Same here. Used to use the unofficial plugin from http://www.andreas-diesner.de/garminplugin/doku.php but it no longer works on Garmin Connect. Back to RunKeeper with FIT2app for now, which still works with the plugin.
Same here. I can't understand why this manual upload option has been disabled :-( Maybe the switch from the old garmin connect plugin to the new garmin express is a good thing for many users, but for all other removing the file upload is just very sad. I couldn't find a workaround to upload my activity, and using a windows virtual machine just for this is not a solution.
I am also a satisfied Ubuntu user. Uploaded my runs via garmin plugin from my Forerunner 210 to Garmin Connect without any problem, UNTIL yesterday when Garmin decided to UPGRADE from classic to modern platform of Garmin Connect. Very disappointed when there is no way that you can upload your activities from your GPS watch to the new modern Garmin Connect. Shame on Garmin. They don't even look into our issues (for Linux user), even from the beginning! I am thinking of NOT using Garmin anymore when I upgraded my GPS watch.
At this moment of time, I still can upload my runs automatically to the CLASSIC Garmin Connect platform through Firefox. But not anymore on Chrome. In the near future, the Firefox plugins also will not be working when Garmin decided to change to MODERN permanently. Sigh....
However, for those who are quite adventurous (I know Linux users are!), what you can do is to install Windows 7 in Virtualbox in Ubuntu. Then download and install Garmin Express in your Windows 7 to connect to your device. It should be quite straightforward, but takes a bit longer time and effort to get it running.
Go to the activities page in the modern interface... http://connect.garmin.com/modern/activities - level with the line that starts "Quick Edit / Delete /..." and to the right is the word "Import". Try clicking on there. Wow! it's the import facility that's been removed and hidden :D
So long as you have your FIT file somewhere accessible (as I assume from your previous use of Andreas Diesner's plugin) you can pick it and upload it.
Another Linux user here. Just about ready to replace my watch, and I'm glad I didn't buy that new Garmin I almost picked up last month. Hello, Strava . . .
Linux still works fine (all my computers at home are linux), you just have to manually upload the activities (as you previously had to in Legacy GC). I believe the confusion stems from the fact that the location of doing this has moved in Modern GC. As MCHUNNYMONSTER points out, it is on the Activities page, off to the right, and call "Import". Click that, browse to your .fit file, and then upload it.