First, reading the console.log I get this message: "DEVONthink 2.8.10, Mac OS X Version 10.11.4 (Build 15E65)
2016-04-01 10:49:28.833 DEVONthink[22921:63942] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead."
Second, the index files. a) are the index files encrypted? b) how are they encrypted? c) is it possible to move the location of the index files? I run my devonthink databases on encrypted sparse images and would like to have my indexes there as well.
The indices are not portable, so no, you can’t move them to a location outside the database. However, why not stored the database itself on the encrypted sparse bundles? (I do this with my financials and accounts databases.)
The correct paths are…
~/Library/Application Support/DEVONthink 2 :: This directory IS the Global Inbox (and only database) for DEVONthink Personal.
~/Library/Application Support/DEVONthink Pro 2 :: The Inbox.dtBase2 file is located here.
Other databases (.dtBase2 files) are located where you have located them. (And to repeat the warning once again: You should never put your databases in a Dropbox (or other cloud-synced) folder or you could irreparably damage them. The safest location is ~/Documents.)
Note: The Global Inbox should not be relocated. It is best to leave it alone where it is.