Try the following commands at first (re-run again if needed):
$ git fsck --full
$ git gc
$ git gc --prune=today
$ git fetch --all
$ git pull --rebase
And then you you still have the problems, try can:
remove all the corrupt objects, e.g.
fatal: loose object 91c5...51e5 (stored in .git/objects/06/91c5...51e5) is corrupt
$ rm -v .git/objects/06/91c5...51e5
remove all the empty objects, e.g.
error: object file .git/objects/06/91c5...51e5 is empty
$ find .git/objects/ -size 0 -exec rm -vf "{}" \;
check a "broken link" message by:
git ls-tree 2d9263c6d23595e7cb2a21e5ebbb53655278dff8
This will tells you what file the corrupt blob came from!
to recover file, you might be really lucky, and it may be the version that you already have checked out in your working tree:
git hash-object -w my-magic-file
again, and if it outputs the missing SHA1 (4b945..) you're now all done!
assuming that it was some older version that was broken, the easiest way to do it is to do:
git log --raw --all --full-history -- subdirectory/my-magic-file
and that will show you the whole log for that file (please realize that the tree you had may not be the top-level tree, so you need to figure out which subdirectory it was in on your own), then you can now recreate the missing object with hash-object again.
to get a list of all refs with missing commits, trees or blobs:
$ git for-each-ref --format='%(refname)' | while read ref; do git rev-list --objects $ref >/dev/null || echo "in $ref"; done
It may not be possible to remove some of those refs using the regular branch -d or tag -d commands, since they will die if git notices the corruption. So use the plumbing command git update-ref -d $ref instead. Note that in case of local branches, this command may leave stale branch configuration behind in .git/config. It can be deleted manually (look for the [branch "$ref"] section).
After all refs are clean, there may still be broken commits in the reflog. You can clear all reflogs using git reflog expire --expire=now --all. If you do not want to lose all of your reflogs, you can search the individual refs for broken reflogs:
$ (echo HEAD; git for-each-ref --format='%(refname)') | while read ref; do git rev-list -g --objects $ref >/dev/null || echo "in $ref"; done
(Note the added -g option to git rev-list.) Then, use git reflog expire --expire=now $ref on each of those.
When all broken refs and reflogs are gone, run git fsck --full in order to check that the repository is clean. Dangling objects are Ok.
Below you can find advanced usage of commands which potentially can cause lost of your data in your git repository if not used wisely, so make a backup before you accidentally do further damages to your git. Try on your own risk if you know what you're doing.
To pull the current branch on top of the upstream branch after fetching:
$ git pull --rebase
You also may try to checkout new branch and delete the old one:
$ git checkout -b new_master origin/master
To find the corrupted object in git for removal, try the following command:
while [ true ]; do f=`git fsck --full 2>&1|awk '{print $3}'|sed -r 's/(^..)(.*)/objects\/\1\/\2/'`; if [ ! -f "$f" ]; then break; fi; echo delete $f; rm -f "$f"; done
For OSX, use sed -E instead of sed -r.
Other idea is to unpack all objects from pack files to regenerate all objects inside .git/objects, so try to run the following commands within your repository:
$ cp -fr .git/objects/pack .git/objects/pack.bak
$ for i in .git/objects/pack.bak/*.pack; do git unpack-objects -r < $i; done
$ rm -frv .git/objects/pack.bak
If above doesn't help, you may try to rsync or copy the git objects from another repo, e.g.
$ rsync -varu git_server:/path/to/git/.git local_git_repo/
$ rsync -varu /local/path/to/other-working/git/.git local_git_repo/
$ cp -frv ../other_repo/.git/objects .git/objects
To fix the broken branch when trying to checkout as follows:
$ git checkout -f master
fatal: unable to read tree 5ace24d474a9535ddd5e6a6c6a1ef480aecf2625
Try to remove it and checkout from upstream again:
$ git branch -D master
$ git checkout -b master github/master
In case if git get you into detached state, checkout the master and merge into it the detached branch.
Another idea is to rebase the existing master recursively:
$ git reset HEAD --hard
$ git rebase -s recursive -X theirs origin/master
See also:
.gitfolder of course) into the freshly cloned repo... and then didgit statusin the new repo... git correctly detects all affected changes to my files and I can start my work again. – Wetzel