DocumentRegistry: Downgrade refcount warnings to debug logging.

It can happen in perfectly sane contexts.

CReDocument: Don't destroy internal engine data when Document just
decreased the refcount (as opposed to actually tore down the document
userdata if it were the last ref).

PdfDocument: Only write edited documents if the Doc instance was torn
down.

PicDocument: Silence some DocumentRegistry related warnings

frontend/document/pdfdocument.lua

@@ -261,9 +261,16 @@ function PdfDocument:writeDocument()
 end
 
 function PdfDocument:close()
-    if self.is_edited then
-        self:writeDocument()
+    -- NOTE: We can't just rely on Document:close's return code for that, as we need self._document
+    --       in :writeDocument, and it would have been destroyed.
+    local DocumentRegistry = require("document/documentregistry")
+    if DocumentRegistry:getReferenceCount(self.file) == 1 then
+        -- We're the final reference to this Document instance.
+        if self.is_edited then
+            self:writeDocument()
+        end
     end
+
     Document.close(self)
 end