diff --git a/code/plugins/reformat_plugin.py b/code/plugins/reformat_plugin.py
index eb68b2a..7985e5f 100644
--- a/code/plugins/reformat_plugin.py
+++ b/code/plugins/reformat_plugin.py
@@ -37,7 +37,7 @@ def append_to_file(filepath, filename, parent, output_file):
     with open(output_file, 'w') as out:
         out.write(text)
 
-def reformat_plugin_dir(plugin_input_dir, plugin_name, plugin_type='wiki'):
+def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'):
     # plugins_output_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins'
     plugin_output_dir = os.path.join('/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins', plugin_name)
     if not os.path.exists(plugin_output_dir):
@@ -58,8 +58,11 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, plugin_type='wiki'):
 parent: Plugins
 categories: plugins
 has_children: true
+nav_order: {order}
 ---
-'''.format(plugin_name=plugin_name)
+To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/{plugin_name}).
+
+'''.format(plugin_name=plugin_name, order=order)
             text = append_text + text
             with open(index_file, 'w') as out:
                 out.write(text)
@@ -77,21 +80,25 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, plugin_type='wiki'):
 title: {plugin_name}
 long_title: {plugin_name}
 parent: Plugins
+nav_order: {order}
 ---
-'''.format(plugin_name=plugin_name)
+To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/{plugin_name}).
+
+'''.format(plugin_name=plugin_name, order=order)
             text = append_text + text
             with open(index_file, 'w') as out:
                 out.write(text)
 
 # main
 def main():
-    if len(sys.argv) != 4:
-        print('Usage: python test.py <plugin_dir_path> <plugin_name> <plugin_type>')
+    if len(sys.argv) != 5:
+        print('Usage: python test.py <plugin_dir_path> <plugin_name> <plugin_type> <nav_order>')
         sys.exit(1)
     dirpath = sys.argv[1]
     plugin_name = sys.argv[2]
     plugin_type = sys.argv[3]
-    reformat_plugin_dir(dirpath, plugin_name, plugin_type)
+    order = sys.argv[4]
+    reformat_plugin_dir(dirpath, plugin_name, order, plugin_type)
 
 if __name__ == "__main__":
     main()
\ No newline at end of file
diff --git a/code/plugins/update_plugins.py b/code/plugins/update_plugins.py
index c3c9c24..5d166af 100644
--- a/code/plugins/update_plugins.py
+++ b/code/plugins/update_plugins.py
@@ -1,5 +1,6 @@
 import os
 import subprocess
+import sys
 
 def run_command(command):
     result = subprocess.run(command, shell=True, capture_output=False, text=True)
@@ -7,7 +8,7 @@ def run_command(command):
         print(f"Command failed: {command}\nError: {result.stderr}")
     return result
 
-def update_repo(repo, script, plugin_type='readme'):
+def update_repo(repo, order, plugin_type='readme'):
     print(f"Updating {repo}...")
     current_dir = os.getcwd()
     repo_path = os.path.join(current_dir, 'github', repo)
@@ -22,16 +23,28 @@ def update_repo(repo, script, plugin_type='readme'):
             run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}')
         
     os.chdir(current_dir)
-    run_command(f'python {script} {repo_path} {repo} {plugin_type}')
+    script = 'reformat_plugin.py'
+    command = f'python {script} {repo_path} {repo} {plugin_type} {order}'
+    run_command(command)
 
 if __name__ == "__main__":
     # if 'github' not in current directory, create it
     if not os.path.exists('github'):
         os.makedirs('github')
-
-    # wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
-    # for plugin in wiki_plugins:
-    #     update_repo(plugin, "reformat_plugin.py", 'wiki')
-    readme_plugins = ['ARfitStudio'] #, 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
-    for plugin in readme_plugins:
-        update_repo(plugin, "reformat_plugin.py", "readme")
+    if len(sys.argv) == 0:
+        order = 1
+        wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
+        for plugin in wiki_plugins:
+            update_repo(plugin, order, 'wiki')
+            order += 1
+        readme_plugins = ['ARfitStudio', 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
+        for plugin in readme_plugins:
+            update_repo(plugin, order, "readme")
+            order += 1
+    elif len(sys.argv) == 3:
+        plugin_name = sys.argv[1]
+        plugin_type = sys.argv[2]
+        update_repo(plugin_name, 1, plugin_type)
+    else:
+        print('Usage: python update_plugins.py <plugin_name> <plugin_type>')
+        sys.exit(1)
diff --git a/code/plugins/update_plugins.sh b/code/plugins/update_plugins.sh
deleted file mode 100644
index 5d61b38..0000000
--- a/code/plugins/update_plugins.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-current_dir=$(pwd)
-
-repo="SIFT"
-if cd ../../$repo; then git pull; else git clone https://github.com/sccn/$repo.wiki.git ../../$repo; fi
-python Wiki_plugin.py ../../$repo $repo
-cd $current_dir
-
-repo="EEG-BIDS"
-if cd ../../$repo; then git pull; else git clone https://github.com/sccn/$repo.git ../../$repo; fi
-python README_plugin.py ../../$repo $repo
-cd $current_dir
-
-repo="roiconnect"
-if cd ../../$repo; then git pull; else git clone https://github.com/sccn/$repo.git ../../$repo; fi
-python README_plugin.py ../../$repo $repo
-cd $current_dir
\ No newline at end of file