You can obtain the Menu from the MenuManager and then modify the contributions. This snippet shows how to access the menu manager and remove a named item.
You'll need to keep track of the removed items and item indices to restore them. The only trouble is that the indexOf method is not visible. Adding this snippet to a type in the same package as MenuManager and adding it to a fragment is one way round that.
IWorkbenchWindow window = Workbench.getInstance().getActiveWorkbenchWindow()
if(window instanceof WorkbenchWindow) {
MenuManager menuManager = ((WorkbenchWindow)window).getMenuManager();
//TODO you may need to remove items from the coolbar as well
ICoolBarManager coolBarManager = null;
if(((WorkbenchWindow) window).getCoolBarVisible()) {
coolBarManager = ((WorkbenchWindow)window).getCoolBarManager2();
}
Menu menu = menuManager.getMenu();
//you'll need to find the id for the item
String itemId = "menuId";
IContributionItem item = menuManager.find(itemId);
// remember position, TODO this is protected
int controlIdx = menu.indexOf(mySaveAction.getId());
if (item != null) {
// clean old one
menuManager.remove(item);
// refresh menu gui
menuManager.update();
}
}