fix: address PR review comments

- Wrap find_nested_git_repos helpers in subshell to prevent bash
  global namespace pollution (_should_skip, _scan_dir)
- Validate --scan-depth is a positive integer in setup-plan.sh
- Remove non-existent nested_repo_scan_depth config reference from
  plan.md template
- Fix duplicate step numbering (two items numbered 5) in plan.md
- Quote repo paths in tasks.md git command template
- Update Find-NestedGitRepos comment to reflect configurable depth

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: sakitA

scripts/bash/common.sh

@@ -294,35 +294,40 @@ find_nested_git_repos() {
                         "__pycache__" ".gradle" "build" "dist" "target" ".idea"
                         ".vscode" "specs")
 
-    _should_skip() {
-        local name="$1"
-        for skip in "${skip_dirs[@]}"; do
-            [ "$name" = "$skip" ] && return 0
-        done
-        return 1
-    }
-
-    _scan_dir() {
-        local dir="$1"
-        local current_depth="$2"
-        for child in "$dir"/*/; do
-            [ -d "$child" ] || continue
-            child="${child%/}"
-            local child_name
-            child_name="$(basename "$child")"
-            _should_skip "$child_name" && continue
+    # Run in a subshell to avoid leaking helper functions into global scope
+    (
+        _should_skip() {
+            local name="$1"
+            local skip
+            for skip in "${skip_dirs[@]}"; do
+                [ "$name" = "$skip" ] && return 0
+            done
+            return 1
+        }
 
-            if [ -e "$child/.git" ]; then
-                if git -C "$child" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-                    echo "$child"
+        _scan_dir() {
+            local dir="$1"
+            local current_depth="$2"
+            local child
+            local child_name
+            for child in "$dir"/*/; do
+                [ -d "$child" ] || continue
+                child="${child%/}"
+                child_name="$(basename "$child")"
+                _should_skip "$child_name" && continue
+
+                if [ -e "$child/.git" ]; then
+                    if git -C "$child" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+                        echo "$child"
+                    fi
+                elif [ "$current_depth" -lt "$max_depth" ]; then
+                    _scan_dir "$child" $((current_depth + 1))
                 fi
-            elif [ "$current_depth" -lt "$max_depth" ]; then
-                _scan_dir "$child" $((current_depth + 1))
-            fi
-        done
-    }
+            done
+        }
 
-    _scan_dir "$repo_root" 1
+        _scan_dir "$repo_root" 1
+    )
 }
 
 # Resolve a template name to a file path using the priority stack:

scripts/bash/setup-plan.sh

@@ -32,8 +32,19 @@ for arg in "$@"; do
             ;;
     esac
 done
-# Reset sentinel if --scan-depth was passed without a value
-[ "$SCAN_DEPTH" = "__NEXT__" ] && SCAN_DEPTH=""
+# Validate --scan-depth argument
+if [ "$SCAN_DEPTH" = "__NEXT__" ]; then
+    echo "ERROR: --scan-depth requires a positive integer value" >&2
+    exit 1
+fi
+if [ -n "$SCAN_DEPTH" ]; then
+    case "$SCAN_DEPTH" in
+        ''|*[!0-9]*|0)
+            echo "ERROR: --scan-depth must be a positive integer, got '$SCAN_DEPTH'" >&2
+            exit 1
+            ;;
+    esac
+fi
 
 # Get script directory and load common functions
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

scripts/powershell/common.ps1

@@ -232,7 +232,7 @@ function Test-DirHasFiles {
 # Searches up to 2 directory levels deep for subdirectories containing .git
 # (directory or file, covering worktrees/submodules). Excludes the root repo
 # itself and common non-project directories.
-# Returns an array of absolute paths.
+# Returns an array of absolute paths. Scan depth is configurable (default 2).
 function Find-NestedGitRepos {
     param(
         [string]$RepoRoot = (Get-RepoRoot),

templates/commands/plan.md

@@ -62,8 +62,6 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 1. **Setup**: Run `{SCRIPT}` from repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH, and NESTED_REPOS. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
 
-   **Nested repo scan depth**: Check `.specify/init-options.json` for `nested_repo_scan_depth`. If present, pass `--scan-depth N` (Bash) or `-ScanDepth N` (PowerShell) to the script.
-
 2. **Load context**: Read FEATURE_SPEC and `/memory/constitution.md`. Load IMPL_PLAN template (already copied).
 
 3. **Identify affected nested repositories**: If NESTED_REPOS is non-empty:
@@ -83,7 +81,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 5. **Stop and report**: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, generated artifacts, and affected nested repos (if any).
 
-5. **Check for extension hooks**: After reporting, check if `.specify/extensions.yml` exists in the project root.
+6. **Check for extension hooks**: After reporting, check if `.specify/extensions.yml` exists in the project root.
    - If it exists, read it and look for entries under the `hooks.after_plan` key
    - If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
    - Filter out hooks where `enabled` is explicitly `false`. Treat hooks without an `enabled` field as enabled by default.

templates/commands/tasks.md

@@ -68,7 +68,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 3. **Execute task generation workflow**:
    - Load plan.md and extract tech stack, libraries, project structure
    - Load spec.md and extract user stories with their priorities (P1, P2, P3, etc.)
-   - If plan.md contains an "Affected Nested Repositories" section: extract the repo paths and reasons. Generate a setup task (in Phase 1) to create the feature branch in each affected nested repo using `git -C <repo_path> checkout -b <BRANCH_NAME>`. The branch name comes from the current feature branch.
+   - If plan.md contains an "Affected Nested Repositories" section: extract the repo paths and reasons. Generate a setup task (in Phase 1) to create the feature branch in each affected nested repo using `git -C "<repo_path>" checkout -b "<BRANCH_NAME>"`. The branch name comes from the current feature branch.
    - If data-model.md exists: Extract entities and map to user stories
    - If contracts/ exists: Map interface contracts to user stories
    - If research.md exists: Extract decisions for setup tasks