Following up on git-annex-import imports outside of directory (posting as a todo since the original bug was fixed):

When git-annex-import imports from a directory remote, if the tree being imported contains symlinks, import these symlinks into git as normal git symlinks. This way, the internal structure of the imported git tree mirrors the internal structure of the original tree, as it does when you archive the tree with tar or copy it with cp -r. If a tree gets imported with symlinks omitted, tools that expect files with specific names in specific subfolders may fail, if symlinks were used to meet these expectations in the original tree.

At least, relative symlinks pointing into the tree being imported should be preserved. This is the most common scenario; any reason not to include these?

Absolute symlinks pointing into the tree being imported should be turned into relative symlinks to the same target, so that they still work in the repo's checkouts.

Absolute symlinks pointing outside the tree are a harder case. I would still suggest importing these as git symlinks, pointing to the same absolute target path. As long as the repo is checked out into a filesystem where the same absolute paths are mounted, the links will work. That's a common scenario when all repo users use the same compute cluster with a shared filesystem.