If I understand you correctly, you want to install the plug-in in the "unpacked" form rather than in the "jar" form. This way the folders of the plug-in project in the Eclipse IDE, will also be "physical" folders when the plug-in is installed in an Eclipse framework.
This can be accomplished in a number of ways, whether the most portable currently seems to be to add the line
Eclipse-BundleShape: dir to the
MANIFEST.MF file. (Some tools - most notably Tycho - does not understand the alternatives.)