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Ask project to gitlab management, there are two branches, merge how to deal with?

Time:04-13

1. Master the main branch is SSM version of the program, is currently in use is this version
2. About 2 months ago, I put the project to upgrade become springboot version, but there is no use, just plan future use
3. As a result of this project will market change function, many developers on the master version (SSM) to add, delete, modify the code
4. Because of the upgrade springboot version is 2 months ago, so now you need to code and SSM version is not the same as
5. Now there is a demand is the main branch to modify the code merge into the deputy branch (springboot version)
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
But I directly use the tortoise git the tools found directly to merge, problem a lot, such as a master of new contents, after the merger is not, and so on, I would like to inquire about
The right way to handle it, is one kind of go on? Or how
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