diff --git a/bin/clean.sh b/bin/clean.sh
index 4549454..b36b231 100755
--- a/bin/clean.sh
+++ b/bin/clean.sh
@@ -129,6 +129,7 @@ PROJECT_ARTIFACT_HINT_EXAMPLES=()
 PROJECT_ARTIFACT_HINT_ESTIMATED_KB=0
 PROJECT_ARTIFACT_HINT_ESTIMATE_SAMPLES=0
 PROJECT_ARTIFACT_HINT_ESTIMATE_PARTIAL=false
+declare -a DRY_RUN_SEEN_IDENTITIES=()
 
 # shellcheck disable=SC2329
 note_activity() {
@@ -137,6 +138,20 @@ note_activity() {
     fi
 }
 
+# shellcheck disable=SC2329
+register_dry_run_cleanup_target() {
+    local path="$1"
+    local identity
+    identity=$(mole_path_identity "$path")
+
+    if [[ ${#DRY_RUN_SEEN_IDENTITIES[@]} -gt 0 ]] && mole_identity_in_list "$identity" "${DRY_RUN_SEEN_IDENTITIES[@]}"; then
+        return 1
+    fi
+
+    DRY_RUN_SEEN_IDENTITIES+=("$identity")
+    return 0
+}
+
 CLEANUP_DONE=false
 # shellcheck disable=SC2329
 cleanup() {
@@ -380,7 +395,12 @@ safe_clean() {
             log_operation "clean" "SKIPPED" "$path" "whitelist"
         fi
         [[ "$skip" == "true" ]] && continue
-        [[ -e "$path" ]] && existing_paths+=("$path")
+        if [[ -e "$path" ]]; then
+            if [[ "$DRY_RUN" == "true" ]]; then
+                register_dry_run_cleanup_target "$path" || continue
+            fi
+            existing_paths+=("$path")
+        fi
     done
 
     if [[ "$show_scan_feedback" == "true" ]]; then
@@ -705,6 +725,7 @@ start_cleanup() {
     # Set current command for operation logging
     export MOLE_CURRENT_COMMAND="clean"
     log_operation_session_start "clean"
+    DRY_RUN_SEEN_IDENTITIES=()
 
     if [[ -t 1 ]]; then
         printf '\033[2J\033[H'
diff --git a/lib/clean/caches.sh b/lib/clean/caches.sh
index 463996b..abda06c 100644
--- a/lib/clean/caches.sh
+++ b/lib/clean/caches.sh
@@ -117,6 +117,8 @@ project_cache_has_indicators() {
 # Discover candidate project roots without scanning the whole home directory.
 discover_project_cache_roots() {
     local -a roots=()
+    local -a unique_roots=()
+    local -a seen_identities=()
     local root
 
     for root in "${MOLE_PURGE_DEFAULT_SEARCH_PATHS[@]}"; do
@@ -147,7 +149,18 @@ discover_project_cache_roots() {
 
     [[ ${#roots[@]} -eq 0 ]] && return 0
 
-    printf '%s\n' "${roots[@]}" | LC_ALL=C sort -u
+    for root in "${roots[@]}"; do
+        local identity
+        identity=$(mole_path_identity "$root")
+        if [[ ${#seen_identities[@]} -gt 0 ]] && mole_identity_in_list "$identity" "${seen_identities[@]}"; then
+            continue
+        fi
+
+        seen_identities+=("$identity")
+        unique_roots+=("$root")
+    done
+
+    [[ ${#unique_roots[@]} -gt 0 ]] && printf '%s\n' "${unique_roots[@]}"
 }
 
 # Scan a project root for supported build caches while pruning heavy subtrees.
diff --git a/lib/core/common.sh b/lib/core/common.sh
index 38f7640..1211685 100755
--- a/lib/core/common.sh
+++ b/lib/core/common.sh
@@ -27,6 +27,45 @@ if [[ -f "$_MOLE_CORE_DIR/sudo.sh" ]]; then
     source "$_MOLE_CORE_DIR/sudo.sh"
 fi
 
+# Normalize a path for comparisons while preserving root.
+mole_normalize_path() {
+    local path="$1"
+    local normalized="${path%/}"
+    [[ -n "$normalized" ]] && printf '%s\n' "$normalized" || printf '%s\n' "$path"
+}
+
+# Return a stable identity for an existing path. Prefer dev+inode so aliased
+# paths on case-insensitive filesystems or symlinks collapse to one identity.
+mole_path_identity() {
+    local path="$1"
+    local normalized
+    normalized=$(mole_normalize_path "$path")
+
+    if [[ -e "$normalized" || -L "$normalized" ]]; then
+        if command -v stat > /dev/null 2>&1; then
+            local fs_id=""
+            fs_id=$(stat -L -f '%d:%i' "$normalized" 2> /dev/null || stat -f '%d:%i' "$normalized" 2> /dev/null || true)
+            if [[ "$fs_id" =~ ^[0-9]+:[0-9]+$ ]]; then
+                printf 'inode:%s\n' "$fs_id"
+                return 0
+            fi
+        fi
+    fi
+
+    printf 'path:%s\n' "$normalized"
+}
+
+mole_identity_in_list() {
+    local needle="$1"
+    shift
+
+    local existing
+    for existing in "$@"; do
+        [[ "$existing" == "$needle" ]] && return 0
+    done
+    return 1
+}
+
 # Update via Homebrew
 update_via_homebrew() {
     local current_version="$1"
diff --git a/tests/clean_core.bats b/tests/clean_core.bats
index 8373378..127b96c 100644
--- a/tests/clean_core.bats
+++ b/tests/clean_core.bats
@@ -125,6 +125,18 @@ PLIST
     [ -f "$HOME/Library/LaunchAgents/com.example.stale.plist" ]
 }
 
+@test "mo clean --dry-run does not export duplicate targets across sections" {
+    mkdir -p "$HOME/Library/Application Support/Code/CachedData"
+    echo "cache" > "$HOME/Library/Application Support/Code/CachedData/data.bin"
+
+    run env HOME="$HOME" MOLE_TEST_MODE=0 "$PROJECT_ROOT/mole" clean --dry-run
+    [ "$status" -eq 0 ]
+
+    run grep -c "Application Support/Code/CachedData" "$HOME/.config/mole/clean-list.txt"
+    [ "$status" -eq 0 ]
+    [ "$output" -eq 1 ]
+}
+
 @test "mo clean honors whitelist entries" {
     mkdir -p "$HOME/Library/Caches/WhitelistedApp"
     echo "keep me" > "$HOME/Library/Caches/WhitelistedApp/data.tmp"
diff --git a/tests/clean_system_caches.bats b/tests/clean_system_caches.bats
index fbd57e7..b81ed42 100644
--- a/tests/clean_system_caches.bats
+++ b/tests/clean_system_caches.bats
@@ -238,6 +238,25 @@ EOF
     rm -rf "$HOME/go"
 }
 
+@test "discover_project_cache_roots dedupes aliased roots by filesystem identity" {
+    mkdir -p "$HOME/code/demo/.dart_tool"
+    touch "$HOME/code/demo/pubspec.yaml"
+    mkdir -p "$HOME/.config/mole"
+    ln -s "$HOME/code" "$HOME/Code"
+    printf '%s\n' "$HOME/Code" > "$HOME/.config/mole/purge_paths"
+
+    run env HOME="$HOME" PROJECT_ROOT="$PROJECT_ROOT" bash --noprofile --norc <<'EOF'
+set -euo pipefail
+source "$PROJECT_ROOT/lib/core/common.sh"
+source "$PROJECT_ROOT/lib/clean/caches.sh"
+roots=$(discover_project_cache_roots)
+printf '%s\n' "$roots"
+printf 'COUNT=%s\n' "$(printf '%s\n' "$roots" | sed '/^$/d' | wc -l | tr -d ' ')"
+EOF
+    [ "$status" -eq 0 ]
+    [[ "$output" == *"COUNT=1"* ]]
+}
+
 @test "clean_project_caches skips stalled root scans" {
     mkdir -p "$HOME/.config/mole"
     mkdir -p "$HOME/SlowProjects/app"