Jack,
Unfortunately there are no places to hook into the deployment process. I’ve been informed, especially now with all the complex support for project dependencies, linked resources and the like, that opening up the deployment process could potentially become a huge can of worms (e.g. “No I don’t want to hook in AFTER its done XYZ, I need to do it BEFORE” or “I want to hook in WHILE its processing the ABC list”).
Unfortunately this leaves you to manually run your substitution scripts before deploying, which I know can get very tedious. If this proves to make MyEclipse painful to use and is not helping you get work done, please let us know in detail what your situation is and what kind of functionality you would need, and we can try and see what we can do.
Right now for the 2.8 release our feature-list is pretty full to the brim, but that isn’t to say this can’t be something that will be in 3.9 or later.