Please describe the problem.

When adding plenty of files to my git annex repository, I encounter recurring sqlite errors.

What steps will reproduce the problem?

Create a git annex repo, add thousands of annexed binary files, and add thousands of small files tracked only with git.

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

>git annex version
git-annex version: 6.20171003
build flags: Assistant Webapp Pairing Testsuite S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify ConcurrentOutput TorrentParser MagicMime Feeds Quvi
dependency versions: aws-0.13.0 bloomfilter-2.0.1.0 cryptonite-0.10 DAV-1.2 feed-0.3.10.4 ghc-7.10.3 http-client-0.4.26.2 persistent-sqlite-2.2 torrent-10000.0.0 uuid-1.3.11 yesod-1.4.2
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external
local repository version: 6
supported repository versions: 3 5 6
upgrade supported from repository versions: 0 1 2 3 4 5
operating system: linux x86_64

>lsb_release -d
Description:    Ubuntu 16.04.3 LTS

>uname -r
4.4.0-43-Microsoft
#(I am using Bash on Windows.)

Please provide any additional information below.

# If you can, paste a complete transcript of the problem occurring here.
>git ls-files --others | grep txt | wc -l
1953
>git add $(git ls-files --others | grep txt)
sqlite worker thread crashed: SQLite3 returned ErrorIO while attempting to perform prepare "SELECT null from content limit 1": disk I/O error
git-annex: sqlite query crashed
error: external filter git-annex smudge --clean %f failed 1
error: external filter git-annex smudge --clean %f failed
# [...] plenty of errors follow
>git ls-files --others | grep txt | wc -l
1953
# End of transcript or log.

Triying to solve this problem, I found a part of answer in the form of a similar problem encountered here : https://git-annex.branchable.com/forum/Problem_with_corrupt_SQLite_DB/

Deleting git annex databases and running git annex fsck didnt do the trick:

rm -rf .git/annex/keys/db .git/annex/keys/db-wal
git annex fsck --incremental -J4
git add $(git ls-files --others | grep txt)
# Again, plenty of sqlite errors :()

It seems like a big overhead to add files tracked only by git in git annex repo. I know there are hooks/filters that catch and recover annexed files after modification but is it possible to disable these git annex hooks/filters when adding files that shouldn't be annexed ?

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)

Oh yeah, I am still discovering this powerfull git annex tool.

In fact, collegues and I are forming a group during the process to exchange about different use cases, encountered problems and help each other.