One issue I run into with long rebases is having to resolve redundant conflicts. Say I have a branch with a sequence of commits that keeps modifying a function, and the final commit removes the function entirely.
When I do rebase master, Git naively applies each of the commits in turn. That means I need to resolve each of these commits with the tip of master - even though ultimately that work is wasted.
What's a good way to deal with this situation? Perhaps I should just generate a single patch for the whole branch, and apply that against master? If so, is there any way to preserve some history? Thoughts, suggestions, etc.
You want to use git rerere combined with teaching the rerere database from historical commits using rerere-train.sh (you may already have it at /usr/share/doc/git/contrib/rerere-train.sh). This allows git to automatically use merge conflict resolutions learned from the history.
Warning: you're basically making git rewrite the source code by blindly using historical string replacements to fix the conflicting merge. You should review all conflicting merges after the rebase. I find that gitk works fine for this (it will show only conflict resolution as the patch for merges). I've had only good experiences with rerere, you might not be that lucky. Basically, if your history does contain broken merges (that is, merges that are technically incorrectly done and then later fixed in following commits), you do not want to train rerere from the version history, unless you want to have similarly broken merges done automatically for you. You can still enable rerere and be careful with future merges so you don't teach bad habits to it.
Long story short, you just run
git config --global rerere.enabled 1
bash /usr/share/doc/git/contrib/rerere-train.sh --all
followed by the rebase you really want to do and it should just magically work.
After you have enabled rerere globally, you no longer need to learn from the history in the future. The learning feature is required only for using rerere after the fact the conflict resolution is already done before enabling rerere.
PS. I found similar answer to another question: https://stackoverflow.com/a/4155237/334451