diff --git a/MANIFEST.in b/MANIFEST.in
index 019c6268bc..f7b4bd542a 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -15,7 +15,7 @@ recursive-include scripts *
 prune build
 prune docs/_build
 prune docs/api
-prune pypeit/deprecated
+prune deprecated
 
 global-exclude *.pyc *.o *.so *.DS_Store
 
diff --git a/pypeit/aroutput.yml b/deprecated/aroutput.yml
similarity index 100%
rename from pypeit/aroutput.yml
rename to deprecated/aroutput.yml
diff --git a/pypeit/archive.py b/pypeit/archive.py
old mode 100755
new mode 100644