### Please describe the problem.

I'm testing whether I can use git-annex to sync binary files to a windows vm (used for development) with v6 adjusted branches.

For testing I use git-annex precompiled binaries for windows, together with git from [msys2](https://sourceforge.net/projects/msys2/), an environment similar to cygwin (it does the usual hacks with path translation, etc).

It seems to more or less work for syncing content from my linux box to the vm, apart from some unexplained clean/smudge errors, which I'll investigate later.

However, when I commit to the adjusted branch in the windows vm, and afterwards do a `git annex sync` to propagate changes to the unadjusted `master`, a broken link for the annexed file `A/B` ends up at the root of the repository in the unadjusted branch.


### What steps will reproduce the problem?

On windows under msys2 do the following:

* Create a v6 annex repo with an adjusted branch.
* Annex a file in a subdirectory, for example `A/B`.
* Commit to the adjusted branch.
* Propagate changes to the original branch.

A file `B` appears in the non-adjusted branch, instead of `A/B`, with broken link (as if it still were in A/B).

### What version of git-annex are you using? On what operating system?

git annex 6.20160418 windows precompiled binaries on windows 10 under msys2. msys2 git is 2.8.1. I haven't tested with other windows git distributions.


### Please provide any additional information below.

Here is a shell transcript while reproducing this

[[!format sh """
$ mkdir test; cd test
$ git init
$ git annex init --version=6
# it automatically puts you in an adjusted master, because of crippled filesystem...
$ git branch
* adjusted/master(unlocked)
  git-annex
  master

$ mkdir A
$ echo "b" > A/B
$ git annex add A/B
$ git commit -m 'annexed A/B'
$ git ls-tree -r --name-only 'adjusted/master(unlocked)'
A/B
$ git ls-tree -r --name-only 'master'

$ git annex sync
commit
On branch adjusted/master(unlocked)
nothing to commit, working directory clean
ok

$ git ls-files -r --name-only 'adjusted/master(unlocked)'
A/B
$ git ls-files -r --name-only 'master'
B
"""]]

### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

Well, git-annex is wonderful!

I use it to sync binary files across linux boxes, I use it for binary distro packages I compile for myself, for my calibre books, pictures, movies...  and I'm very happy with it on linux.

> [[fixed|done]] --[[Joey]]