Skip excluded directory subtrees during copy

Author: helizaga

CHANGELOG.md

@@ -6,6 +6,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com), and this
 
 ## [Unreleased]
 
+### Fixed
+
+- Directory copying now skips excluded child subtrees during copy instead of cloning them and deleting them afterward.
+
 ## [2.7.1] - 2026-04-28
 
 ### Added

lib/copy.sh

@@ -338,6 +338,80 @@ $excludes
 EOF
 }
 
+# Check whether any exclude pattern applies beneath a copied directory.
+# Usage: _has_subdir_excludes <dir_path> <excludes>
+_has_subdir_excludes() {
+  local dir_path="$1" excludes="$2"
+
+  [ -z "$excludes" ] && return 1
+
+  local exclude_pattern
+  while IFS= read -r exclude_pattern; do
+    [ -z "$exclude_pattern" ] && continue
+
+    if _is_unsafe_path "$exclude_pattern"; then
+      continue
+    fi
+
+    case "$exclude_pattern" in
+      */*)
+        local pattern_prefix="${exclude_pattern%%/*}"
+        local pattern_suffix="${exclude_pattern#*/}"
+
+        [ -z "$pattern_suffix" ] && continue
+
+        case "$exclude_pattern" in
+          .git|*/.git|.git/*|*/.git/*) continue ;;
+        esac
+
+        # Intentional glob pattern matching for directory prefix
+        # shellcheck disable=SC2254
+        case "$dir_path" in
+          $pattern_prefix) return 0 ;;
+        esac
+        ;;
+    esac
+  done <<EOF
+$excludes
+EOF
+
+  return 1
+}
+
+# Copy a directory one direct child at a time, skipping excluded child subtrees
+# before they are copied. Deeper excludes are still removed after copy.
+# Usage: _selective_copy_dir <dir_path> <dest_parent> <excludes>
+_selective_copy_dir() {
+  local dir_path="$1" dest_parent="$2" excludes="$3"
+  local dest_dir="$dest_parent/$dir_path"
+
+  mkdir -p "$dest_dir" || return 1
+
+  local find_results
+  find_results=$(find "$dir_path" -mindepth 1 -maxdepth 1 2>/dev/null || true)
+
+  local child_path child_name child_rel
+  while IFS= read -r child_path; do
+    [ -z "$child_path" ] && continue
+
+    child_name=$(basename "$child_path")
+    child_rel="$dir_path/$child_name"
+
+    if is_excluded "$child_rel" "$excludes"; then
+      log_info "Skipped excluded directory $child_rel"
+      continue
+    fi
+
+    if ! _fast_copy_dir "$child_path" "$dest_dir/"; then
+      return 1
+    fi
+  done <<EOF
+$find_results
+EOF
+
+  _apply_directory_excludes "$dest_parent" "$dir_path" "$excludes"
+}
+
 # Copy directories matching patterns (typically git-ignored directories like node_modules)
 # Usage: copy_directories src_root dst_root dir_patterns excludes [dry_run]
 # dir_patterns: newline-separated directory names to copy (e.g., "node_modules", ".venv")
@@ -403,7 +477,14 @@ copy_directories() {
       mkdir -p "$dest_parent"
 
       # Copy directory using CoW when available (preserves symlinks as symlinks)
-      if _fast_copy_dir "$dir_path" "$dest_parent/"; then
+      if _has_subdir_excludes "$dir_path" "$excludes"; then
+        if _selective_copy_dir "$dir_path" "$dest_parent" "$excludes"; then
+          log_info "Copied directory $dir_path"
+          copied_count=$((copied_count + 1))
+        else
+          log_warn "Failed to copy directory $dir_path"
+        fi
+      elif _fast_copy_dir "$dir_path" "$dest_parent/"; then
         log_info "Copied directory $dir_path"
         copied_count=$((copied_count + 1))
         _apply_directory_excludes "$dest_parent" "$dir_path" "$excludes"

tests/copy_safety.bats

@@ -203,3 +203,66 @@ teardown() {
 
   [ -e "$dest/node_modules/.git" ]
 }
+
+@test "_has_subdir_excludes returns true for child exclude" {
+  _has_subdir_excludes ".claude" $'.claude/worktrees'
+}
+
+@test "_has_subdir_excludes returns false for unrelated exclude" {
+  ! _has_subdir_excludes ".claude" $'node_modules\n.venv'
+}
+
+@test "_has_subdir_excludes returns false for exact parent exclude" {
+  ! _has_subdir_excludes ".claude" ".claude"
+}
+
+@test "_has_subdir_excludes supports glob prefixes" {
+  _has_subdir_excludes ".claude" $'*/worktrees'
+}
+
+@test "_selective_copy_dir skips excluded direct child" {
+  _test_tmpdir=$(mktemp -d)
+  local src="$_test_tmpdir/src" dst="$_test_tmpdir/dst"
+  mkdir -p "$src/.claude/settings" "$src/.claude/worktrees" "$dst"
+  echo "keep" > "$src/.claude/settings/config.json"
+  echo "skip" > "$src/.claude/worktrees/session.json"
+
+  cd "$src"
+  _selective_copy_dir ".claude" "$dst" $'.claude/worktrees'
+
+  [ -f "$dst/.claude/settings/config.json" ]
+  [ ! -e "$dst/.claude/worktrees" ]
+}
+
+@test "_selective_copy_dir still applies deeper excludes after copy" {
+  _test_tmpdir=$(mktemp -d)
+  local src="$_test_tmpdir/src" dst="$_test_tmpdir/dst"
+  mkdir -p "$src/.claude/worktrees/cache" "$src/.claude/worktrees/keep" "$dst"
+  echo "skip" > "$src/.claude/worktrees/cache/blob"
+  echo "keep" > "$src/.claude/worktrees/keep/session.json"
+
+  cd "$src"
+  _selective_copy_dir ".claude" "$dst" $'.claude/worktrees/cache'
+
+  [ ! -e "$dst/.claude/worktrees/cache" ]
+  [ -f "$dst/.claude/worktrees/keep/session.json" ]
+}
+
+@test "copy_directories does not copy excluded direct child subtree" {
+  _test_tmpdir=$(mktemp -d)
+  local src="$_test_tmpdir/src" dst="$_test_tmpdir/dst" copy_log="$_test_tmpdir/copy.log"
+  mkdir -p "$src/.claude/settings" "$src/.claude/worktrees" "$dst"
+  echo "keep" > "$src/.claude/settings/config.json"
+  echo "skip" > "$src/.claude/worktrees/session.json"
+
+  _fast_copy_dir() {
+    printf '%s\n' "$1" >> "$copy_log"
+    cp -RP "$1" "$2"
+  }
+
+  copy_directories "$src" "$dst" ".claude" $'.claude/worktrees'
+
+  [ -f "$dst/.claude/settings/config.json" ]
+  [ ! -e "$dst/.claude/worktrees" ]
+  ! grep -qx ".claude/worktrees" "$copy_log"
+}