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Copytree Same-File Crash

Home > Troubleshooting > Copytree Same-File Crash

Symptoms

When AMPLIHACK_HOME is set to the amplihack source tree itself (or to a path that resolves to the same directory via symlinks), copytree_manifest() crashes with:

shutil.SameFileError: '/home/user/src/amplihack/bin' and '/home/user/src/amplihack/bin' are the same file

This typically happens during:

  • Local development with AMPLIHACK_HOME=.
  • Symlinked installs where source and staging directory converge
  • CI pipelines that reuse the checkout as the install target

Root Cause

copytree_manifest() in install.py iterates over ESSENTIAL_DIRS and copies each from the source tree into the destination. When source and destination resolve to the same filesystem path, shutil.copytree() detects the overlap and raises SameFileError.

Fix

An os.path.samefile() guard now runs before each shutil.copytree() call. If source and target resolve to the same inode, the copy is silently skipped with a warning:

  ⚠️  Skipping bin: source and target are the same path

The guard:

  • Resolves symlinks — os.path.samefile() compares real device/inode pairs, so symlinked paths that converge are correctly detected.
  • Fails open — If samefile() raises OSError or ValueError (e.g., on platforms where it is unsupported), the guard is bypassed and the normal copy proceeds.
  • Has no side effects — It is a read-only stat check with no filesystem mutations.

Verifying the Fix

# Reproduce the original crash (before fix):
AMPLIHACK_HOME=$(pwd) python -c "from amplihack.install import copytree_manifest; copytree_manifest('.', '.')"
# Expected (after fix): prints skip warnings, exits cleanly

# Run the regression tests:
pytest tests/unit/test_copytree_samefile.py -v

Equivalent Rust Guard

The Rust CLI (amplihack-rs) has an identical guard in every copy_dir_recursive function. It uses std::fs::canonicalize() to resolve both paths and compares the results:

if let (Ok(canon_src), Ok(canon_dst)) = (source.canonicalize(), dest.canonicalize()) {
    if canon_src == canon_dst {
        // skip copy, log warning
        return Ok(());
    }
}

The Rust guard appears in:

Crate File Function
amplihack-cli src/auto_stager.rs copy_dir_recursive
amplihack-launcher src/auto_stager.rs copy_dir_recursive
amplihack-context src/migration.rs copy_dir_recursive
amplihack-cli src/commands/mode/migration.rs copy_dir_recursive