file1=file) == {"out": "a string\n"}
 
@@ -87,7 +88,7 @@ def test_value_from_two_concatenated_expressions_podman(
     with monkeypatch.context() as m:
         m.setenv("PATH", new_paths)
         echo = factory.make(get_data("tests/wf/vf-concat.cwl"))
-        file = {"class": "File", "location": get_data("tests/wf/whale.txt")}
+        file = CWLFileType(**{"class": "File", "location": get_data("tests/wf/whale.txt")})
         assert echo(file1=file) == {"out": "a string\n"}
 
 
@@ -112,7 +113,7 @@ def test_value_from_two_concatenated_expressions_singularity(
         m.setenv("CWL_SINGULARITY_CACHE", str(singularity_cache))
         m.setenv("PATH", new_paths)
         echo = factory.make(get_data("tests/wf/vf-concat.cwl"))
-        file = {"class": "File", "location": get_data("tests/wf/whale.txt")}
+        file = CWLFileType(**{"class": "File", "location": get_data("tests/wf/whale.txt")})
         assert echo(file1=file) == {"out": "a string\n"}
 
 
diff --git a/tests/test_load_tool.py b/tests/test_load_tool.py
index 2b9e9b6ed..c1c1ce017 100644
--- a/tests/test_load_tool.py
+++ b/tests/test_load_tool.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 
 import pytest
+from cwl_utils.types import CWLObjectType
 from schema_salad.exceptions import ValidationException
 
 from cwltool.context import LoadingContext, RuntimeContext
@@ -13,7 +14,6 @@
 from cwltool.loghandler import _logger, configure_logging
 from cwltool.process import use_custom_schema, use_standard_schema
 from cwltool.update import INTERNAL_VERSION
-from cwltool.utils import CWLObjectType
 
 from .util import get_data
 
diff --git a/tests/test_parallel.py b/tests/test_parallel.py
index 2d76e07a7..367714f27 100644
--- a/tests/test_parallel.py
+++ b/tests/test_parallel.py
@@ -1,6 +1,8 @@
 import json
 from pathlib import Path
 
+from cwl_utils.types import CWLFileType
+
 from cwltool.context import RuntimeContext
 from cwltool.executors import MultithreadedJobExecutor
 from cwltool.factory import Factory
@@ -17,7 +19,7 @@ def test_sequential_workflow(tmp_path: Path) -> None:
     runtime_context.select_resources = executor.select_resources
     factory = Factory(executor, None, runtime_context)
     echo = factory.make(get_data(test_file))
-    file_contents = {"class": "File", "location": get_data("tests/wf/whale.txt")}
+    file_contents = CWLFileType(**{"class": "File", "location": get_data("tests/wf/whale.txt")})
     assert echo(file1=file_contents) == {"count_output": 16}
 
 
diff --git a/tests/test_path_checks.py b/tests/test_path_checks.py
index 096de9942..c01d84944 100644
--- a/tests/test_path_checks.py
+++ b/tests/test_path_checks.py
@@ -4,6 +4,7 @@
 from typing import IO, Any, cast
 
 import pytest
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
@@ -14,7 +15,7 @@
 from cwltool.main import main
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION
-from cwltool.utils import CONTENT_LIMIT, CWLObjectType, bytes2str_in_dicts
+from cwltool.utils import CONTENT_LIMIT, bytes2str_in_dicts
 
 from .util import needs_docker
 
diff --git a/tests/test_pathmapper.py b/tests/test_pathmapper.py
index 4ffac24bd..c0005cc77 100644
--- a/tests/test_pathmapper.py
+++ b/tests/test_pathmapper.py
@@ -1,14 +1,17 @@
+from collections.abc import MutableSequence
+
 import pytest
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType
 
 from cwltool.pathmapper import PathMapper
-from cwltool.utils import CWLObjectType, normalizeFilesDirs
+from cwltool.utils import normalizeFilesDirs
 
 
 def test_subclass() -> None:
     class SubPathMapper(PathMapper):
         def __init__(
             self,
-            referenced_files: list[CWLObjectType],
+            referenced_files: MutableSequence[CWLFileType | CWLDirectoryType],
             basedir: str,
             stagedir: str,
             new: str,
@@ -89,7 +92,7 @@ def test_basename_field_generation(filename: str, expected: tuple[str, str]) ->
         "nameext": nameext,
     }
 
-    my_file = {"class": "File", "location": "/foo/" + filename}
+    my_file = CWLFileType(**{"class": "File", "location": "/foo/" + filename})
 
     normalizeFilesDirs(my_file)
     assert my_file == expected2
diff --git a/tests/test_secrets.py b/tests/test_secrets.py
index 206b001bd..b6c316ce1 100644
--- a/tests/test_secrets.py
+++ b/tests/test_secrets.py
@@ -1,13 +1,14 @@
 import shutil
 import tempfile
-from collections.abc import Callable
+from collections.abc import Callable, MutableMapping
 from io import StringIO
+from typing import cast
 
 import pytest
+from cwl_utils.types import CWLObjectType, CWLOutputType
 
 from cwltool.main import main
 from cwltool.secrets import SecretStore
-from cwltool.utils import CWLObjectType
 
 from .util import get_data, needs_docker, needs_singularity
 
@@ -27,7 +28,7 @@ def test_obscuring(secrets: tuple[SecretStore, CWLObjectType]) -> None:
     storage, obscured = secrets
     assert obscured["foo"] != "bar"
     assert obscured["baz"] == "quux"
-    result = storage.retrieve(obscured)
+    result = cast(MutableMapping[str, CWLOutputType], storage.retrieve(obscured))
     assert isinstance(result, dict) and result["foo"] == "bar"
 
 
diff --git a/tests/test_streaming.py b/tests/test_streaming.py
index aef4a7efe..c68454409 100644
--- a/tests/test_streaming.py
+++ b/tests/test_streaming.py
@@ -5,6 +5,7 @@
 from typing import cast
 
 import pytest
+from cwl_utils.types import CWLObjectType
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
@@ -13,7 +14,6 @@
 from cwltool.errors import WorkflowException
 from cwltool.job import JobBase
 from cwltool.update import INTERNAL_VERSION, ORIGINAL_CWLVERSION
-from cwltool.utils import CWLObjectType
 
 from .util import get_data
 
diff --git a/tox.ini b/tox.ini
index 305603343..69d0d1437 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,9 +4,9 @@ envlist =
   py3{10,11,12,13,14}-unit
   py3{10,11,12,13,14}-bandit
   py3{10,11,12,13,14}-mypy
-  py312-lintreadme
-  py312-shellcheck
-  py312-pydocstyle
+  py313-lintreadme
+  py313-shellcheck
+  py313-pydocstyle
 
 skip_missing_interpreters = True
 
@@ -31,9 +31,9 @@ description =
   py3{10,11,12,13,14}-lint: Lint the Python code
   py3{10,11,12,13,14}-bandit: Search for common security issues
   py3{10,11,12,13,14}-mypy: Check for type safety
-  py312-pydocstyle: docstring style checker
-  py312-shellcheck: syntax check for shell scripts
-  py312-lintreadme: Lint the README.rst→.md conversion
+  py313-pydocstyle: docstring style checker
+  py313-shellcheck: syntax check for shell scripts
+  py313-lintreadme: Lint the README.rst→.md conversion
 
 passenv =
   CI
@@ -52,27 +52,27 @@ deps =
   py3{10,11,12,13,14}-lint: -rlint-requirements.txt
   py3{10,11,12,13,14}-bandit: bandit
   py3{10,11,12,13,14}-mypy: -rmypy-requirements.txt
-  py312-pydocstyle: pydocstyle
-  py312-pydocstyle: diff-cover
-  py312-lintreadme: twine
-  py312-lintreadme: build
-  py312-lintreadme: readme_renderer[rst]
+  py313-pydocstyle: pydocstyle
+  py313-pydocstyle: diff-cover
+  py313-lintreadme: twine
+  py313-lintreadme: build
+  py313-lintreadme: readme_renderer[rst]
 
 setenv =
   LC_ALL = C.UTF-8
   HOME = {envtmpdir}
 
 commands_pre =
-  py312-lintreadme: python -m build --outdir {pkg_dir}
+  py313-lintreadme: python -m build --outdir {pkg_dir}
 
 commands =
   py3{10,11,12,13,14}-unit: make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
   py3{10,11,12,13,14}-bandit: bandit -r cwltool
   py3{10,11,12,13,14}-lint: make flake8 format-check codespell-check
   py3{10,11,12,13,14}-mypy: make mypy mypyc PYTEST_EXTRA="{posargs}"
-  py312-shellcheck: make shellcheck
-  py312-pydocstyle: make diff_pydocstyle_report
-  py312-lintreadme: twine check {pkg_dir}/*
+  py313-shellcheck: make shellcheck
+  py313-pydocstyle: make diff_pydocstyle_report
+  py313-lintreadme: twine check {pkg_dir}/*
 
 skip_install =
   py3{10,11,12,13,14}-{bandit,lint,mypy,shellcheck,pydocstyle,lintreadme}: true