Seems easy, but git ls-files can't list the right subset of files.
So, I wrote a whole new parser for git status output, and converted the
status command to use that.
There are a few other small behavior changes. The order changed. Unlocked
files show as T. In indirect mode, deleted files were not shown before, and
that's fixed. Regular files checked directly into git and modified
were not shown before, and are now.
i found that most man pages only had references to the main git-annex
manpage, which i stillfind pretty huge and hard to navigate through.
i tried to sift through all the man pages and add cross-references
between relevant pages. my general rule of thumb is that links should
be both ways unless one of the pages is a more general page that would
become ridiculously huge if all backlinks would be added
(git-annex-preferred-content comes to mind).
i have also make the links one per line as this is how it was done in
the metadata pages so far.
i did everything but the plumbing, utility and test commands, although
some of those are linked from the other commands so cross-links were
added there as well.
