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For the filetype issue there are two (at least for my design) caveats. The first is I'm only sending (for the most part) documents and created files to my centralized Cloud storage, so most of the names won't be generic or common. But of course your point is still valid as occasionally there will be duplicates. Syncovery automatically appends a copy number (1) to every file thats a duplicate, so while they will have a number on them, at least they are still saved, sync-ed and then flagged for manual curation later in the database (I understand DevonThink isn't a 'real' database per se, but I'll keep referring to it as such), while leaving the original files saved in the system tree untouched.
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It's not that the search was insufficient, as I've never used Spotlight before anyway (and in fact, believe it or not, I bought my first-ever Mac JUST to use DevonThink (though I think DevonThink seriously needs a direct competitor, as their lack of competition is very obvious from the lack of streamlining of the software)).
I basically saw the opportunity to create a huge centralized cloud repository of my documents, images, and some other misc files and then overlay a meta database-like program (DevonThink) over that data, which would not merely allow me to search all of it (already possible as you note, though DT search IS much faster and better I think), but more importantly, set up meta frameworks on the SAME data without worrying about creating file structures or disturbing the original files.
I have a paranoid backup strategy, and I like having a clean save of every original user-created file on the system that is centralized in the user folder say. DevonThink allows the creation, for example, of project-specific databases where you can meta tag data, annotate files with notes/comments/attachments, hyperlink files to one-another, and a bunch of other data analysis and supposed 'AI' features that some people love, and which I haven't really bothered to explore (yet).
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Opus came in as you mentioned - I use it on my 4 Windows machines and I always loved the flatten-folder feature, and knew it could sync, so I just figured I'd look into it first.
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I know VERY little about OSX - and I will look into native rsync (though I'm not really familiar with how it works either necessarily). My current solution is I have the cloud storage WebDav mounted as a drive in MacOSX (using the solid FTP client Transmit v.4), and DevonThink can actually pull the cloud data (which is from the 4 windows machines) off these mounted-as-local WebDav folders itself, and import them into the database sorter.
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I'm almost afraid to find out that there's a much better way to do this at this point because I'm spent SO much time and energy figuring out how to do all this! LOL. From first learning MacOSX for the first time, navigating the opaque and virtually documentation-less DevonThink, making sure WebDav folders mount stably in the face of interrupted internet, making sure DevonThink can reliably read WebDav, and THEN setting up everything on the Windows side (where I need yet a different WebDav client (since neither OSX or Win7 can connect to WebDav natively - extremely slow in the former, basically doesn't work in the latter) on the Windows machines, specifically WebDrive).
Under this complex multi-sync-over-the-WAN-to-cloud-server-and-then-sync-to-MacBookWithDevonThink-and-import data flow, I have a fairly complicated Backup system which involves 3 types of backup: 1. one-way-sync copies of user-created data in native format sent to onboard AND onsite HDDs, 2. HDD images of the System Drive, AND 3. bootable clone backups of the system drive to allow near-instant reboot of the failed volume, which itself is a hardware RAID10 array of SSDs.
Because of the backup system, and just out of my SOP, I don't like reorganizing the original files in the file system.
I would obviously though, be interested in hearing if there are solutions I haven't thought of to do something similar with the cloud data, DevonThink, databases, etc.
Conceptually - it feels simple to set up in an era of cloud computing, internet-everything, etc. but in reality, it requires a LOT of extraneous one-purpose programs to accomplish.