diff --git a/src/doc/Makefile b/src/doc/Makefile
index 2d433b3727c..98a3d138baf 100644
--- a/src/doc/Makefile
+++ b/src/doc/Makefile
@@ -42,7 +42,7 @@ doc-inventory-reference: doc-src
 	$(eval BIBLIO = $(firstword $(DOCS)))
 	$(eval OTHER_DOCS = $(wordlist 2, 100, $(DOCS)))
 	$(MAKE) doc-inventory--$(subst /,-,$(BIBLIO))
-	$(MAKE) SAGE_DOCBUILD_OPTS="$(SAGE_DOCBUILD_OPTS) --no-prune-empty-dirs" $(foreach doc, $(OTHER_DOCS), doc-inventory--$(subst /,-,$(doc)))
+	$(MAKE) $(foreach doc, $(OTHER_DOCS), doc-inventory--$(subst /,-,$(doc)))
 	$(MAKE) SAGE_DOCBUILD_OPTS="$(SAGE_DOCBUILD_OPTS) --no-prune-empty-dirs" doc-inventory--reference_top
 endif
 
@@ -63,7 +63,7 @@ doc-html-reference: doc-html-reference-sub
 doc-html-other: doc-html-reference
 	$(eval DOCS = $(shell sage --docbuild --all-documents all))
 	@if [ -z "$(DOCS)" ]; then echo "Error: 'sage --docbuild --all-documents' failed"; exit 1; fi
-	$(MAKE) SAGE_DOCBUILD_OPTS="$(SAGE_DOCBUILD_OPTS) --no-prune-empty-dirs" $(foreach doc, $(wordlist 2, 100, $(DOCS)), doc-html--$(subst /,-,$(doc)))
+	$(MAKE) $(foreach doc, $(wordlist 2, 100, $(DOCS)), doc-html--$(subst /,-,$(doc)))
 
 doc-html: doc-html-reference doc-html-other
 
diff --git a/src/sage_docbuild/__main__.py b/src/sage_docbuild/__main__.py
index 844e1ebee17..a7b7b39880b 100644
--- a/src/sage_docbuild/__main__.py
+++ b/src/sage_docbuild/__main__.py
@@ -46,7 +46,7 @@
                         option: nitpicky)
   --check-nested        check picklability of nested classes in DOCUMENT 'reference'
   --no-prune-empty-dirs
-                        do not prune empty directories in the documentation sources
+                        do not prune empty directories in the documentation source
   --use-cdns            assume internet connection and use CDNs; in particular,
                         use MathJax CDN
   -N, --no-colors       do not color output; does not affect children
@@ -325,7 +325,7 @@ def setup_parser():
                           help="check picklability of nested classes in DOCUMENT 'reference'")
     standard.add_argument("--no-prune-empty-dirs", dest="no_prune_empty_dirs",
                           action="store_true",
-                          help="do not prune empty directories in the documentation sources")
+                          help="do not prune empty directories in the documentation source")
     standard.add_argument("--use-cdns", dest="use_cdns", default=False,
                           action="store_true",
                           help="assume internet connection and use CDNs; in particular, use MathJax CDN")
@@ -508,22 +508,24 @@ def excepthook(*exc_info):
 
     build_options.ABORT_ON_ERROR = not args.keep_going
 
+    # Set up Intersphinx cache
+    _ = IntersphinxCache()
+
+    builder = get_builder(name)
+
     if not args.no_prune_empty_dirs:
         # Delete empty directories. This is needed in particular for empty
         # directories due to "git checkout" which never deletes empty
         # directories it leaves behind. See Issue #20010.
         # Issue #31948: This is not parallelization-safe; use the option
         # --no-prune-empty-dirs to turn it off
-        for dirpath, dirnames, filenames in os.walk(SAGE_DOC_SRC, topdown=False):
+        for dirpath, dirnames, filenames in os.walk(builder.dir, topdown=False):
             if not dirnames + filenames:
                 logger.warning('Deleting empty directory {0}'.format(dirpath))
                 os.rmdir(dirpath)
 
-    # Set up Intersphinx cache
-    _ = IntersphinxCache()
-
-    builder = getattr(get_builder(name), typ)
-    builder()
+    build = getattr(builder, typ)
+    build()
 
 
 if __name__ == '__main__':