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better index file refresh method

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Use git update-index --refresh, since it's a little bit more
efficient and the user can be told to run it if a locked index prevents
git-annex from running it.

This also fixes the problem where an annexed file was deleted in the index
and a get of another file that uses the same key caused the index update to
add back the deleted file. update-index will not add back the deleted file.

Documented in tips/unlocked_files.mdwn the gotcha that the index update
may conflict with other operations. I can't see any way to possibly avoid
that conflict.

One new todo about a race that causes a modification to be accidentially
staged.

Note that the assistant only flushes the git command queue when it
commits a modification. I have not tested the assistant with v6 unlocked
files, but assume most users of the assistant won't care if the index
shows a file as modified for a while.

This commit was supported by the NSF-funded DataLad project.
This commit is contained in:
Joey Hess 2018-08-16 13:51:32 -04:00
parent 5e87389f40
commit 82cfcfc838
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19
doc/tips/unlocked_files.mdwn
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@ -110,6 +110,23 @@ to having them all unlocked, you can do so using `git annex adjust
useful when using filesystems like FAT, and OS's like Windows that don't
support symlinks.
## index gotchas
When git-annex gets or drops the content of an unlocked file, it updates
the file in git's worktree accordingly. Then it needs to update the index
file to reflect the change. Otherwise, `git status` would show the file
as modified, even though there are no changes to commit.
This means that when git-annex is running a command that gets or drops the
content of an unlocked file, the index will sometimes be locked. This might
prevent you from `git commit` at the same time. Or, if you have a git
commit in progress, or are running multiple git-annex processes, git-annex
may complain that the index is locked.
To manually update the index when git-annex was not able to, you can run:
git update-index -q --refresh $file
## using less disk space
Unlocked files are handy, but they have one significant disadvantage
@ -154,7 +171,7 @@ So, using `git checkout` to check out a different branch, or even
working tree, and using more disk space. A warning will be printed out in
this situation. You can always run `git annex fix` to re-thin such files.
## tradeoffs
## annex.thin tradeoffs
[[!template id=note text="""
When a [[direct_mode]] repository is upgraded, annex.thin is automatically