### Please describe the problem.

I'm starting to slowly migrate my personal data collection (530GB 3.7M files) under git-annex.  I'm going piece by piece, and not yet giving up my other synchronization methods (yet); thus I need to stay in direct mode.  

I initially found that `git annex` commands [were quite slow](https://github.com/datalad/datalad/issues/17), but I was able to address that by adding all my "not yet included" directories to `.gitignore` at the root of the working tree.  Unfortunately, `git annex proxy` remains super slow, because I notice that it does not include `--exclude-standard` in its calls to ls-files, and thus does not respect `.gitignore`.  Here's an example from the `--debug` log:

```
 read: git ["--git-dir=../../../../../.git","--work-tree=../../../../..","--literal-pathspecs","-c","core.bare=false","ls-files","--others","-z","--","../../../../.."]
```

As a result, I was very shocked to learn that (25 min later), `git annex proxy` was still setting up, and had duplicated 140GB of untracked files!

My end goal is actually just to add files directly to the git repo, bypassing the annex, in spite of being in direct mode.  (I can do this with the largefiles attribute, but I'd like to be able to control it directly irrespective of size.)

### What steps will reproduce the problem?

```
git annex proxy --debug -- git commit myfile -m foo
```

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

Version 6.20170520 on Mac OS 10.13.4.

### Please provide any additional information below.

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log


# End of transcript or log.
"""]]

### 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)

Today is my first day trying it out!  It's fabulous so far, but I'm at the beginning of the learning curve.

