Please describe the problem.

Even if -c annex.largefiles=nothing is used with git add, then git commit commits file into annex.

This script demonstrates initial finding: http://www.onerussian.com/tmp/ga.sh

Even if we use -c annex.largefiles=nothing with both add and commit, subsequent git status migrates that file into annex (which is even more weird)

Adjusted script demonstrates it: http://www.onerussian.com/tmp/ga-2.sh

What steps will reproduce the problem?

see above

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

6.20170101+gitg93d69b1-1~ndall+1

Please provide any additional information below.

For completeness here is the output of the 2nd script run:

$> /tmp/ga-2.sh
++ mktemp -d
+ d=/home/yoh/.tmp/tmp.WXTv2cULD0
+ echo 'directory: /home/yoh/.tmp/tmp.WXTv2cULD0'
directory: /home/yoh/.tmp/tmp.WXTv2cULD0
+ cd /home/yoh/.tmp/tmp.WXTv2cULD0
+ git init
Initialized empty Git repository in /tmp/tmp.WXTv2cULD0/.git/
+ git annex init --version=6
init  ok
(recording state in git...)
+ sed -i -e 's,pre-commit ,pre-commit --debug ,g' .git/hooks/pre-commit
+ echo 'I: creating a file'
I: creating a file
+ echo whatever
+ git -c annex.largefiles=nothing add file5
+ git annex lookupkey file5
+ echo 'not in annex as it should'
not in annex as it should
+ git annex find
+ ls -lR .git/annex/objects
ls: cannot access '.git/annex/objects': No such file or directory
+ :
+ git -c annex.largefiles=nothing commit -m sdf
[2017-01-27 09:43:27.569648245] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","diff","--cached","--name-only","-z","--diff-filter=ACMRT","--","."]
[2017-01-27 09:43:27.576498829] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","symbolic-ref","-q","HEAD"]
[2017-01-27 09:43:27.581039152] process done ExitSuccess
[2017-01-27 09:43:27.581134039] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","refs/heads/master"]
[2017-01-27 09:43:27.585093046] process done ExitFailure 1
[master (root-commit) 9ec3fe6] sdf
 1 file changed, 1 insertion(+)
 create mode 100644 file5
+ ls -lR .git/annex/objects
ls: cannot access '.git/annex/objects': No such file or directory
+ :
+ echo 'I: before git status'
I: before git status
+ ls -lR .git/annex/objects
ls: cannot access '.git/annex/objects': No such file or directory
+ :
+ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   file5

no changes added to commit (use "git add" and/or "git commit -a")
+ echo 'I: after git status'
I: after git status
+ ls -lR .git/annex/objects
.git/annex/objects:
total 0
drwx------ 3 yoh yoh 60 Jan 27 09:43 XF

.git/annex/objects/XF:
total 0
drwx------ 3 yoh yoh 60 Jan 27 09:43 pp

.git/annex/objects/XF/pp:
total 0
dr-x------ 2 yoh yoh 60 Jan 27 09:43 SHA256E-s9--cd293be6cea034bd45a0352775a219ef5dc7825ce55d1f7dae9762d80ce64411

.git/annex/objects/XF/pp/SHA256E-s9--cd293be6cea034bd45a0352775a219ef5dc7825ce55d1f7dae9762d80ce64411:
total 4
-rw------- 1 yoh yoh 9 Jan 27 09:43 SHA256E-s9--cd293be6cea034bd45a0352775a219ef5dc7825ce55d1f7dae9762d80ce64411
+ git diff
diff --git a/file5 b/file5
index 982793c..8fdffc0 100644
--- a/file5
+++ b/file5
@@ -1 +1 @@
-whatever
+/annex/objects/SHA256E-s9--cd293be6cea034bd45a0352775a219ef5dc7825ce55d1f7dae9762d80ce64411

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)

yeap