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You can't use unstable, as it doesn't have any 3.0 breaking API changes. The 3.x branch needs to be merged onto master and unstable when 3.0 is released.
Extensions that already work OK on 3.0 can be released as a new minor release with the dependency updated to something like cytoscape: '^2.4 | ^3.0'. Small changes that can easily support both versions can do the same (e.g. event.target || event.cyTarget).
Where the extension could work on 3.0 only by breaking support for 2.x, we'll need to make the changes in a cytoscape3 branch. The branch can be merged in for each of those extensions after 3.0 is officially released.
Probably most extensions will need little or no changes to work with 3.0
@maxkfranz Also found that for 3.x after calling the layout function, you need to add a .run() in order to make the layout function actually work. In 2.x, this appears to be done for you so .run() is not required. Is this intentional? See cytoscape/cytoscape.js-automove@b7972e0 for example. This is a breaking change and applies to all the built-in layouts (eg. circle etc.).
Otherwise I am done with all the extensions, which are all backwards compatible.