Could it be that this is the 
solution? 
http://stackoverflow.com/questions/42798006/how-to-disable-automatic-build-from-scm-change-in-jenkinsfile
The flow in my case is:

PR to GHE > GHE sends pull_request webhook to Jenkins > Jenkins uses the 
Jenkinsfile to run unit tests > Jenkins makes a call to merge the PR to the 
master branch.
The merge to the master branch is essentially a push webhook, so: GHE sends 
a push webhook to Jenkins > Jenkins uses the same Jenkinsfile to run again 
unit tests > there is logic to not-merge in case the branch is the master 
branch > Instead publish to npm > bump the version number > commit & push 
to git.

This time because the the whole thing worked from a checkout of the master 
branch and not based on a PR, the option to "Suppress automatic SCM 
triggering" should hopefully stop the loop from starting...

On Thursday, March 23, 2017 at 4:09:09 PM UTC+2, Idan Adar wrote:
>
> Unfortunately I am not versed enough in programming to add this 
> functionality... 
>
> I think that the workaround will add lots of "red rows" in the job view, 
> because it first has to checkout the repo, check the messages and then 
> abort...
>
> On Thursday, March 23, 2017 at 3:59:07 PM UTC+2, Mark Waite wrote:
>>
>> The git plugin as used in pipeline doesn't support ignoring commits from 
>> certain users, or ignoring commits with certain messages.  Until it does, 
>> you will probably need to "short circuit" and exit from the pipeline after 
>> using git commands to extract the latest commit message from the 
>> repository.  It's not a pretty solution, but it can work now.
>>
>> Another alternative is to fork the git plugin and add the "ignore commits 
>> from specific user" support to the pipeline.
>>
>> Mark Waite
>>
>> On Thu, Mar 23, 2017 at 7:43 AM Idan Adar <[email protected]> wrote:
>>
>>> I should add that the job is of multibranch type.
>>>
>>>
>>> On Thursday, March 23, 2017 at 3:10:51 PM UTC+2, Idan Adar wrote:
>>>>
>>>> Hi all,
>>>>
>>>> In a declarative pipeline (a Jenkinsfile in the repo), how can I stop a 
>>>> job from getting re/triggered due to a push event in GitHub?
>>>> For example:
>>>>
>>>> stage ("Publish to npm") {
>>>>    steps {
>>>>       sh '''
>>>>          npm publish
>>>>          npm --no-git-tag-version version minor
>>>>       '''
>>>>       
>>>>       sh '''
>>>>          git commit -am 'Bumped version number'
>>>>          git push
>>>>       '''
>>>>    }
>>>> }
>>>>
>>>> The "git push" will trigger the push webhook in GitHub that makes a 
>>>> call to Jenkins, which will in turn start the same Jenkinsfile and again 
>>>> bump the version, commit, push and again... a loop.
>>>> How can we not-trigger the job in this scenario?
>>>>
>>>>
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