diff --git a/apio/__main__.py b/apio/__main__.py
index cbc4a9f4..4c36c382 100644
--- a/apio/__main__.py
+++ b/apio/__main__.py
@@ -11,8 +11,8 @@
 # --------------------------------------------
 
 import string
-import click
 import re
+import click
 
 from apio import util
 
@@ -128,7 +128,8 @@ def cli(ctx):
         # -- We later split the command lines into command groups.
         index = help_lines.index("Commands:")
         header_lines = help_lines[:index]
-        command_lines = help_lines[index + 1 :]
+        index += 1  # Skip the Commands: line.
+        command_lines = help_lines[index:]
 
         # -- Select project commands:
         project_help = select_commands_help(
diff --git a/apio/util.py b/apio/util.py
index b6e81df7..62cdb537 100644
--- a/apio/util.py
+++ b/apio/util.py
@@ -86,7 +86,8 @@ def run(self):
         """DOC: TODO"""
 
         for line in iter(self._pipe_reader.readline, ""):
-            line = line.strip()
+            # We do preserve trailing whitespace and indentation.
+            line = line.rstrip()
             self._buffer.append(line)
             if self.outcallback:
                 self.outcallback(line)