diff --git a/cwltool/main.py b/cwltool/main.py
index 65da89ed0..79038907b 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -73,6 +73,7 @@
     CWL_IANA,
     Process,
     add_sizes,
+    mergedirs,
     scandeps,
     shortname,
     use_custom_schema,
@@ -620,7 +621,9 @@ def loadref(base: str, uri: str) -> Union[CommentedMap, CommentedSeq, str, None]
         nestdirs=nestdirs,
     )
     if sfs is not None:
-        deps["secondaryFiles"] = cast(MutableSequence[CWLOutputAtomType], sfs)
+        deps["secondaryFiles"] = cast(
+            MutableSequence[CWLOutputAtomType], mergedirs(sfs)
+        )
 
     return deps
 
diff --git a/cwltool/process.py b/cwltool/process.py
index 7898782cb..d6975e5ce 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -1104,42 +1104,38 @@ def nestdir(base: str, deps: CWLObjectType) -> CWLObjectType:
         sp = s2.split("/")
         sp.pop()
         while sp:
+            loc = dirname + "/".join(sp)
             nx = sp.pop()
-            deps = {"class": "Directory", "basename": nx, "listing": [deps]}
+            deps = {
+                "class": "Directory",
+                "basename": nx,
+                "listing": [deps],
+                "location": loc,
+            }
     return deps
 
 
-def mergedirs(listing: List[CWLObjectType]) -> List[CWLObjectType]:
+def mergedirs(
+    listing: MutableSequence[CWLObjectType],
+) -> MutableSequence[CWLObjectType]:
     r = []  # type: List[CWLObjectType]
     ents = {}  # type: Dict[str, CWLObjectType]
-    collided = set()  # type: Set[str]
     for e in listing:
         basename = cast(str, e["basename"])
         if basename not in ents:
             ents[basename] = e
+        elif e["location"] != ents[basename]["location"]:
+            raise ValidationException(
+                "Conflicting basename in listing or secondaryFiles, '%s' used by both '%s' and '%s'"
+                % (basename, e["location"], ents[basename]["location"])
+            )
         elif e["class"] == "Directory":
             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"]))
-            if cast(str, ents[basename]["location"]).startswith("_:"):
-                ents[basename]["location"] = e["location"]
-        elif e["location"] != ents[basename]["location"]:
-            # same basename, different location, collision,
-            # rename both.
-            collided.add(basename)
-            e2 = ents[basename]
-
-            e["basename"] = urllib.parse.quote(cast(str, e["location"]), safe="")
-            e2["basename"] = urllib.parse.quote(cast(str, e2["location"]), safe="")
-
-            e["nameroot"], e["nameext"] = os.path.splitext(cast(str, e["basename"]))
-            e2["nameroot"], e2["nameext"] = os.path.splitext(cast(str, e2["basename"]))
-
-            ents[cast(str, e["basename"])] = e
-            ents[cast(str, e2["basename"])] = e2
-    for c in collided:
-        del ents[c]
     for e in ents.values():
         if e["class"] == "Directory" and "listing" in e:
             e["listing"] = cast(
@@ -1162,6 +1158,30 @@ def scandeps(
     urljoin: Callable[[str, str], str] = urllib.parse.urljoin,
     nestdirs: bool = True,
 ) -> MutableSequence[CWLObjectType]:
+
+    """Given a CWL document or input object, search for dependencies
+    (references to external files) of 'doc' and return them as a list
+    of File or Directory objects.
+
+    The 'base' is the base URL for relative references.
+
+    Looks for objects with 'class: File' or 'class: Directory' and
+    adds them to the list of dependencies.
+
+    Anything in 'urlfields' is also added as a File dependency.
+
+    Anything in 'reffields' (such as workflow step 'run') will be
+    added as a dependency and also loaded (using the 'loadref'
+    function) and recursively scanned for dependencies.  Those
+    dependencies will be added as secondary files to the primary file.
+
+    If "nestdirs" is true, create intermediate directory objects when
+    a file is located in a subdirectory under the starting directory.
+    This is so that if the dependencies are materialized, they will
+    produce the same relative file system locations.
+
+    """
+
     r: MutableSequence[CWLObjectType] = []
     if isinstance(doc, MutableMapping):
         if "id" in doc:
@@ -1268,7 +1288,7 @@ def scandeps(
                         )
                         if sf:
                             deps2["secondaryFiles"] = cast(
-                                MutableSequence[CWLOutputAtomType], sf
+                                MutableSequence[CWLOutputAtomType], mergedirs(sf)
                             )
                         if nestdirs:
                             deps2 = nestdir(base, deps2)
@@ -1313,7 +1333,6 @@ def scandeps(
 
     if r:
         normalizeFilesDirs(r)
-        r = mergedirs(cast(List[CWLObjectType], r))
 
     return r
 
diff --git a/tests/test_examples.py b/tests/test_examples.py
index ad617c740..418d1ccf0 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -512,6 +512,53 @@ def loadref(
     assert scanned_deps2 == expected_deps
 
 
+def test_scandeps_samedirname() -> None:
+    obj: CWLObjectType = {
+        "dir1": {"class": "Directory", "location": "tests/wf/dir1/foo"},
+        "dir2": {"class": "Directory", "location": "tests/wf/dir2/foo"},
+    }
+
+    def loadref(
+        base: str, p: Union[CommentedMap, CommentedSeq, str, None]
+    ) -> Union[CommentedMap, CommentedSeq, str, None]:
+        if isinstance(p, dict):
+            return p
+        raise Exception("test case can't load things")
+
+    scanned_deps = cast(
+        List[Dict[str, Any]],
+        cwltool.process.scandeps(
+            "",
+            obj,
+            {"$import", "run"},
+            {"$include", "$schemas", "location"},
+            loadref,
+            nestdirs=False,
+        ),
+    )
+
+    scanned_deps.sort(key=lambda k: cast(str, k["basename"]))
+
+    expected_deps = [
+        {"basename": "foo", "class": "Directory", "location": "tests/wf/dir1/foo"},
+        {"basename": "foo", "class": "Directory", "location": "tests/wf/dir2/foo"},
+    ]
+
+    assert scanned_deps == expected_deps
+
+
+def test_scandeps_collision() -> None:
+    stream = StringIO()
+
+    assert (
+        main(
+            ["--print-deps", "--debug", get_data("tests/wf/dir_deps.json")],
+            stdout=stream,
+        )
+        == 1
+    )
+
+
 def test_trick_scandeps() -> None:
     stream = StringIO()
 
diff --git a/tests/wf/dir_deps.json b/tests/wf/dir_deps.json
new file mode 100644
index 000000000..60b2805e6
--- /dev/null
+++ b/tests/wf/dir_deps.json
@@ -0,0 +1,7 @@
+"dir1": {
+    "class": "Directory",
+    "listing": [
+        {"class": "File", "basename": "foo", "location": "tests/wf/foo1"},
+        {"class": "File", "basename": "foo", "location": "tests/wf/foo2"}
+    ]
+}