I found that on OSX you can change this setting in the following file:
~/Library/Preferences/IntelliJIdea2016.1/options/options.xml
Add the following properties:
<property name="decompiler.use.line.mapping" value="true" />
<property name="decompiler.dump.original.lines" value="true" />
ok, as there are no news regarding this, I've created a little plugin which decompiles the jar file with compiled code to new *-sources.jar file using build-in Intellij fernflower decompiler and attaches sources to project. anyone interested, can take a look at decompile and attach plugin in jetbrains plugin repository
Update
answering my question about line numbers in decompiled code using fernflower. I found 'decompiler.use.line.table' flag in Intellij's fernflower which preserves line numbers.
As the author has forgotten to add a detailed usage listing
No, I haven't :) See readme.txt in your jar for the full documentation.
Current source code and documentation of Fernflower is available here: https://github.com/fesh0r/fernflower
Command line options are listed there, I do not copy-paste them from github.
Online version of Fernflower is now available on this site: http://www.javadecompilers.com/