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I seem to have managed to create a branch that does not stem from the initial commit.
It seemed to happen when pulling changes from the repo. I have managed to get a point where my working branch has all the necessary commits, but my branch history is confusing.
Can I correct it?
Git does not require a single root commit. In fact, git.git itself has several root commits (it contains at least root commits for git‘s, gitk‘s and gitweb‘s history)
Since you have already merged successfully, there is no need to “fix” your history, Git will do the right thing™ during future merges.