diff --git a/docs/tutorials/command_line_client.md b/docs/tutorials/command_line_client.md
index 5cc7da890..d3a6758d5 100644
--- a/docs/tutorials/command_line_client.md
+++ b/docs/tutorials/command_line_client.md
@@ -108,17 +108,31 @@ synapse get [-h] [-q queryString] [-v VERSION] [-r] [--followLink] [--limitSearc
 
 ### `manifest`
 
-Generate manifest for uploading directory tree to Synapse.
+Generate a TSV manifest describing the files in a local directory tree for
+later upload with `synapse sync`.
+
+!!! warning "Folders are created in Synapse during manifest generation"
+    While walking the directory tree, `synapse manifest` **also creates the
+    corresponding folder structure under `--parent-id` in Synapse**, including
+    any empty subfolders. Only the files themselves are deferred to the
+    subsequent `synapse sync` call. That is why `--parent-id` is required even
+    when you only want to generate a manifest: each row in the manifest needs
+    to reference the Synapse ID of its (already-created) parent folder.
+
+To upload a subset of files, run `synapse manifest` first, delete the rows for
+files you do not want to upload from the generated manifest, then run
+`synapse sync <manifest>`. The empty folders created in Synapse during manifest
+generation will remain.
 
 ```bash
 synapse manifest [-h] --parent-id syn123 [--manifest-file OUTPUT] PATH
 ```
 
-| Name              | Type       | Description                                                    | Default |
-|-------------------|------------|----------------------------------------------------------------|---------|
-| `PATH`            | Positional | A path to a file or folder whose manifest will be generated.   |         |
-| `--parent-id`     | Named      | Synapse ID of project or folder where to upload data.          |         |
-| `--manifest-file` | Named      | A TSV output file path where the generated manifest is stored. | stdout  |
+| Name              | Type       | Description                                                                                                                                                                                                                                                                  | Default                     |
+|-------------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------|
+| `PATH`            | Positional | Local path to the directory whose contents will be described in the manifest. The directory tree is walked recursively.                                                                                                                                                      |                             |
+| `--parent-id`     | Named      | Synapse ID of the project or folder that will be the parent of the uploaded tree. Required even when only generating a manifest, because the matching folder structure (including empty folders) is created in Synapse under this parent as the manifest is generated.       |                             |
+| `--manifest-file` | Named      | Path where the generated TSV manifest will be written (for example `./manifest.tsv`). If omitted, the manifest is printed to stdout; pass an explicit path if you intend to edit it before running `synapse sync`.                                                            | stdout                      |
 
 
 ### `sync`
diff --git a/docs/tutorials/python/upload_data_in_bulk.md b/docs/tutorials/python/upload_data_in_bulk.md
index b017163b1..f3725e2ea 100644
--- a/docs/tutorials/python/upload_data_in_bulk.md
+++ b/docs/tutorials/python/upload_data_in_bulk.md
@@ -67,6 +67,20 @@ It walks our local directory and produces a CSV manifest that maps each file to
 the correct parent folder in Synapse (creating folders as needed). The output
 is ready to hand directly to `sync_to_synapse`.
 
+!!! warning "Folders are created in Synapse during manifest generation"
+    While walking the directory tree, `generate_sync_manifest` **creates the
+    corresponding folder structure on the project/folder it is called on**,
+    including any empty subfolders . Only the files themselves are deferred
+    to the later `sync_to_synapse` call. This is why the call still needs a
+    target Synapse Project/Folder even when you only want to produce a manifest
+    — each row in the manifest references the Synapse ID of its (already-created)
+    parent folder.
+
+    To upload a subset of files, generate the manifest first, delete the rows
+    for files you do not want to upload from `PATH_TO_MANIFEST_FILE`, then run
+    `sync_to_synapse`. The empty folders created during manifest generation
+    will remain in Synapse.
+
 ```python
 --8<-- "docs/tutorials/python/tutorial_scripts/upload_data_in_bulk.py:generate_manifest"
 ```
diff --git a/synapseclient/__main__.py b/synapseclient/__main__.py
index fa462bb4c..34338112d 100644
--- a/synapseclient/__main__.py
+++ b/synapseclient/__main__.py
@@ -1006,13 +1006,26 @@ def build_parser():
     parser_get.set_defaults(func=get)
 
     parser_manifest = subparsers.add_parser(
-        "manifest", help="Generate manifest for uploading directory tree to Synapse."
+        "manifest",
+        help="Generate manifest for uploading directory tree to Synapse.",
+        description=(
+            "Generate a TSV manifest describing the files in a local directory tree "
+            "for later upload with `synapse sync`. "
+            "IMPORTANT: this command will also create the corresponding folder structure "
+            "in Synapse while walking the directory under --parent-id "
+            "(including any empty folders); only the files are deferred to "
+            "the subsequent `synapse sync` call. "
+            "To upload a subset of files, run `synapse manifest` first, delete the rows "
+            "for files you do not want to upload from the generated manifest, then run "
+            "`synapse sync <manifest>`."
+        ),
     )
     parser_manifest.add_argument(
         "path",
         metavar="PATH",
         type=str,
-        help="A path to a file or folder whose manifest will be generated.",
+        help="Local path to the directory whose contents will be described in the "
+        "manifest. The directory tree is walked recursively.",
     )
     parser_manifest.add_argument(
         "--parent-id",
@@ -1020,13 +1033,18 @@ def build_parser():
         type=str,
         required=True,
         dest="parentid",
-        help="Synapse ID of project or folder where to upload data.",
+        help="Synapse ID of the project or folder that will be the parent of the "
+        "uploaded tree. Required even when only generating a manifest, because the "
+        "matching folder structure (including empty folders) is created in Synapse "
+        "under this parent as the manifest is generated, so that each row in the "
+        "manifest can reference the Synapse ID of its parent folder.",
     )
     parser_manifest.add_argument(
         "--manifest-file",
         metavar="OUTPUT",
-        help="A TSV output file path where the generated manifest is stored. "
-        "(default: stdout)",
+        help="Path where the generated TSV manifest will be written (for example "
+        "`./manifest.tsv`). If omitted, the manifest is printed to stdout; pass an "
+        "explicit path if you intend to edit it before running `synapse sync`.",
     )
     parser_manifest.set_defaults(func=manifest)