See if this helps

http://blogs.atlassian.com/2013/05/git-automatic-merges-with-server-side-hooks-for-the-win/

u may not be doing server side hooks, but u can write the similar script 
and invoke from pipeline.

On Thursday, February 9, 2017 at 11:31:48 AM UTC+5:30, Sharan Basappa wrote:
>
> The issues is, the files generated during testing cannot be predicted and 
> can keep changing. Also, even if I put them in Git ignore, how would 
> checkout still work as the files are still local to my repo branch? 
>
> On 9 Feb 2017 11:17 a.m., "Indra Gunawan (ingunawa)" <[email protected] 
> <javascript:>> wrote:
>
>> I would recommend that you include these files in a .gitignore so they 
>> are ignored by git.
>>
>>  
>>
>> -Indra
>>
>>  
>>
>> *From: *<[email protected] <javascript:>> on behalf of Sharan 
>> Basappa <[email protected] <javascript:>>
>> *Reply-To: *"[email protected] <javascript:>" <
>> [email protected] <javascript:>>
>> *Date: *Wednesday, February 8, 2017 at 6:27 PM
>> *To: *Jenkins Users <[email protected] <javascript:>>
>> *Subject: *Pipeline - merge and push
>>
>>  
>>
>>  
>>
>> I have created a pipeline script. The pipeline script runs in a 'topic' 
>> branch (e.g. my_feature).
>>
>> Once test stage is successful, I would like to merge this into the master 
>> branch and then push the changes to remote.
>>
>>  
>>
>> However, I have some doubts. My test stage creates many intermediate 
>> files that would not be checked-in but are necessary for debug and analysis.
>>
>> So, in order to merge, I need to first checkout the master branch. Doing 
>> this creates issue as I have untracked files.
>>
>> But if I do git clean, I lose important log files that I might need for 
>> the next few days.
>>
>> How can I handle this? Would git stash help in this case?
>>
>>  
>>
>> Thanks,
>>
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