How to fix corrupted git repository

Question

I tried cloning my repository which I keep on my Ubuntu one folder to a new machine and I got this   christopher christopher-laptop   source personal  git clone   Ubuntu  One  Side  Work projects git  Cloning into  projects     done  fatal  unable to read tree 29a422c19251aeaeb907175e9b3219a9bed6c616 christopher christopher-laptop   source personal     So I tried looking at the many other questions like this that have been asked here and most of them say to run git fsck --full and then I get this when I try that   christopher christopher-laptop   Ubuntu One Side Work projects git  git fsck --full Checking object directories  100   256 256   done  Checking objects  100   447 447   done  broken link from  commit 235ae1f48701d577d71ebd430344a159e5ba4881               to  commit 984c11abfc9c2839b386f29c574d9e03383fa589 broken link from    tree 632a9cf0ef9fccea08438b574e2f1c954f4ff08b               to    blob 25a742dff0a403b2b3884f2ffddf63eb45721fac broken link from    tree 632a9cf0ef9fccea08438b574e2f1c954f4ff08b               to    blob dd4e97e22e159a585b20e21028f964827d5afa4e broken link from    tree 632a9cf0ef9fccea08438b574e2f1c954f4ff08b               to    tree 29a422c19251aeaeb907175e9b3219a9bed6c616 broken link from    tree 632a9cf0ef9fccea08438b574e2f1c954f4ff08b               to    tree 8084e8e04d510cc28321f30a9646477cc50c235c broken link from    tree 774b5b4157b4caae1c6cad96c8eaf5d4eba2c628               to    blob a0daa0c1567b55d8de2b4d7a3bc010f58c047eab broken link from    tree 774b5b4157b4caae1c6cad96c8eaf5d4eba2c628               to    blob e9052d35bfb6d30065b206fc43f4200a04d5281b broken link from    tree 774b5b4157b4caae1c6cad96c8eaf5d4eba2c628               to    blob 1a3a5e4dd2502ac121c22f743c4250e254a94eeb broken link from    tree 4aa336dc1a5838e8918e03b85580069d83f4ad09               to    tree 8cc55ec952dc192a233e062201d1e7e873ac3db0 broken link from    tree e5674a91a53e15575a1f3bf5786bc5cc719fb483               to    blob 4a994e1e7bb7ce28dcec98bad48b9a891d7dec51 broken link from    tree e5674a91a53e15575a1f3bf5786bc5cc719fb483               to    blob ac033bf9dc846101320c96a5ce8aceb8c96ec098 broken link from    tree 252ab84542264e1589576b6ee51e7a31e580a0e2               to    tree 2069041cd5950e529e2991d37b7290ec021d90d4 broken link from    tree 2d4964aa4d4f5d8c7228518ce72ef6a63f820c6d               to    blob d83690e1b9a6bdd8a08754b38231799acefcb2ab broken link from    tree c7192e82fc581bd6448bda1a25e8729bdac5f4ff               to    blob 30d54d47ae82add1917ca173d42e58b396df580b broken link from    tree 7c66306901fc71389623286936cef172d4ffe408               to    blob bc7e05d705401273b1df4e939de0f540597c0931 broken link from    tree 0940f5fd227d4c84d6e6749d872db50a4522ae3a               to    tree 923767594ac22023e824948d65622fe5b407d1a1 broken link from    tree 8eadcd2a971e8357d24f0d80f993d2963452209f               to    blob 2598bde3dc8cb80ee49510b8159344004b88645f broken link from    tree ffa302dd0d969172ef23caeefe856ab2f57a4e4d               to    blob d6925fa431be1ac585bf9a481e98f75107a6e6fb broken link from    tree 7045b8870a49ce30a2027537a96d73d162bda773               to    blob 25688652dea26f61f576ca1b52b9d1a18fbfd01d broken link from    tree 37e4705d34bd440ce681ae32ae9a180a13256d72               to    tree 246f564d4cee53339b8a4244f3173b61caa518eb missing blob d6925fa431be1ac585bf9a481e98f75107a6e6fb missing blob ac033bf9dc846101320c96a5ce8aceb8c96ec098 missing tree 29a422c19251aeaeb907175e9b3219a9bed6c616 missing tree 8084e8e04d510cc28321f30a9646477cc50c235c missing blob 30d54d47ae82add1917ca173d42e58b396df580b missing tree 8cc55ec952dc192a233e062201d1e7e873ac3db0 missing blob e9052d35bfb6d30065b206fc43f4200a04d5281b dangling tree 4b26e95db542c72ac4a22ec25abe38fb2de79752 missing blob d83690e1b9a6bdd8a08754b38231799acefcb2ab missing blob 25a742dff0a403b2b3884f2ffddf63eb45721fac missing tree 923767594ac22023e824948d65622fe5b407d1a1 missing blob 25688652dea26f61f576ca1b52b9d1a18fbfd01d missing blob 2598bde3dc8cb80ee49510b8159344004b88645f dangling tree 3a683869f1bb0c1634de75700c316b3b36570dbd dangling blob 4098d30843380d798a811f1aa9a02994f0dbbb27 missing tree 2069041cd5950e529e2991d37b7290ec021d90d4 missing blob 4a994e1e7bb7ce28dcec98bad48b9a891d7dec51 missing blob 1a3a5e4dd2502ac121c22f743c4250e254a94eeb missing blob a0daa0c1567b55d8de2b4d7a3bc010f58c047eab dangling tree 6c7b5162aa7a303fa3fe8dc393c5da564e309521 missing commit 984c11abfc9c2839b386f29c574d9e03383fa589 missing blob bc7e05d705401273b1df4e939de0f540597c0931 missing blob dd4e97e22e159a585b20e21028f964827d5afa4e missing tree 246f564d4cee53339b8a4244f3173b61caa518eb dangling commit a01f5c1e5315dc837203d6dee00d3493be9c5db9   That looks really bad  When I do a git log   head I get this  christopher christopher-laptop   Ubuntu One Side Work projects git  git log   head error  Could not read 984c11abfc9c2839b386f29c574d9e03383fa589 fatal  Failed to traverse parents of commit 235ae1f48701d577d71ebd430344a159e5ba4881 commit 2fb0d2d0643b445440f01b164f11ee9ee71fca48 Author  christopher  lt christopher christopher christopher gt  Date    Wed Aug 7 15 51 42 2013 -0400      finishing chapter 7   Other questions here have said to look at   git refs heads master  It s a bare repo and refs heads  exists but refs heads master does not  HEAD in the bare repo says ref  refs heads master though   packed-refs does say this though    pack-refs with  peeled  2fb0d2d0643b445440f01b164f11ee9ee71fca48 refs heads master   Still other questions have suggested running git reflog and no output shows up when I run that   So I really have no idea what to do here  What strategy should be taken  Is it possible to reset head to this last commit on Aug 7  EDIT   Doing a git log and going to the bottom of the screen output shows this   commit 996e03b949aea176238e3c7a8452700bbb987ac9 Author  christopher  lt christopher christopher gt  Date    Wed Jul 3 23 00 44 2013 -0400      many many changes error  Could not read 984c11abfc9c2839b386f29c574d9e03383fa589 fatal  Failed to traverse parents of commit 235ae1f48701d577d71ebd430344a159e5ba4881   That seems to be preventing the git prune from working

User · Answer

Remove the index and do reset  rm -f  git index git reset

User · Answer

I tried moving away the object files with 0 bytes and fetching them again from the remote  and it worked   find   -type f -size 0 -exec mv     tmp    git fetch   It fetched the missing objects from the remote and allowed me to continue working without reinitializing the whole repo

User · Answer

In my case  I was creating the repository from source code already in my pc and that error appeared  I deleted the  git folder and did everything again and it worked

User · Answer

TL DR  Git doesn t really store history the way you think it does  It calculates history at run-time based on an ancestor chain  If your ancestry is missing blobs  trees  or commits then you may not be able to fully recover your history   Restore Missing Objects from Backups  The first thing you can try is to restore the missing items from backup  For example  see if you have a backup of the commit stored as  git objects 98 4c11abfc9c2839b386f29c574d9e03383fa589  If so you can restore it   You may also want to look into git-verify-pack and git-unpack-objects in the event that the commit has already been packed up and you want to return it to a loose object for the purposes of repository surgery   Surgical Resection  If you can t replace the missing items from a backup  you may be able to excise the missing history  For example  you might examine your history or reflog to find an ancestor of commit 984c11abfc9c2839b386f29c574d9e03383fa589  If you find one intact  then    Copy your Git working directory to a temporary directory somewhere  Do a hard reset to the uncorrupted commit  Copy your current files back into the Git work tree  but make sure you don t copy the  git folder back  Commit the current work tree  and do your best to treat it as a squashed commit of all the missing history    If it works  you will of course lose the intervening history  At this point  if you have a working history log  then it s a good idea to prune your history and reflogs of all unreachable commits and objects   Full Restores and Re-Initialization  If your repository is still broken  then hopefully you have an uncorrupted backup or clone you can restore from  If not  but your current working directory contains valid files  then you can always re-initialize Git  For example   rm -rf  git git init git add   git commit -m  Re-initialize repository without old history     It s drastic  but it may be your only option if your repository history is truly unrecoverable  YMMV

User · Answer

As an alternative to CodeGnome s last option  if only the local repo is corrupted  and you know the url to the remote  you can use this to re-set your  git to match the remote  replacing   url  with the remote url    mv -v  git  git old  amp  amp               remove old git git init  amp  amp                          initialise new repo git remote add origin    url    amp  amp    link to old repo git fetch  amp  amp                         get old history git reset origin master --mixed     force update to old history   This leaves your working tree intact  and only affects git s bookkeeping  I also recently made a bash script for this very purpose   Appendix A   which wraps a bit of safety around this operation   Note   If your repo has submodules  this process will mess them up somehow  and the only solution I ve found so far is deleting them and then using git submodule update --init  or re-cloning the repo  but that seems too drastic    Appendix A - Full script     bin bash    Author  Zoey Llewellyn  Zobean  Hewll     Usage  fix-git  REMOTE-URL      Must be run from the root directory of the repository      If a remote is not supplied  it will be read from  git config      For when you have a corrupted local repo  but a trusted remote    This script replaces all your history with that of the remote    If there is a  git  it is backed up as  git old  removing the last backup    This does not affect your working tree      This does not currently work with submodules    This will abort if a suspected submodule is found    You will have to delete them first   and re-clone them after  with  git submodule update --init       Error codes    1  If a url is not supplied  and one cannot be read from  git config   4  If the url cannot be reached   5  If a git submodule is detected   if       find -name  git -not -path    git   wc -l   -gt 0      then     echo  It looks like this repo uses submodules   gt  amp 2     echo  You will need to remove them before this script can safely execute   gt  amp 2     echo  Then use   git submodule update --init   to re-clone them   gt  amp 2     exit 5 fi  if       -ge 1      then     url   1  else     if   url    git config --local --get remote origin url         then         echo  Unable to find remote  origin   missing in   git config    gt  amp 2         exit 1     fi fi url base    echo    url     sed -E  s                             2     echo  Attempting to access   url base  before continuing  if   wget -p    url base   -O  dev null -q --dns-timeout 5 --connect-timeout 5   then     echo  Unable to reach   url base   Aborting before any damage is done   gt  amp 2     exit 4 fi  echo echo  This operation will replace the local repo with the remote at   echo    url   echo echo  This will completely rewrite history   echo  but will leave your working tree intact  echo -n  Are you sure   y N      read confirm if     -t 0       i m open in a pipe then       print the piped input     echo    confirm   fi if echo    confirm   grep -Eq   Yy   EeSs        it looks like a yes then     if    -e  git          then           remove old backup         rm -vrf  git old   tail -n 1  amp  amp            backup  git iff it exists         mv -v  git  git old     fi  amp  amp      git init  amp  amp      git remote add origin    url    amp  amp      git config --local --get remote origin url   sed  s   Added remote origin at     amp  amp      git fetch  amp  amp      git reset origin master --mixed else     echo  Aborting without doing anything  fi

User · Answer

I wanted to add this as a comment under Zoey Hewil s awesome answer above  but I don t currently have enough rep to do so  so I have to add it here and give credit for her work  P  If you re using Poshgit and are feeling exceptionally lazy  you can use the following to automatically extract your URL from your git config and make an easy job even easier  Standard caveats apply about testing this on a copy backing up your local repo first in case it blows up in your face    config   get-content  git config  url    config -match   url      lt content gt       url    url trim   Substring 6   url  move-item -v  git  git old  git init  git remote add origin   url   git fetch  git reset origin master --mixed

User · Answer

This command worked for me     git reset --mixed

User · Answer

Before trying any of the fixes described on this page  I would advise to make a copy of your repo and work on this copy only  Then at the end if you can fix it  compare it with the original to ensure you did not lose any file in the repair process   Another alternative which worked for me was to reset the git head and index to its previous state using   git reset --keep  You can also do the same manually by opening the Git GUI and selecting each  Staged changes  and click on  Unstage the change   When everything is unstaged  you should now be able to compress your database  check your database and commit   I also tried the following commands but they did not work for me  but they might for you depending on the exact issue you have   git reset --mixed git fsck --full git gc --auto git prune --expire now git reflog --all   Finally  to avoid this problem of synchronization damaging your git index  which can happen with DropBox  SpiderOak  or any other cloud disk   you can do the following    Convert your  git folder into a single  bundle  git file by using  git bundle create my repo git --all  then it should work just the same as before  but since everything is in a single file you won t risk the synchronization damaging your git repo anymore  Disable instantaneous synchronization  SpiderOak allows you to set the scheduling for checking changes to  automatic   which means that it is as soon as possible  being monitoring file changes thanks to the OS notifications   This is bad because it will start to upload changes as soon as you are doing a change  and then download the change  so it might erase the latest changes you were just doing  A solution to fix this issue is to set the changes monitoring delay to 5 minutes or more  This also fixes issues with instant saving note taking applications  such as Notepad

User · Answer

Quick way if you have change on your current project and don t want to lose it   move your current project some where   clone the project from github to this folder and make some change an try to commit again  Or just delete the repo and clone it again   it worked form me

User · Answer

I was facing the same issue  so I replaced the   git  folder with a backed up version and it still wasn t working because  gitconfig file was corrupted  The BSOD on my laptop corrupted it  I replaced it with the following code and sourcetree restored all my repositories    user  name    your username  email    your email address   core  autocrlf   true excludesfile   C   Users   user name   Documents  gitignore global txt   I don t know if this will help anybody  but this is just another solution that worked for me

User · Answer

If you are desperate you can try this   git clone ssh   me my git server path to project destination --depth 1   It will get your data  but you ll lose the history  I went with trial and error on my repo and --depth 10 worked  but --depth 50 gave me failure

User · Answer

If you have a remote configured and you have   don t care about losing some unpushed code  you can do    git fetch  amp  amp  git reset --hard

User · Answer

I experienced similar issues using git version 2 7 1 under Ubuntu 18 04 3 lately  Here is how I did   sudo apt install git-repair git-repair    fix a broken git repository or git-repair --force    force repair  even if data is lost git fsck    to verify it was fixed   Most of the time the recovery process was successful

User · Answer

Here s a script  bash  to automate the first solution by  CodeGnome to restore from a backup  run from the top level of the corrupted repo   The backup doesn t need to be complete  it only needs to have the missing objects   git fsck 2 gt  amp 1   grep -e missing -e invalid   awk   print  NF     sort -u       while read entry  do         mkdir -p  git objects   entry 0 2          cp   BACKUP  objects   entry 0 2    entry 2   git objects   entry 0 2    entry 2      done

[git] How to fix corrupted git repository?

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