The "tree" door leads to the second treasure room, where you can pick up Nathaniel's Ring Of The Ram. You get there by teleporting from the portrait room.
You get into the shadow room the same way. Once there, you'll see a shadow across the inner door. Someone has to step on the shadow (usually taking damage) and that opens the exit door. THEN you can shoot the gun, which will get rid of the shadow, and you can finally enter the altar room.
Unfortunately, it's been some time now since I played the game, and I don't recall the phrases needed to enter the above two places.
Nightowl2
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