To keep the work of the core devs as less as possible you should get your code rebased on master.
First update your github repo to current master:
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# in your FreeCAD source directory
# change to your master branch
git checkout master
git remote add fcmaster git://github.com/FreeCAD/FreeCAD/
# fetch the changes from github
git fetch fcmaster
# make your master branch follow the fetched master
git branch --set-upstream-to=remotes/fcmaster/master master
# pull the changes
git pull
# push the current master to your github
git push https://github.com/makkemal/FreeCAD.git
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# in future you only need to do the following to update your master branch on github (may be it works by leaving git fetch out too.)
git checkout master
git fetch fcmaster
git pull
git push https://github.com/makkemal/FreeCAD.git
Now you need to rebase your code on current master. Means your code base should not be revision 5560 but HEAD of master instead (
https://github.com/FreeCAD/FreeCAD, currently on 5793). For this it would be much more simpler for you if you would compile FreeCAD yourself. You do not need to know any of C++ for this. But it works without compiling FreeCAD yourself too. since you are not common with git I would not recomend usining git rebase for an automatic rebase. Means you need to do it by yourself.
# download the latest windows binary from
https://github.com/FreeCAD/FreeCAD/releases This is the base you should your code get rebased too. You will spend some time in coding to get your code to running on your new FreeCAD. If your code runs on the up to date FreeCAD you should push it on github again on exact the revision you are working with.
Up to date revisionID for windows dev is 5764. Start FreeCAD --> Help --> about --> click on copy to clipboard. Copy to an editor. The number behind hash is the commitID. The one we need to checkout in git, because it is the version your FreeCAD is based on. For an checkout you only need the first 7 character. For 5764 it should be eff2799
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# in your FreeCAD source directory
# make sure you are on master
git checkout master
# test the commitID by
git rev-list eff2799 | wc -l
# should be 5764
# checkout a new branch
git checkout -b predeformation2 eff2799
git status
# on branch predeformation2 nothing to commit
# now you just need to do what you did for before
# copy your code to the FreeCAD git source
git status
# on branch predeformation2 lots of canges to commit, all the stuff you changed
# add to index, commit and push to github
git add .
git commit -m "your_commit_message"
git push https://github.com/makkemal/FreeCAD.git predeformation2
Hope that helps. YEAH again lots of stuff, but I promise as soon as you are used to git you will be happy. Learning git is not that easy. But we all have been thought this
BTW: There have been changes in FEM resently. If I where you I would not take revision 5764 and waiting for the next Windows dev instead.