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@everyone - Full Fix, no hacks required, just your own work:
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So I have to agree with everyone's posts above; given that the only thing needed to support Boxcryptor Classic in 10.11 is a symlink, I think it is BS that they are using this to force people to a different product. It would be one thing is Apple switched the FS layer, but they did not, so there is no technical reason not to support it.
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After looking at the guts, I took a guess to fix it and figured it out...very simple if boxcryptor wants to update a current version.
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I understand the proposed advantages to Boxcryptor, but I use Boxcryptor Classic precisely since it has encFS support. As such, it's the only package I've found that lets me sync encrypted stuff between Mac, Windows and Linux easily.
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1) install the latest version of boxcryptor classic (1.5.409 at the time of this guide) if not already installed
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Anyway, since they refuse to support it, an even easier way to have full support in El Capitain is:
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2) open the applications folder in finder view or wherever boxcryptor classic is installed.
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1. Download an older version of Boxcryptor Classic. I used 1.5.409.246 (https://www.boxcryptor.com/download/Boxcryptor_Classic_v1.5.409.246_Installer.dmg).
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3) right click boxcryptor classic and select show package contents
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2. Install the application and open it once (you need to open it before modifying so Gatekeeper doesn't compain to you).
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4) expand into Contents, MacOS, Filesystems
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3. Close out Boxcryptor Classic
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5) right click on bccfs.fs and select show package contents
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4. Open Terminal.
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6) expand into Contents, Extensions.
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5. Run the following command: ln -s /Applications/Boxcryptor\ Classic.app/Contents/MacOS/Filesystems/bccfs.fs/Contents/Extensions/10.9 /Applications/Boxcryptor\ Classic.app/Contents/MacOS/Filesystems/bccfs.fs/Contents/Extensions/10.11 && ln -s /Applications/Boxcryptor\ Classic.app/Contents/Resources/bccfs.fs/Contents/Extensions/10.9 /Applications/Boxcryptor\ Classic.app/Contents/Resources/bccfs.fs/Contents/Extensions/10.11
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7) copy the 10.10 shortcut and paste it into the same folder...it defaults to the contents folder for me, just drag it back.
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6. Enjoy!
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8) rename 10.10 copy to 10.11
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7. If Gatekeeper gives you a message saying Boxcryptor Classic is corrupted, open System Preferences -> Security & Privacy and switch "Allow apps downloaded from" to "Anywhere". Open the app, then switch the setting back. 
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9) close the window
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10) open the applications folder in finder view or wherever boxcryptor classic is installed.
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11) right click boxcryptor classic and select show package contents
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