So I tested running eclipse -clean just after build, to verify the order
of bundles - and it looks like that calling that before initializer has
no effect - bundle numbers are exactly the same.

What I have noticed that in my original Eclipse (platform only) SWT has
number 153, but when I install more things using dropins, SWT gets
bigger numbers (774, 759).

I think that bundles get consistent numbers within one configuration
(shared or user) but consistency between those two is not maintained.

What is the best place to start code investigation/patching?

Regards,
Chris

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