Upgrade other repos than the current one by running git-annex upgrade
inside them, which avoids problems with upgrade code making assumptions
that the cwd will be inside the repo being upgraded.
In particular, this fixes a problem where upgrading a v7 repo to v8 caused
an ugly git error message.
I actually could not find a way to make Upgrade.V7 work properly
without changing directory to the remote. Once I got git ls-files to work,
the git cat-file failed because :path can only be used in the current git
repo.
Can be set to false to prevent any automatic repository upgrades.
Also, removed direct mode specific upgrade code in Annex.Init, and made
needsUpgrade always include the name/path of the repo, so if
there's a problem it's clear what repo has the problem.
And, made needsUpgrade catch any exceptions that might occur during the
upgrade, so it can display a more useful error message than just the
exception.
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.
