diff --git a/template/build/core/phing/tasks/validate.xml b/template/build/core/phing/tasks/validate.xml
index 8c7c9887b..7c425e5ce 100644
--- a/template/build/core/phing/tasks/validate.xml
+++ b/template/build/core/phing/tasks/validate.xml
@@ -33,6 +33,7 @@
     <if>
       <istrue value="${filteredFileList}"/>
       <then>
+        <!--@todo Pass an entire fileset to PHPCS rather than looping over a list. -->
         <foreach list="${filteredFileList}" target="validate:phpcs:file" param="file"/>
       </then>
     </if>
diff --git a/template/scripts/blt/update-scaffold b/template/scripts/blt/update-scaffold
index e0f79bdf1..38e2167c2 100755
--- a/template/scripts/blt/update-scaffold
+++ b/template/scripts/blt/update-scaffold
@@ -37,6 +37,6 @@ done
 
 # Restore execute permissions.
 chmod 755 blt.sh
-chmod 755 scripts/git-hooks/pre-commit
+chmod -R 755 scripts/git-hooks/pre-commit
 
 echo "Changes have been pulled down. Please review and commit desired changes."
diff --git a/template/tests/phpunit/Bolt/GitTest.php b/template/tests/phpunit/Bolt/GitTest.php
index c60c03eae..bbd80a1b2 100644
--- a/template/tests/phpunit/Bolt/GitTest.php
+++ b/template/tests/phpunit/Bolt/GitTest.php
@@ -87,13 +87,11 @@ protected function assertCommitMessageValidity($is_valid, $commit_message, $mess
     chdir($this->projectDirectory);
 
     // "2>&1" redirects standard error output to standard output.
-    $command = "git commit --amend -m '$commit_message' 2>&1";
+    $command = "mkdir -p {$this->projectDirectory}/tmp && echo '$commit_message' > {$this->projectDirectory}/tmp/blt_commit_msg && {$this->projectDirectory}/.git/hooks/commit-msg {$this->projectDirectory}/tmp/blt_commit_msg 2>&1";
     print "Executing \"$command\" \n";
 
-    $output = shell_exec($command);
-    $invalid_commit_text = 'Invalid commit message';
-    $output_contains_invalid_commit_text = (bool) strstr($output, $invalid_commit_text);
-    $this->assertNotSame($is_valid, $output_contains_invalid_commit_text, $message);
+    exec($command, $output, $return);
+    $this->assertNotSame($is_valid, (bool) $return, $message);
   }
 
 }