How to fix modified content in Git

First, navigate to the submodule directory and see what Git thinks has changed:

cd path/to/submodule
git status
git diff

This shows you whether there are:
- Modified files (local edits)
- Untracked files (new files not in the submodule's .gitignore)
- A detached HEAD at a different commit

Understanding the cause helps you choose the right fix.

If you want to discard all changes and return the submodule to the exact state the parent repository expects:

git submodule update --checkout

Or for all submodules recursively:

git submodule update --checkout --recursive

This checks out the commit SHA that the parent repository has recorded for each submodule.

If the regular update doesn't work because of local modifications, use the force flag:

git submodule update --force --recursive

Or reset changes manually inside the submodule:

cd path/to/submodule
git checkout .
git clean -fd

Warning: This discards all uncommitted changes in the submodule.

To reset all submodules in your project to their clean state:

git submodule foreach --recursive git checkout .
git submodule foreach --recursive git clean -fd

This runs the checkout and clean commands inside each submodule directory.

If you intentionally updated the submodule to a new commit and want to record this in the parent repository:

# First, commit any changes inside the submodule
cd path/to/submodule
git add .
git commit -m "Your changes"
git push

# Then, update the parent repository to point to the new commit
cd ..
git add path/to/submodule
git commit -m "Update submodule to latest version"

The parent repository stores only the commit reference, not the submodule's files.

If you want Git to stop showing "modified content" for submodules with local changes, add the ignore setting to your .gitmodules file:

[submodule "path/to/submodule"]
    path = path/to/submodule
    url = https://github.com/example/repo.git
    ignore = dirty

Or set it via command line:

git config -f .gitmodules submodule.path/to/submodule.ignore dirty

Options for ignore:
- untracked: Ignore only untracked files
- dirty: Ignore all working tree changes
- all: Ignore all changes including new commits

For a quick one-time check without seeing dirty submodules:

git status --ignore-submodules=dirty

Or to ignore all submodule changes:

git status --ignore-submodules=all

You can also set this as your default behavior:

git config --global diff.ignoreSubmodules dirty

Sometimes "modified content" appears when there's an accidental nested Git repository. Check if there's a .git folder inside a regular directory:

find . -name ".git" -type d

If you find unexpected .git directories that aren't proper submodules, you may need to either:
- Remove the nested .git folder and add the files normally
- Convert the directory to a proper submodule using git submodule add