Why did MultiMarkdown Composer stop working?
On February 14, 2016 Apple's certificates expired, which means that apps from the App Store need new receipts.
According to Apple:
Users running OS X El Capitan (v10.11 or v10.11.1) may receive a notification that your Mac app is damaged if it utilizes receipt validation to request a new receipt from Apple. They can resolve this issue by restarting their Mac or updating to OS X El Capitan (v10.11.2) or later. Mac App Store customers running OS X Snow Leopard (v10.6.8) will be unable to purchase new apps or run previously purchased apps that utilize receipt validation until they install the Mac App Store Update for OS X Snow Leopard which is available via OS X Software Update.
To get MultiMarkdown Composer working again:
Ensure you have upgraded your Mac's OS as above.
Restart your Mac.
Run the App Store version of MultiMarkdown Composer. It should trigger the OS to have you log into your iTunes/App Store account in order to update the receipt. If you have deleted the App Store version of Composer from your machine, you'll have to reinstall it. (You don't have to purchase it again.)
Once the App Store version is running, you can run the non-sandboxed build or demo of version 3 again. If you're running the non-sandboxed build of version 2, you'll need to follow the original instructions to replace the old receipt with the new receipt. If you are using the version 3 demo, it will take care of this automatically. I definitely suggest using the v3 beta.
My apologies for any inconvenience this caused. I'm not any happier than you are.