I have the same problem. I'm stuck at the main quest line.
http://gameswiki.net/pillars-of-eternity-act-ii-all-side-quests-guide/2/
If this page is correct, my quest does not update when I enter the ruins. Its objective is "Enter the Ruins via Stormwall Gorge" after I enter and explore everywhere.
There is no ancient weapons, only cladhaliath, in the sarcophagus; whether I kill the spider boss or not.
https://drive.google.com/file/d/0BxonmKN54einV0ktVVVPa1JnT1k/view?usp=sharing
I upload the save file, hoping that it will be fixed, my previous save is tens hours before.
Also I play it on windows, version is v1.0.3.0526 -steam