Cherry picking changes to specific files from a range of commits

So if I understand you correctly, what you want to do first is cherry pick the range, i.e. git cherry-pick --no-commit. Then, remove the changes to your index with git reset. Then git add all of the files you want to commit, git commit those files, and finally git checkout . to get rid of the other local changes. This will result in a single, flattened commit that contains your changes.

Now, if instead what you want to do is include just those commits that have touched a particular set of files, you may want to take a look at an example given towards the bottom of this page that uses git rev-list to feed a list of all commits that have touched a particular filespec to cherry-pick. So if, for example, all your files were in mydir, something like git rev-list --reverse master -- mydir | git cherry-pick --stdin should do it.

If there is a single commit that you used to merge in, that you can avoid, then use git rebase to skip the merging commit.

-----origin/foo-------A----------------------------B----C----D (where you merged in) (commits on top of that) AFTER REBASE -----origin/foo-------B'----C'----D' (your commits, skipping A) 

If instead your changes (B, C, and D above) actually touch the files you're trying to avoid, you'll need to use git filter-branch to rewrite those commits and avoid changing those files. Using the --tree-filter command, you can reset the part of each tree that you don't want to touch.