This may not be the whole answer to your problem but you can change the
runtime workspace used in Run -> Run ... -> Eclipse Application
Just click on the "Workspace...", "Filesystem..." or "Varables..." buttons
on the "main" page of the run dialog.
I would warn against running your plugins using your development workspace
(the one containing the source for your plugin) as your plugin may
inadvertantly change/damage/delete the source code you are working on!!
A better idea is to keep using a separate runtime workspace but preserve
the workspace between runtimes by unchecking "clear workspace data before
launching".
I recommend also looking at the approaches to test workspaces discussed in
the book "Contributing to Eclipse" by Gamma & Beck: