Please describe the problem.
Originally spotted/reported: https://github.com/datalad/datalad/issues/1020
If that is mandatory, then I guess there should be some error message.
What steps will reproduce the problem?
create a remote repo without specifying version, i.e. of version 5 and copy data into it
What version of git-annex are you using? On what operating system?
6.20160923+gitgd1dabb3-1~ndall+1
Please provide any additional information below.
Output from running http://www.onerussian.com/tmp/v6-push.sh with argument which specifies annex version within remote
$> ./v6-push.sh 5 2>&1 | grep '>>>'
>>> /annex/objects/SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat
>>> /annex/objects/SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat
$> ./v6-push.sh 6 2>&1 | grep '>>>'
>>> /annex/objects/SHA256E-s4--181210f8f9c779c26da1d9b2075bde0127302ee0e3fca38c9a83f5b1dd8e5d3b.dat
>>> 123
The data loss bugs are fixed in ee309d694161d0f416420db6c4efb834c813351e.
I am not sure yet why the keys database lacked an entry for the file; perhaps something to do with it being a v6 unlocked file in a v5 repository.
Ok.. Seems that cloning to a v5 repository, and then copying/getting objects into it, and then upgrading to v6 reproduces the problem with the keys database. The inode cache does not get populated for unlocked files on upgrade. Also, unlocked files stay as pointer files even when their content is present in annex/objects. Fixed the upgrade process to handle this case.