There is a bug reported against Sourcetree that when doing a subtree pull it puts the new files/folders under the root of the repository instead of under the subtree. The original bug is SRCTREEWIN-1621 and I was going to create a new one and link it to this one since I see this issue when using Sourcetree 3.0.15, but all I see when trying to create the bug is this:
If you do the pull from git bash it adds it correctly under the subtree as expected. From what I see from within Sourcetree it looks like it ignores the local relative path as the starting point for the merge and instead uses the path that is coming from the subtree repository.
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