In the world of git, we're not scared about internal implementation details, and sometimes we like to dive in and tweak things by hand. Here's some documentation to that end.

The .git/ directory


This is where locally available file contents are actually stored. Files added to the annex get a symlink checked into git that points to the file content.

First there are two levels of directories used for hashing, to prevent too many things ending up in any one directory. See hashing for details.

Each subdirectory has the name of a key in one of the key-value backends. The file inside also has the name of the key. This two-level structure is used because it allows the write bit to be removed from the subdirectories as well as from the files. That prevents accidentally deleting or changing the file contents. See lockdown for details.

In direct mode, file contents are not stored in here, and instead are stored directly in the file. However, the same symlinks are still committed to git, internally.

Also in direct mode, some additional data is stored in these directories. .cache files contain cached file stats used in detecting when a file has changed, and .map files contain a list of file(s) in the work directory that contain the key.


This directory contains partially transferred objects.


This is a temp directory for miscellaneous other temp files.

While .git/annex/objects and .git/annex/tmp can be put on different filesystems if desired, .git/annex/misctmp has to be on the same filesystem as the work tree and git repository.


git-annex fsck puts any bad objects it finds in here.


Contains information files for uploads and downloads that are in progress, as well as any that have failed. Used especially by the assistant. It is safe to delete these files.


ssh connection caching files are written in here. It is safe to delete these files.


This is a git index file which git-annex uses to stage files when preparing commits to the git-annex branch.

It's pretty safe to delete this file if git-annex is not currently running. It will be re-created as necessary.


git-annex uses this to journal changes to the git-annex branch, before committing a set of changes.

The git-annex branch

This branch is managed by git-annex, with the contents listed below.

This branch is not connected to your master, etc branches. It it used for internal tracking of information about git-annex repositories and annexed objects.

The files stored in this branch are all designed to be auto-merged using git's union merge driver. So each line has a timestamp, to allow the most recent information to be identified.


Records the UUIDs of known repositories, and associates them with a description of the repository. This allows git-annex to display something more useful than a UUID when it refers to a repository that does not have a configured git remote pointing at it.

The file format is simply one line per repository, with the uuid followed by a space and then the description, followed by a timestamp. Example:

e605dca6-446a-11e0-8b2a-002170d25c55 laptop timestamp=1317929189.157237s
26339d22-446b-11e0-9101-002170d25c55 usb disk timestamp=1317929330.769997s


Records the global numcopies setting.

The file format is simply a timestamp followed by a number.


Holds persistent configuration settings for special remotes such as Amazon S3.

The file format is one line per remote, starting with the uuid of the remote, followed by a space, and then a series of var=value pairs, each separated by whitespace, and finally a timestamp.

Encrypted special remotes store their encryption key here, in the "cipher" value. It is base64 encoded, and unless shared encryption is used, is encrypted to one or more gpg keys. The first 256 bytes of the cipher is used as the HMAC SHA1 encryption key, to encrypt filenames stored on the special remote. The remainder of the cipher is used as a gpg symmetric encryption key, to encrypt the content of files stored on the special remote.


Records the trust information for repositories. Does not exist unless trust values are configured.

The file format is one line per repository, with the uuid followed by a space, and then either 1 (trusted), 0 (untrusted), ? (semi-trusted), X (dead) and finally a timestamp.


e605dca6-446a-11e0-8b2a-002170d25c55 1 timestamp=1317929189.157237s
26339d22-446b-11e0-9101-002170d25c55 ? timestamp=1317929330.769997s

Repositories not listed are semi-trusted.


Used to group repositories together.

The file format is one line per repository, with the uuid followed by a space, and then a space-separated list of groups this repository is part of, and finally a timestamp.


Used to indicate which repositories prefer to contain which file contents.

The file format is one line per repository, with the uuid followed by a space, then a boolean expression, and finally a timestamp.

Files matching the expression are preferred to be retained in the repository, while files not matching it are preferred to be stored somewhere else.


Used to indicate which repositories are required to contain which file contents.

File format is identical to preferred-content.log.


Contains standard preferred content settings for groups. (Overriding or supplementing the ones built into git-annex.)

The file format is one line per group, staring with a timestamp, then a space, then the group name followed by a space and then the preferred content expression.


These log files record location tracking information for file contents. These are placed in two levels of subdirectories for hashing. See hashing for details.

The name of the key is the filename, and the content consists of a timestamp, either 1 (present) or 0 (not present) or X (dead), and the UUID of the repository that has or lacks the file content.


1287290776.765152s 1 e605dca6-446a-11e0-8b2a-002170d25c55
1287290767.478634s 0 26339d22-446b-11e0-9101-002170d25c55


These log files record urls used by the web special remote and sometimes by other remotes. Their format is similar to the location tracking files, but with urls rather than UUIDs.


These log files are used by remotes that need to record their own state about keys. Each remote can store one line of data about a key, in its own format.


1287290776.765152s e605dca6-446a-11e0-8b2a-002170d25c55 blah blah
1287290767.478634s 26339d22-446b-11e0-9101-002170d25c55 foo=bar


These log files are used to store arbitrary metadata about keys. Each key can have any number of metadata fields. Each field has a set of values.

Lines are timestamped, and record when values are added (field +value), but also when values are removed (field -value). Removed values are retained in the log so that when merging an old line that sets a value that was later unset, the value is not accidentally added back.

For example:

1287290776.765152s tag +foo +bar author +joey
1291237510.141453s tag -bar +baz

The value can be completely arbitrary data, although it's typically reasonably short. If the value contains any whitespace (including \r or \n), it will be base64 encoded. Base64 encoded values are indicated by prefixing them with "!".


These log files are used when objects are stored in chunked form on remotes. They record the size(s) of the chunks, and the number of chunks.

For example, this logs that a remote has an object stored using both 9 chunks of 1 mb size, and 1 chunk of 10 mb size.

1287290776.765152s e605dca6-446a-11e0-8b2a-002170d25c55:10240 9
1287290776.765153s e605dca6-446a-11e0-8b2a-002170d25c55:102400 1

(When those chunks are removed from the remote, the 9 is changed to 0.)


Used to record scheduled events, such as periodic fscks.

The file format is simply one line per repository, with the uuid followed by a space and then its schedule, followed by a timestamp.

There can be multiple events in the schedule, separated by "; ".

The format of the scheduled events is the same described in git-annex-schedule.


42bf2035-0636-461d-a367-49e9dfd361dd fsck self 30m every day at any time; fsck 4b3ebc86-0faf-4892-83c5-ce00cbe30f0a 1h every year at any time timestamp=1385646997.053162s


Used to record the times of activities, such as fscks.


42bf2035-0636-461d-a367-49e9dfd361dd Fsck timestamp=1422387398.30395s


Used to record transitions, eg by git annex forget

Each line of the file is a transition, followed by a timestamp.


ForgetGitHistory 1387325539.685136s
ForgetDeadRemotes 1387325539.685136s


Used when a repository has fundamental differences from other repositories, that should prevent merging.


e605dca6-446a-11e0-8b2a-002170d25c55 [ObjectHashLower] timestamp=1422387398.30395s