I have a copy of a source controlled folder with a lot of changes that's not currently linked to our Source control.
The contents of both copies this folder have been heavily edited since the copy was taken and no I've to merge them somehow.
How can I merge a copy not linked to source control to a copy that is?
The procedure is simple:
Make sure you have an unmodifed repository state in your repository. Commit your modifications, if there are some.
In the repository: Update to the predecessor of the commit with which you want to merge your unversioned files.
Now copy all files of the unversioned directory into the working directory of your repository. Add the needed untracked files and commit the changes. This will result in a new head in the repository and you'll have at least two: your previously tracked one and the previously untracked ones
Now merge the two heads and solve any conflict in a manner which suits you.
It's always a good idea to keep a copy of things (both, original repository and unversioned directory) should things go differently than you bid for... it's easier to start anew than undo a commit or even an unwanted merge.