Like korm, I do not use DEVONthink as a Finder replacement.
There are many files on my Macs that would add no value to a DEVONthink database, for example zipped files, Microsoft Office user data, applications (which cannot be added) and the vast majority of my image, audio and video files.
I have a number of DEVONthink Pro Office databases that I created to meet specific interests and needs. I don’t put all the files on my computers into those databases.
My own preference is for self-contained databases. I almost never do Index captures, in order to minimize problems in moving databases among my computers, or sometimes running them off an external drive mounted to the computer I’m using at the moment, without worrying about ‘missing file’ message that would result if dangling external files had their Paths broken.
When I Import files from the Finder, I’ll delete them from the Finder, or archive them to an external drive. Literally, I no longer care about those files.
But I’m a stickler about data integrity. I keep the operating system clean and error-free. Every two or three weeks (or immediately if something flaky happens) I’ll run an OS X maintenance utility (I use C0cktail, but others such as OnyX can be used) to clear caches and do a number of other procedures that help keep OS X clean and efficient, and then restart the computer. Once in a while I’ll run the Verify Disk routine of Disk Utility, to check for any possible disk directory errors, and repair them if found.
I use a multilevel backup system for my DEVONthink database, which contain the most important files on my computers.
First level: DEVONthink’s internal Backup folders, which are set for daily backup, and which I sometimes manually invoke when I’ve done a major surgery on a database and verified it is error-free by running Tools > Verify & Repair. On occasion I’ve been known to do something dumb to a database. The Tools > Restore Backup procedure allows me to return to an earlier state of the database. Any new content I’ve added after the date of that internal backup will be available in an Orphan folder, after I’ve run Verify & Repair. But this first level wouldn’t protect me were my hard drive to crash.
Second level: A backup system that stores my data on an external medium. I use Apple’s free Time Machine to automatically backup all changes to an external drive. Now I’m protected against a hard drive failure. My preference is for backups that I can control, so I don’t like cloud backups of my databases. A related issue is that it would take a long time to recover them from cloud backup. Because Time Machine would faithfully backup my databases even if they were damaged, once in a while I run Verify & Repair to ensure they are in good shape. But this level of backup wouldn’t protect my data if a burglar stole all my computer equipment, or in case of a fire.
Third level: Periodically, I backup my most important databases as Database Archives (the smallest possible zipped versions of databases), which are updated to a portable drive that I store in a bank safety deposit box.
I’m in my 12th year of using DEVONthink. My databases have been stable and error-free, and they are better protected against loss than any other content on my computers.