How can I clean up Eclipse “run configurations”

Question

I set my java runtime options in Eclipse\'s Window > Prefs > Java > Installed JREs > Default VM Arguments. Since this setting is sufficient for all my main() entry

Answer 1

One simple way would be to organize your projects by Eclipse workspace, which would limit the "run configurations" list only to the project referenced in a given workspace.
Switching workspaces would reset that list to the ones recorded for the projects of the new workspace.

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Note: the OP's answer regarding launches file location isn't the only location possible.
The official one is:

${WORKSPACE}/.metadata/.plugins/org.eclipse.debug.core/.launches

But you can copy them enywhere else you want (as explained in "How do I save Eclipse launch profiles across workspaces?"), either by manually copying those files or by sharing them:
See "Which eclipse files belong under Version Control".

Once you know where they are saved, a simple delete is enough to make them disappear from the launcher menu.