I am a DT personal edition user. I use DT exclusively as a pdf database for the time being. I keep all the pdfs in the Application Support folder reserved for that purpose.
It’s very reassuring to know that they are not baked into some kind of database structure but still accessible via the finder.
I am now thinking about using DT also to build a database of notes. Now for my question: Where are the notes (i.e. rtf files) stored? I think in DT personal they are inside the database. But what about the pro version? Is it possible to store them within the ordinary file structure (as described for pdfs above).
I am sure the answer is somewhere in this forum, but I could not find it …
Text (plain and rich), HTML, XML and some other file types are still stored in the monolithic body of the database. That will change when version 2.0 is released.
I applaud your concern for data integrity, but I don’t let it keep me from storing text files in my databases. In fact, as most of my many thousands of files captured from the Web are RTF or RTFD formats, they are stored in the main body of my database. And as I do most of my writing and editing in DT Pro, so are my project text files. I don’t worry about them, because I make backup copies of the database externally, and make internal backup using Verify & Repair followed by Backup & Optimize manually, after I’ve made significant additions or invested time in editing or organizing data. In sum, I simply don’t lose data – and I’ve been putting them into my database since 2004. I haven’t seen an error reported by Verify & Repair for almost a year, and that was corrected by a rerun. I haven’t had to use a backup file in over a year – and that was because of a System problem that I caused (playing with invisible files!), and resulted in no data loss (yes, I did something stupid, but backed up first).
It is possible to corrupt a DT database (and perhaps everything else, too). Here are some of the things that can go wrong:
 A power outage, brownout or voltage surge occurs. This is probably the most common cause of file problems, and might not be noticed at the time, e.g., low voltage or a voltage surge. In the worst case, this happens while data is being written to disk and results in a corrupt file. But corruption of the HD can happen even if the database isn’t being written to. Preventive measures: Use an uninterruptible power supply (UPS) for desktop computers, or work on a PowerBook or MacBook. Note: A UPS protects not only your investment of time and effort in your data, it also protects your computer hardware. I’ve never had a hardware failure on any of my Macs.
 Dumping already corrupted files into your database. The older a collection of files and the more diverse their origin (such as collections of files from 20-year old floppy disks that may be failing, or from web collections with poor quality control), the more likely this can happen. Preventive measures: Make a backup of your database before importing a batch of files of unknown quality, and immediately run Verify & Repair afterwards. If problems occur, either run Restore Backup to restore your database to its state before the import, or run Rebuild Database to kick out the bad files. Note: This problem will be somewhat mitigated under the version 2.0 file structure, but dumping bad files into your database won’t add information to your database!
 Poor maintenance of your operating system and disk directory. Although OS X is a very stable operating system, failure to do routine and preventive maintenance can ultimately result in poor performance, a damaged operating system, an unreadable hard drive and/or unreadable or corrupted files – not just DT databases but any or all of your files. At a minimum, run permissions repair before and after OS and Security updates, and run Disk Repair anytime flaky operations appear. Corrupt fonts can cause all kinds of problems, as can corrupt caches and permissions. Whenever Apple releases an OS update, there are users reporting that their computers have been rendered unusable. Guess why?
 Operating a computer without sufficient free disk space. Apple engineers recommend keeping at least 10% to 15% (the more, the better – some engineers recommend 25%) of the capacity of your hard disk free to accommodate the operating system’s Virtual Memory swap files and other temporary files during operation. And of course applications often need to maintain caches and other temporary files on your hard drive. In addition to performance deterioration, very bad things can happen when disk drives fill up, including overwriting of files that will render them unusable. This problem can occur unexpectedly, if an application or process goes wild and writes huge log or cache files to your disk. Once in a while, launch Activity Monitor and check out your free disk space. If it is low, try utilities such as Onyx or Cocktail that can clean out caches and rotated log files, and perhaps delete or archive to a CD files that are no longer needed.
 Hardware failures. IMHO, this is the least likely cause of problems, but hardware failures can and do happen. In many years on many Macs, I’ve never experienced one. But I periodically store backups of my databases and other important files on external drives or CDs, and I periodically clone my hard drive so that I’ve got a complete, bootable backup.
To copy a DT Pro database to an external drive, simply select the package file (with DT Pro quit!) and option drag it to the external drive. To copy a DT Personal database to an external drive, locate it in the Finder in your user directory/Library/Application Support/ (it’s the folder named “DEVONthink”) and (with DT quit!) copy (Option-drag) it to the location of your choice.
Referring to your last point, I already had two hardware failures on my iBook since I bought it August 2004.
First, the mainboard crashed last summer, and just a couple of weeks ago, the hard drive went dead.
So it is indeed, as you suggest, very very important to make backups (as I, fortunately, did).