I just opened IDEA (10781) with my last project opening by default and it Indexed and Scanned files 5 times!
Once it completed, as a test, I closed IDEA and reopened it and it started scanning and indexing again!
What is most strange is that the JDK is being indexed multiple times as well, which makes the process extremely lengthy.
Why would the JDK need to be rescanned? Thats not going to change between sessions.
I tried Invalidating the caches, but not only did that not work, on top on the scanning and indexing I was left with the Idea 4.5 Look and Feel without the Alloy LAFs available to choose!