diff --git a/thicken-manifests.py b/thicken-manifests.py
index 17a19e3..2921420 100755
--- a/thicken-manifests.py
+++ b/thicken-manifests.py
@@ -83,14 +83,14 @@ def maybe_thicken_manifest(pkg_dir):
 	manifest_entries = []
 	for root in pkg_dir, os.path.join(pkg_dir, 'files'):
 		for filename in dir_contents[root]:
-			if filename == 'Manifest':
+			if filename == 'Manifest' and root == pkg_dir:
 				continue
 
 			file_mtime = math.floor(os.stat(os.path.join(root, filename)).st_mtime)
 			if file_mtime > newest_mtime:
 				newest_mtime = file_mtime
 
-			if os.path.split(root)[1] == 'files':
+			if root != pkg_dir:
 				manifest_entries.append('AUX ' + filename)
 			elif filename.endswith('.ebuild'):
 				manifest_entries.append('EBUILD ' + filename)
@@ -164,18 +164,20 @@ location = %s
 					subdirectories.remove(dirname)
 
 		if (not subdirectories or subdirectories == ['files']) and 'metadata.xml' in files:
+			if os.path.sep not in os.path.split(root)[0]:
+				# EDGE CASE: category with single package called "files"
+				continue
 			pkg_dirs.append(root[2:])
 			dir_contents[root[2:]] = files
-		elif os.path.split(root)[1] == 'files' and 'metadata.xml' not in files:
-			dir_contents[root[2:]] = files
-			for dirname in subdirectories[:]:
-				subdirectories.remove(dirname)
-			os.chdir(root)
-			for root2, subdirectories2, files2 in os.walk('.'):
-				if root2 != '.':
+			if 'files' in subdirectories:
+				subdirectories.remove('files')
+				filesdir = os.path.join(root, 'files')
+				dir_contents[filesdir[2:]] = []
+				os.chdir(filesdir)
+				for root2, subdirectories2, files2 in os.walk('.'):
 					for filename in files2:
-						dir_contents[root[2:]].append(os.path.join(root2[2:], filename))
-			os.chdir(args.location)
+						dir_contents[filesdir[2:]].append(os.path.join(root2[2:], filename))
+				os.chdir(args.location)
 
 	pkg_dirs.sort()
 	pool = multiprocessing.Pool(args.jobs, worker_init)