diff --git a/agentstack/generation/files.py b/agentstack/generation/files.py
index f2ad90a..fa21857 100644
--- a/agentstack/generation/files.py
+++ b/agentstack/generation/files.py
@@ -1,4 +1,5 @@
 from typing import Optional, Union
+import string
 import os, sys
 from pathlib import Path
 
@@ -20,6 +21,10 @@ class EnvFile:
     and instead just append new lines to the end of the file. This preseres
     comments and other formatting that the user may have added and prevents
     opportunities for data loss.
+    
+    If the value of a variable is None, it will be commented out when it is written
+    to the file. This gives the user a suggestion, but doesn't override values that
+    may have been set by the user via other means. 
 
     `path` is the directory where the .env file is located. Defaults to the
     current working directory.
@@ -57,7 +62,7 @@ def append_if_new(self, key, value):
     def read(self):
         def parse_line(line):
             key, value = line.split('=')
-            return key.strip(), value.strip()
+            return key.strip(string.whitespace + '#'), value.strip(string.whitespace + '"')
 
         if os.path.exists(conf.PATH / self._filename):
             with open(conf.PATH / self._filename, 'r') as f:
@@ -69,7 +74,10 @@ def parse_line(line):
     def write(self):
         with open(conf.PATH / self._filename, 'a') as f:
             for key, value in self._new_variables.items():
-                f.write(f"\n{key}={value}")
+                if value is None:
+                    f.write(f'\n#{key}=""')  # comment-out empty values
+                else:
+                    f.write(f'\n{key}={value}')
 
     def __enter__(self) -> 'EnvFile':
         return self