Have either of you trialed DEVONsphere Express?
I tried DEVONsphere Express but I could not get the AI / see also list / recommendations (or whatever itās called) to work. Iām sorry that I canāt provide a more detailed description of what the problem was, since I tried it a couple of months ago and I no longer have it installed. I tried everything I could think of to get it to work, including letting it run all night to index things, but it never worked. Iām running Mavericks 10.9.5. If it only indexes the startup disk, that may have been the problem since most of my files are on an external drive. Itās definitely worth trying though; it looks like a promising tool.
Thanks for the support, Nat.
Diving off in pursuit of alternatives til DEVONthink offers tighter file system integration.
and thanks all 
Come on back anytime. 
Just as a follow up - hereās an example of a less powerful product storing their files via the file system.
āNotebooks stores all your documents as regular files on your computerās hard drive, so you can always access them through Finder to open and edit with other applications, too.ā
If only they offered a decent editing tool.
Notebooks (which I use extensively) has watched folders, as do many other apps. If a document is moved in the file system outside of one of Notebooksā watched folders then Notebooks loses track of it. Which was your frequent criticism of DEVONthinkās indexing method. DEVONthinkās indexing virtually similar to Notebooksā process.
So why is Notebooks an example of something better?
(BTW, DEVONthink can index Notebooksā folders ā which is how I use the two apps together. Why? I prefer Notebookās side-by-side editor, a feature no version of DTTG on iOS has.)
btw Iām not advocating Notebooks here - just their approach which is ārightā. It has other holes.
They have one home directory.
Everything that happens under that directory is synched between the file system and Notebooks.
Create a subfolder in Notesbooks, it appears in Finder.
Create a subfolder in Finder, it appears in Notebooks.
Simple.
Which is exactly what DEVONthink does with indexing. So the betterment is ā¦ ?
When you create a subfolder under an indexed folder in DT, does it appear in the file system?
When you move a file in DT from one indexed folder to another, does the file move in Finder?
When you delete a file in DTā¦ (you know the rest)
Even though itās been pointed out here, in the suggested links, and elsewhere in places easily found ā how to do all these things in DEVONthink, I finally realized that is not the point of this pointless thread.
Please donāt shoot the messenger.
Happy to be wrong butā¦
If you move a file from one indexed folder to another in DT, does the file move in filing system?
ārightā is a subjective term here. 
Iām with jamesmicfish on some (but not all) of the points mentioned above, and I understand what he is trying to say, unlike some of the other commenters. Some of you seem to think that DEVONthink is perfect as it is, but itās not from our perspective. You could listen to us and see an opportunity here to make the app usable for more users, or you can call this thread āpointlessā (as korm did above) and lose users. DEVONthink has been working fairly well for me, but I agree that what jamesmicfish has said points toward some optional features that would improve the product for users like us.
While DEVONthink does use Appleās file system to store Imported document files within the database, in the folder named Files.noindex, those document files are not organized into folders corresponding to the userās organizational scheme for a database. Thereās a good reason for that.
In the Finder a Mac user works with folders and files. Folders can be opened to view their contained files. Files can be opened and displayed under an application capable of viewing/editing them, or under Appleās Quick Look. Folders and files may be duplicated or aliased.
In DEVONthink a database user works with groups and documents. A group can be opened to display its contained (located) documents, so is really metadata about organizational location. A document can be opened to view it within the database via viewing code for its file type built into OS X, or a Quick Look plugin or opened externally under another application, so is metadata pointing to a file. Groups and documents can be duplicated or replicated. Unlike an alias of a file, which points to the original file and remains as a useless artifact if the original is deleted, all replicants are pointers to the original group or document, so that if one of a pair is deleted, the āoriginalā remains, no matter which was deleted.
Replication makes it possible to organizationally locate a document within multiple groups, which can be very useful. The memory and srtorage space overhead for doing that is small, unlike duplication of the document into multiple locations. And if any replicated instance of the document is edited, all instances are edited.
Suppose Iāve replicated a document into 4 groups. If I export that database to the Finder, the replicants will be translated into duplicates, increasing storage space. If I were then to edit one of those duplicates, the others would not change, but would have to be individually edited or copied if I wanted them all to change.
I find replication very useful for a number of purposes. The inability of the Finder to honor replication is one of the reasons I donāt want my databases to be mirrored in the Finder via Indexing. I can do useful things in DEVONthink that would be lost be in translation to the Finder.
Bill, I am wondering whether you also use tags? Tags also make it āpossible to organizationally locate a document within multiple groupsā (where a tag is a group), both in DEVONthink and in the Mac file system.
For sure. Thatās why I said that tighter integration with the file system in indexed folders would have to be an āoptionalā feature, not a replacement of existing functionality. Thereās no point in dropping or replacing functionality that users depend upon.
I have absolutely no idea what anyone thinks about anything; so that kind of insight would be enviable. But DEVONthink is not perfect for sure. Pretty good; pretty flexible; pretty workable; takes effort; not perfect. What is?
We are in total agreement on that point! I think there is at least one good idea for improving DEVONthink in this thread. That makes this thread worthwhile and not pointless.
Having just installed the latest MSOffice on the Mac, Iām really put off by the amount of traffic going back to Microsoft.
I can see people becoming a lot more privacy savvy - and less willing to share their data with large companies and even public clouds.
There needs to be a worthy replacement for OneNote and the like - that does not monitor the user or require internet access.
It should store files on the local drive in a standard format - letting users manage synching however they choose (maybe their own private cloud).
It has solid file management tools.
It has an advanced editing tool - letting users push text and images anywhere they want around a page. Perhaps stored as HTML5. This will be big.
Some outlining and mind mapping tools would be nice.
Thatās enough to capture a huge chunk of market.
just saynā
Again, I agree with jamesmicfish. There is a need here that is not perfectly filled by current software tools. But until the software utopia arrives, see also: How to Program Yourself for Productivity and Stop Searching for the Ideal Software. For outlining and diagramming, check out OmniOutliner and OmniGraffle. They work together very well.