how to identify between a 'pure/plain' java project or a 'plug-in java project'?

Have a look at the “.project” file. This file contains the description of your project. It contains a XML tag “natures” where the nature of the project is described. A plugin project has the nature “org.eclipse.pde.PluginNature” and a java project has the nature “org.eclipse.jdt.core.javanature”.

These tags will also steer some behavior of the development environment, e.g. a project with PluginNature will update the java class path if you change the dependency information in a plugin project. For example if you add the “org.eclipse.pde.PluginNature” to an existing Java project you get the PDE menu for your project.

http://www.vogella.de/blog/tag/pde/