I like how Eclipse IDE indents my source code but I would like to keep my comments intact. How do I make Eclipse not touch comments in Java source code?
I am using Eclipse Luna.
Window -> Preferences -> Java -> Code Style -> Formatter here you have to create a copy of the default rules and change then as you like. Have a look at the Comments tab.

In Eclipse, Goto Window->Preferences->Java->Formatter and click on Edit your active profile. In the Comments tab, you will have the options to achieve what you want with a preview. Hope this helps
(Note: You may want to duplicate the existing profile if you need to revert back)
You can define your custom formatting rules in eclipse. Go to Eclipse Preferences--> Java --> Code Style --> Formatter and add your rules.