There is a checkbox under Items>Town Run. "Stash gems on 2nd to last page"
It wont organize an existing stash, but any new gems stashed (rubies/topaz etc and legendary gems) should be placed on 2nd to last page.
You can manually organize the existing stash or dump them all into your backpack to be re-stashed.
Its a short term solution to my last stash tab being full with crafting materials. In future i want to let you pick with more detail what kinds of items go where.