Here are two options I have used so far:

== Two PRs

- create one PR against branch "master"
- create a second PR against "master-legacy-version" into which you cherry-pick 
the changes from the first PR

== Merging branches (this is the one I usually use)

- this requires that "master" and "master-legacy-version" have some common 
history
- tell git that all changes against "master-legacy-version" have been merged 
into master by calling "git merge -s ours master-legacy-version" on a 
checked-out "master"
- create a PR against the "master-legacy-version" and merge it
- repeat for other PRs if you like
- merge the "master-legacy-version" into master (or create a PR to do this 
merge if you cannot push to master directly)

Considering what you write, I think you'd also like to go with option 2. I use 
option 1 usually only if I accidentally did a bugfix PR against master which 
should have gone into "master-legacy-version"

For uimaFIT, I have so-far used only option 1 but it is tedious. I'd prefer 
switching to option 2 at some point.

-- Richard

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