Currently, Indigo stores its files in /Library. Can I instead store them in ~/Library? The reason is that Apple Backup now backs up only files in the user's home directory.
George

No, Indigo requires them to be in the top-level /Library directory. Are you talking about Time Machine? That seems to be working fine for me.

No, Apple Backup, which I use to back up to my iDisk. v3.2 of the app removes the ability to select directories outside the user's home.
George

If backup follows aliases or symbolic links then you might can create an alias or symlink in your home directory. Not sure if it's that smart though. The other thing you can do is have Indigo kick off a script that tells the Finder to make a copy of that directory in your home directory sometime before the backup runs.

I thought that dropped that app a long time ago...

The main database file can actually be moved out of the /Library folder. Make sure you ONLY move your active database file (not the entire databases folder) and Indigo should still be able to find it.

The preferences files, however, cannot be moved.