You cannot in a simple way.
What I'm doing usually (when i want to work on top of synergies) is this :
I create a first mod, in which are included all the Synergies files. This allows me to do whatever change I want, even if it uses Synergies files, because all the bindings are there.
Then I create a second mod, in which there is no Synergies file. But, I look at the modification date, and include there (this means copy/pasting basically) all the text files (the binary ones are automatically generated - only text files matter) that have been created or modified by my session.
This way, I develop on the first mod, and I release the second mod. And the second mod contains only the files you have created/modified.
This means that users still need Synergies to run your mod (otherwise, there might be some weird issue - like the game not finding an ability, and replacing it by a default one for example). But the big advantage is that you don't include Synergies in your mod, so people don't have the extra 50 MB to download everytime.