Following this instruction, I could run headless Eclipse plugin in side Eclipse IDE.
An instance of headless Eclipse needs to include many plugins, not just your plugin. A minimal product includes:
org.eclipse.core.runtime
org.eclipse.core.variables
EDIT
I generated the product, and here is the list of plugins used by my "minimal" headless Eclipse:
I output the product, and here is the list of plugins loaded:
org.eclipse.core.contenttype_3.4.100.v20100505-1235.jar
org.eclipse.core.jobs_3.5.1.R36x_v20100824.jar
org.eclipse.core.runtime.compatibility.auth_3.2.200.v20100517.jar
org.eclipse.core.runtime.compatibility.registry_3.3.0.v20100520
org.eclipse.core.runtime_3.6.0.v20100505.jar
org.eclipse.equinox.app_1.3.1.R36x_v20100803.jar
org.eclipse.equinox.common_3.6.0.v20100503.jar
org.eclipse.equinox.launcher.win32.win32.x86_64_1.1.2.R36x_v20101222
org.eclipse.equinox.launcher_1.1.1.R36x_v20101122_1400.jar
org.eclipse.equinox.preferences_3.3.0.v20100503.jar
org.eclipse.equinox.registry_3.5.0.v20100503.jar
org.eclipse.osgi.services_3.2.100.v20100503.jar
org.eclipse.osgi.util_3.2.100.v20100503.jar
org.eclipse.osgi_3.6.2.R36x_v20110210.jar
So, might I recommend that you create a product for this Eclipse application you are building, and try that. Looking for a FAQ I found this. http://wiki.eclipse.org/FAQ_What_is_the_minimal_Eclipse_configuration%3F