fix: skip dot-paths already declared in Mackup built-in app definitions

Previously ssr-custom cfg generation only checked whether the path was
already in the cloud backup directory.  It did not consult Mackup's
~400 built-in app definitions, causing duplicates like ssr-claude.cfg
when Mackup already has a 'claude-code' entry covering .claude.

Changes:
- _ssr_mackup_declared_paths(): parses all built-in *.cfg files from
  Mackup's Python package apps/ dir + hand-written ~/.mackup/*.cfg
  (excluding our own ssr-*.cfg) into a sorted path set
- generate_custom_cfg now skips any path already in that set
- Stale ssr-*.cfg files that now duplicate a built-in are removed
  automatically on the next sync run

Co-authored-by: Cursor <cursoragent@cursor.com>

lib/mackup.sh

@@ -71,11 +71,44 @@ _ssr_mackup_write_cfg() {
     printf '%s\n' "$desired" > "$cfg_file"
 }
 
+# Build a newline-separated list of all paths already declared in Mackup's
+# built-in app definitions AND user-defined ~/.mackup/*.cfg files.
+# Our own generated ssr-*.cfg files are excluded to avoid circular checks.
+_ssr_mackup_declared_paths() {
+    local apps_dir=""
+
+    # Locate Mackup's built-in apps/ directory via Python.
+    if command -v python3 >/dev/null 2>&1; then
+        apps_dir="$(python3 -c \
+            'import os, mackup; print(os.path.join(os.path.dirname(mackup.__file__), "apps"))' \
+            2>/dev/null || true)"
+    fi
+
+    # Also include hand-written user definitions (not our generated ssr-*.cfg).
+    local user_cfg_dir="$HOME/.mackup"
+
+    {
+        [[ -d "$apps_dir" ]] \
+            && grep -rh '' "$apps_dir"/*.cfg 2>/dev/null || true
+        [[ -d "$user_cfg_dir" ]] \
+            && grep -rhl '' "$user_cfg_dir"/*.cfg 2>/dev/null \
+            | grep -v '/ssr-' \
+            | xargs grep -h '' 2>/dev/null || true
+    } | awk '
+        /^\[configuration_files\]/ { in_section=1; next }
+        /^\[/                      { in_section=0 }
+        in_section && /^[^#[:space:]]/ { print $1 }
+    ' | sort -u
+}
+
 # Generate one ~/.mackup/ssr-<name>.cfg per uncovered dot-dir/file.
-#   1. Curated entries that exist in $HOME and are not yet in the Mackup backup.
+#   1. Curated entries that exist in $HOME and are not yet covered.
-#   2. Auto-discovered dot-dirs in $HOME not in the skip list and not in backup.
+#   2. Auto-discovered dot-dirs in $HOME not in the skip list and not covered.
 #
-# Removes the old combined ssr-custom.cfg if found (migration from old format).
+# "Covered" means: already declared in a built-in or hand-written Mackup app
+# definition OR already materialised in the Mackup backup directory.
+#
+# Removes the old combined ssr-custom.cfg if found (migration).
 # Each file is picked up automatically by `mackup backup/restore`.
 ssr::mackup::generate_custom_cfg() {
     local mackup_dir="$1"
@@ -85,8 +118,34 @@ ssr::mackup::generate_custom_cfg() {
     # Remove legacy combined file if present.
     [[ -f "$cfg_dir/ssr-custom.cfg" ]] && rm -f "$cfg_dir/ssr-custom.cfg"
 
+    # Build declared-paths lookup early so we can also purge stale ssr-*.cfg
+    # files that now duplicate a built-in definition (e.g. ssr-claude.cfg after
+    # Mackup added a built-in "claude-code" app).
+    local declared
+    declared="$(_ssr_mackup_declared_paths)"
+
+    local stale_cfg stale_path
+    for stale_cfg in "$cfg_dir"/ssr-*.cfg; do
+        [[ -f "$stale_cfg" ]] || continue
+        # Extract the single path from [configuration_files].
+        stale_path="$(awk '/^\[configuration_files\]/{f=1;next}/^\[/{f=0}f&&/^[^#[:space:]]/{print $1;exit}' "$stale_cfg")"
+        if printf '%s\n' "$declared" | grep -qxF "$stale_path"; then
+            ssr::log "Removing stale duplicate: ${stale_cfg##*/} ($stale_path now covered by built-in)"
+            rm -f "$stale_cfg"
+        fi
+    done
+
     local skip_set=" ${_SSR_MACKUP_SKIP[*]} "
 
+    # Build declared-paths lookup (newline-separated, sorted).
+    local declared
+    declared="$(_ssr_mackup_declared_paths)"
+
+    # Return true when <path> is already declared in any existing app definition.
+    _is_declared() {
+        printf '%s\n' "$declared" | grep -qxF "$1"
+    }
+    # Return true when <path> is already present in the Mackup cloud backup.
     _in_backup() { [[ -e "$mackup_dir/$1" ]]; }
 
     local -a items=()
@@ -95,6 +154,7 @@ ssr::mackup::generate_custom_cfg() {
     local item
     for item in "${_SSR_MACKUP_CURATED[@]}" ${SSR_MACKUP_EXTRA_PATHS:-}; do
         [[ -e "$HOME/$item" ]] || continue
+        _is_declared "$item"   && continue
         _in_backup "$item"     && continue
         items+=("$item")
     done
@@ -104,6 +164,7 @@ ssr::mackup::generate_custom_cfg() {
     while IFS= read -r dotdir; do
         name="${dotdir##*/}"
         [[ "$skip_set" == *" $name "* ]] && continue
+        _is_declared "$name"   && continue
         _in_backup "$name"     && continue
         local dup=false
         for item in "${items[@]:-}"; do [[ "$item" == "$name" ]] && dup=true && break; done
@@ -118,12 +179,11 @@ ssr::mackup::generate_custom_cfg() {
 
     local written=0 it
     for it in "${items[@]}"; do
-        if _ssr_mackup_write_cfg "$cfg_dir" "$it"; then
+        _ssr_mackup_write_cfg "$cfg_dir" "$it"
         written=$((written + 1))
-        fi
     done
 
-    ssr::ok "~/.mackup/ssr-*.cfg: ${#items[@]} app definitions written (${written} new/updated)"
+    ssr::ok "~/.mackup/ssr-*.cfg: ${written} definition(s) written"
     ssr::log "  → ${items[*]}"
 }