I recommend Referencer. You can download it using apt-get. It supports tagging files with fields such as author, title, journal and publisher, etc. For many research papers it will automatically download the data for you provided there is a DOI identifier inside the file. It can also generate BibTex files automatically.

However, it does not store your references online. I use it with git myself, and it works nicely.

Short answer

It seems there's no good enough up to date open source Flash player project. And apparently current Lightspark won't work with Chromium version 34 and higher.

Current Status

Starting from version 34 (April 2014) Chromium/Chrome start to drop support for the Netscape-API plugins (NPAPI) in favor to new Pepper API (PPAPI) which runs plugins in sandbox mode (which, IMHO, closed the main web security hole of the last years named Flash). To keep Flash support under Linux Google made deal with Adobe to maintain its own version of Flash (still proprietary and close sourced) available as pepperflashplugin-nonfree.

Since the latest version of Lightspark was long before (2013-03-16) the API switch (2014-02-17) it doesn't supported by current version of Chromium project. The other active FOSS Flash player projects are even older.

What to do

Depends on reasons you're seeking FOSS Flash player.

• In case of security, you could safely use Google's Pepper Flash, since it's sandboxed. Install it via Ubuntu Software Center as pepperflashplugin-nonfree or command line sudo apt-get install pepperflashplugin-nonfree. Chrome already includes plugin build-in.

• In case you believe in FOSS software and want to support it - it's better to not use Flash at all (ignore it), as using any FOSS players still promote closed proprietary RIA standard (which, IMHO, harmed industry enough). It's not so hard, since many sites going to use HTML5 as Flash replacement. And as backup feature you can install Pepper Flash, but set Chromium to run it only by request (entering URL chrome://settings/content and selecting "Click to play" for Plug-ins).