org-babel-expand-references: Fix :noweb-ref expansion

* lisp/ob-core.el (org-babel-expand-noweb-references): Do not rely on
reference cache being populated as a condition that all the references
in buffer have been processed.  Set this information explicitly.
* testing/lisp/test-ob.el (test-ob/noweb-expansion): Add new test.

lisp/ob-core.el

@@ -2994,7 +2994,8 @@ block but are passed literally to the \"example-block\"."
 		      ;; run.  Yet, ID is not in cache (see the above
 		      ;; condition).  Process missing reference in
 		      ;; `expand-references'.
-		      ((hash-table-p org-babel-expand-noweb-references--cache)
+		      ((and (hash-table-p org-babel-expand-noweb-references--cache)
+                            (gethash 'buffer-processed org-babel-expand-noweb-references--cache))
 		       (expand-references id))
 		      ;; Though luck.  We go into the long process of
 		      ;; checking each source block and expand those
@@ -3010,6 +3011,7 @@ block but are passed literally to the \"example-block\"."
 			    (let* ((info (org-babel-get-src-block-info t))
 				   (ref (cdr (assq :noweb-ref (nth 2 info)))))
 			      (push info (gethash ref org-babel-expand-noweb-references--cache))))))
+                       (puthash 'buffer-processed t org-babel-expand-noweb-references--cache)
 		       (expand-references id)))))
 	       ;; Interpose PREFIX between every line.
                (if noweb-prefix

testing/lisp/test-ob.el

@@ -883,7 +883,52 @@ x
 #+begin_src emacs-lisp :noweb yes<point>
 <<AA>>
 #+end_src"
-	    (org-babel-expand-noweb-references)))))
+	    (org-babel-expand-noweb-references))))
+  ;; Test :noweb-ref expansion.
+  (should
+   (equal "(message \"!! %s\" \"Running confpkg-test-setup\")
+
+(message \"- Ran `%s'\" 'confpkg-test-strip-package-statements)
+
+(message \"!! %s\" \"Still running confpkg-test-setup\")
+
+(message \"- Ran elisp blocks in `%s'\" 'confpkg-test-dependency-analysis)
+
+(message \"!! %s\" \"End of confpkg-test-setup\")"
+          (org-test-with-temp-text "
+* Setup
+
+#+name: confpkg-test-setup
+#+begin_src emacs-lisp :results silent :noweb no-export
+(message \"!! %s\" \"Running confpkg-test-setup\")
+
+<<confpkg-test-strip-package-statements>>
+
+(message \"!! %s\" \"Still running confpkg-test-setup\")
+
+<<confpkg-test-dependency-analysis>>
+
+(message \"!! %s\" \"End of confpkg-test-setup\")
+#+end_src
+
+#+call: confpkg-test-setup[:results none]()
+
+* Identify cross-package dependencies
+
+#+begin_src emacs-lisp :noweb-ref confpkg-test-dependency-analysis
+(message \"- Ran elisp blocks in `%s'\" 'confpkg-test-dependency-analysis)
+#+end_src
+
+* Commenting out ~package!~ statements
+
+#+name: confpkg-test-strip-package-statements
+#+begin_src emacs-lisp
+(message \"- Ran `%s'\" 'confpkg-test-strip-package-statements)
+#+end_src
+"
+            (goto-char (point-min))
+            (search-forward "begin_src")
+            (org-babel-expand-noweb-references)))))
 
 (ert-deftest test-ob/splitting-variable-lists-in-references ()
   (org-test-with-temp-text ""