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Editorial Team
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Asked: 2026-05-20T05:51:29+00:00

Yesterday I did one of these operations (see code snippet below) on my git

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Yesterday I did one of these operations (see code snippet below) on my git repo in order to effectively move my project up a few folders in the folder hierarchy. This basically lists all files and adds a prefix folder name to them and updates the index accordingly.

Old layout:

+ Root
  - Sublevel 1
    - Sublevel 2
      - .git was here

New, desired layout:

+ Root
  - .git moved to here, so prefix all index files with "Sublevel 1/Sublevel 2/"
  - Sublevel 1
    - Sublevel 2

Command:

git filter-branch --index-filter '
    git ls-files -s | sed "s-\t-&newRoot/sub1/sub2/-" |
        GIT_INDEX_FILE=$GIT_INDEX_FILE.new git update-index --index-info && mv $GIT_INDEX_FILE.new $GIT_INDEX_FILE
    ' HEAD

However, this command, unbeknownst to me, only modified the master branch. I have about 8 other branches off of master. When I checkout one of these other branches, it checks out all files (some 11,000) in my repo in their original folder structure at the new root folder level where I moved the .git folder to.

How do I repair this snafu? The damage is already done. I have a backup of the .git folder before I did ran the filter-branch but I have commits after this backup was made, not many but enough to warrant finding a patch-like fix on the current repo. I don’t see any obvious branch-specific arguments to the filter-branch command.

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1 Answer

  1. Editorial Team

    filter-branch will “rewrite only the positive refs mentioned in the command line“. So you need to specify “–branches” to rewrite all branches. You specified HEAD, so it just rewrote HEAD (i.e. master)

    After you run filter-branch, the original refs are backed up in refs/original (i.e. refs/original/master is master before filtering): the objects are still available, and I believe the reflogs are kept intact too, so recovering from a bad filter-branch operation is fairly straightforward.

    So your options are:

    • Undo the filter-branch command by checking out master and doing git reset --hard refs/original/master

    • Filter the other branches so they are transformed as well: redo the filter-branch command but specify --branches --not master instead of HEAD, or more safely by naming the branches to be modified explicity

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