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+Git-annex supports a wide variety of workflows, a spectrum that ranges from completely automatic behavior where git-annex handles everything, through manual behavior where git-annex does only what you say, when you tell it to, down to internal behavior, where you have complete control and understand how everything is stored and exactly what changes are happening.
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+I will proceed to summarize all of these. Your question sounds like a high-level question, so I will begin at the automatic end, hoping that this is most useful, and drill down to the low level approaches. Note, however, that this the opposite order of how git-annex was apparently developed. A list of workflows that started from manual, commandline usage would be much more intuitive, but you'd have to be willing to read the man page and wiki pages to get started, and that's pretty much what's already out there anyway.
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+Note that for each of these levels of interaction, all the levels following will also work as well. So you can actually manually move annexed files around while the webapp is running, etc.
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+(0) git annex webapp. This command launches a local web server which serves a graphical user interface and automatically manages git annex. It will attempt to guide you through the whole process and do everything for you. I think the intent is that no other commands are needed. This should be run on every machine that may produce file changes.
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+(1) git annex assistant without running the webapp. You could call this the command-line version of the webapp, giving you more control over creating and connecting your repositories, and configuring how files are moved between them. The assistant, when running, will automatically watch for file changes and synchronize them to other repositories, but you must manually create the repositories and configure the rules for syncing. To create a repository, use git init and then git annex init, and then git remote add it to any other repositories. If you want more than one annex, you can add their paths to ~/.config/git-annex/autostart if you would like them to automatically begin syncing when git annex assistant --autostart is run, perhaps on boot or login. You can configure rules for where files are copied using the repository setup commands such as preferred content expressions, git annex numcopies, and git config annex.largefiles; most of the settings are accessible in one place with git annex vicfg.
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+(2) git annex watch without running the assistant. This command is like the assistant but has no automatic network behavior, giving you complete control over when repositories are pushed and pulled, and when files are moved between systems. The repository is watched, and any file changes are added to git-annex. In order to synchronize between repositories, you must run git annex sync --content in the repository with the changes, which will merge the git history and logs with your remotes, and automatically transfer files to match your preferred and required content expressions.
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+(3) No background processes, allowing you to decide when and what files are annexed. In order to tell git-annex to manage files, you must git annex add the files.
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+(4) Plain git annex sync without --content, giving you fine-grained control of where copies of your files are stored. This tells git-annex to merge git histories, but it does not automatically transfer your large files between systems. To transfer files and directories, you can use git annex get, git annex drop, git annex move, and git annex copy. Git-annex will not violate a required content expression or your numcopies setting unless you pass --force, so your files are still safe. This is the workflow I mostly use, and I find it the most stable. I'm trying to migrate up to --content, but I have too many large files that haven't reached their numcopies yet for that to be effective.
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+(5) Manual management of git history without running the syncronizer, allowing you to control precisely what is committed, what commit message is used, and how your history is merged between repositories. You must have an understanding of git, and run git commit after git annex add to store the change. You must manage the git history yourself, using git pull and git push, to synchronize repositories. You may freely use git normally side-by-side with git-annex.
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+(6) Manual management of git annex keys, giving you control of what and where git annex stores your files under the hood, and how they are associated with your working tree, rather than using the git annex add and git annex get commands which reference files automatically. Git-annex has a variety of plumbing commands listed in the man page that let you directly store and retrieve data in an annex associated with your git repository, where every datafile is enumerated by a unique hashkey.