diff --git a/docs/source/manual/file_formats/reference_file.rst b/docs/source/manual/file_formats/reference_file.rst
index f2240df62..1a57939a8 100644
--- a/docs/source/manual/file_formats/reference_file.rst
+++ b/docs/source/manual/file_formats/reference_file.rst
@@ -14,63 +14,63 @@ An example of the file is shown as follows.
 
 .. code-block:: yaml
 
-Date: Mon Sep  9 16:41:53 2024
+  Date: Mon Sep  9 16:41:53 2024
 
-#the instance names are given during netlist generation
-references:
-- module: grid_io_top
-  count: 1
-  instances:
-    - grid_io_top_1__2_
-- module: grid_io_right
-  count: 1
-  instances:
-    - grid_io_right_2__1_
-- module: grid_io_bottom
-  count: 1
-  instances:
-    - grid_io_bottom_1__0_
-- module: grid_io_left
-  count: 1
-  instances:
-    - grid_io_left_0__1_
-- module: grid_clb
-  count: 1
-  instances:
-    - grid_clb_1__1_
-- module: sb_0__0_
-  count: 1
-  instances:
-    - sb_0__0_
-- module: sb_0__1_
-  count: 1
-  instances:
-    - sb_0__1_
-- module: sb_1__0_
-  count: 1
-  instances:
-    - sb_1__0_
-- module: sb_1__1_
-  count: 1
-  instances:
-    - sb_1__1_
-- module: cbx_1__0_
-  count: 1
-  instances:
-    - cbx_1__0_
-- module: cbx_1__1_
-  count: 1
-  instances:
-    - cbx_1__1_
-- module: cby_0__1_
-  count: 1
-  instances:
-    - cby_0__1_
-- module: cby_1__1_
-  count: 1
-  instances:
-    - cby_1__1_
-          direct_interc
+  #the instance names are given during netlist generation
+
+  references:
+    - module: grid_io_top
+      count: 1
+      instances:
+        - grid_io_top_1__2_
+    - module: grid_io_right
+      count: 1
+      instances:
+        - grid_io_right_2__1_
+    - module: grid_io_bottom
+      count: 1
+      instances:
+        - grid_io_bottom_1__0_
+    - module: grid_io_left
+      count: 1
+      instances:
+        - grid_io_left_0__1_
+    - module: grid_clb
+      count: 1
+      instances:
+        - grid_clb_1__1_
+    - module: sb_0__0_
+      count: 1
+      instances:
+        - sb_0__0_
+    - module: sb_0__1_
+      count: 1
+      instances:
+        - sb_0__1_
+    - module: sb_1__0_
+      count: 1
+      instances:
+        - sb_1__0_
+    - module: sb_1__1_
+      count: 1
+      instances:
+        - sb_1__1_
+    - module: cbx_1__0_
+      count: 1
+      instances:
+        - cbx_1__0_
+    - module: cbx_1__1_
+      count: 1
+      instances:
+        - cbx_1__1_
+    - module: cby_0__1_
+      count: 1
+      instances:
+        - cby_0__1_
+    - module: cby_1__1_
+      count: 1
+      instances:
+        - cby_1__1_
 
 In this example, the parent module is ``fpga_top``.
 The child modules under ``fpga_top`` are ``grid_io_top``, ``grid_io_right``, and etc.
diff --git a/docs/source/manual/openfpga_shell/openfpga_commands/setup_commands.rst b/docs/source/manual/openfpga_shell/openfpga_commands/setup_commands.rst
index b2e10d1b6..2c0cde183 100644
--- a/docs/source/manual/openfpga_shell/openfpga_commands/setup_commands.rst
+++ b/docs/source/manual/openfpga_shell/openfpga_commands/setup_commands.rst
@@ -535,7 +535,7 @@ report_reference
 
   .. option:: --file <string> or -f <string>
 
-    Specify the file name to write the reference information
+    Specify the file name to write the reference information. See details in :ref:`file_format_reference_file`.
 
   .. option:: --module <string>
 
@@ -547,4 +547,4 @@ report_reference
 
   .. option:: --verbose
 
-    Show verbose info
\ No newline at end of file
+    Show verbose info