How to fix error: Entry 'file.txt' not uptodate. Cannot merge. in Git

First, identify what files Git considers changed:

git status
git diff

This will show you which files have uncommitted changes. If git status shows changes but git diff shows nothing, the issue is likely related to file metadata or index corruption.

The safest approach is to temporarily save your changes using git stash:

git stash
git pull
git stash pop

This saves your local modifications, performs the merge, and then reapplies your changes. If there are conflicts after git stash pop, you'll need to resolve them manually.

If you've used git add -N (intent-to-add), you need to fully stage those files:

# Check for intent-to-add files
git status

# Fully stage the files
git add <filename>

# Or stage all pending files
git add .

After staging, you can either commit these changes or use git stash to temporarily save them.

If you don't need your local changes, you can restore the file to match the repository:

# Using git restore (Git 2.23+)
git restore <filename>

# Or using the older checkout command
git checkout -- <filename>

Warning: This will discard any uncommitted changes to that file.

If the error persists despite no visible changes, refresh the Git index:

# Refresh the index
git update-index --refresh

# Or force a hard reset (WARNING: discards all uncommitted changes)
git reset --hard HEAD

The hard reset should only be used if you've backed up any important changes.

Files with special flags can cause this error. Check and remove these flags:

# List files with assume-unchanged
git ls-files -v | grep '^[a-z]'

# List files with skip-worktree
git ls-files -v | grep '^S'

# Remove assume-unchanged flag
git update-index --no-assume-unchanged <filename>

# Remove skip-worktree flag
git update-index --no-skip-worktree <filename>

If backup software or file indexers are modifying file metadata:

git config core.trustctime false

This tells Git to ignore the ctime (inode change time) when determining if files have changed.