What should I do about com.apple.quarantine?

You don't have to deal with it. Open it and OS X will ask for your permission. Or like richard suggested, delete it using something like:

xattr -d com.apple.quarantine my_jar.jar

To do this automatically for any downloaded file you can attach a folder action to the download folder, like described on macosxhints.com in 10.5: Remove the 'downloaded file' warning flag.

And the following was posted on macosxhints.com a long time ago, for Safari: 10.5: Disable the 'downloaded from internet' file warning, claiming one can remove VerifiedDownloadPlugin.plugin from /Library/Internet Plug-Ins. I did not test that.

As an aside: sometimes one needs to start a single program multiple times on a Mac. That can be done using cd /Applications/some-application/ followed by open -n "Application Name.app". This really needs the .app suffix; running open -n "Application Name" might get one GateKeeper stopping access:

"Application Name" can't be opened because it is from an unidentified developer.

Your security preferences allow installation of only apps from the Mac App Store and identified developers.

Above, even removing the extended attribute com.apple.quarantine does not fix that, but using the .app suffix works just fine.

(I am not advising anyone to actually get rid of the security measures.)

This attribute is added so that it can ask for user confirmation the first time the downloaded program is run, to help stop malware. Upon confirmation the attribute should be removed automatically, and then the program will run normally.

 xattr -d com.apple.quarantine /path/to/file