fix: harden bash scripts against shell injection and improve robustness (#1809)

- Replace eval of unquoted get_feature_paths output with safe pattern:
  capture into variable, check return code, then eval quoted result
- Use printf '%q' in get_feature_paths to safely emit shell assignments,
  preventing injection via paths containing quotes or metacharacters
- Add json_escape() helper for printf JSON fallback paths, handling
  backslash, double-quote, and control characters when jq is unavailable
- Use jq -cn for safe JSON construction with proper escaping when
  available, with printf + json_escape() fallback
- Replace declare -A (bash 4+) with indexed array for bash 3.2
  compatibility (macOS default)
- Use inline command -v jq check in create-new-feature.sh since it
  does not source common.sh
- Guard trap cleanup against re-entrant invocation by disarming traps
  at entry
- Use printf '%q' for shell-escaped branch names in user-facing output
- Return failure instead of silently returning wrong path on ambiguous
  spec directory matches
- Deduplicate agent file updates via realpath to prevent multiple writes
  to the same file (e.g. AGENTS.md aliased by multiple variables)

scripts/bash/check-prerequisites.sh

@@ -79,15 +79,28 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths and validate branch
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 
 # If paths-only mode, output paths and exit (support JSON + paths-only combined)
 if $PATHS_ONLY; then
     if $JSON_MODE; then
         # Minimal JSON paths payload (no validation performed)
+        if has_jq; then
+            jq -cn \
+                --arg repo_root "$REPO_ROOT" \
+                --arg branch "$CURRENT_BRANCH" \
+                --arg feature_dir "$FEATURE_DIR" \
+                --arg feature_spec "$FEATURE_SPEC" \
+                --arg impl_plan "$IMPL_PLAN" \
+                --arg tasks "$TASKS" \
+                '{REPO_ROOT:$repo_root,BRANCH:$branch,FEATURE_DIR:$feature_dir,FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,TASKS:$tasks}'
+        else
             printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
-            "$REPO_ROOT" "$CURRENT_BRANCH" "$FEATURE_DIR" "$FEATURE_SPEC" "$IMPL_PLAN" "$TASKS"
+                "$(json_escape "$REPO_ROOT")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$TASKS")"
+        fi
     else
         echo "REPO_ROOT: $REPO_ROOT"
         echo "BRANCH: $CURRENT_BRANCH"
@@ -141,14 +154,25 @@ fi
 # Output results
 if $JSON_MODE; then
     # Build JSON array of documents
+    if has_jq; then
+        if [[ ${#docs[@]} -eq 0 ]]; then
+            json_docs="[]"
+        else
+            json_docs=$(printf '%s\n' "${docs[@]}" | jq -R . | jq -s .)
+        fi
+        jq -cn \
+            --arg feature_dir "$FEATURE_DIR" \
+            --argjson docs "$json_docs" \
+            '{FEATURE_DIR:$feature_dir,AVAILABLE_DOCS:$docs}'
+    else
         if [[ ${#docs[@]} -eq 0 ]]; then
             json_docs="[]"
         else
             json_docs=$(printf '"%s",' "${docs[@]}")
             json_docs="[${json_docs%,}]"
         fi
-    
+        printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"
-    printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$FEATURE_DIR" "$json_docs"
+    fi
 else
     # Text output
     echo "FEATURE_DIR:$FEATURE_DIR"

scripts/bash/common.sh

@@ -120,7 +120,7 @@ find_feature_dir_by_prefix() {
         # Multiple matches - this shouldn't happen with proper naming convention
         echo "ERROR: Multiple spec directories found with prefix '$prefix': ${matches[*]}" >&2
         echo "Please ensure only one spec directory exists per numeric prefix." >&2
-        echo "$specs_dir/$branch_name"  # Return something to avoid breaking the script
+        return 1
     fi
 }
 
@@ -134,21 +134,42 @@ get_feature_paths() {
     fi
 
     # Use prefix-based lookup to support multiple branches per spec
-    local feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch")
+    local feature_dir
+    if ! feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch"); then
+        echo "ERROR: Failed to resolve feature directory" >&2
+        return 1
+    fi
 
-    cat <<EOF
+    # Use printf '%q' to safely quote values, preventing shell injection
-REPO_ROOT='$repo_root'
+    # via crafted branch names or paths containing special characters
-CURRENT_BRANCH='$current_branch'
+    printf 'REPO_ROOT=%q\n' "$repo_root"
-HAS_GIT='$has_git_repo'
+    printf 'CURRENT_BRANCH=%q\n' "$current_branch"
-FEATURE_DIR='$feature_dir'
+    printf 'HAS_GIT=%q\n' "$has_git_repo"
-FEATURE_SPEC='$feature_dir/spec.md'
+    printf 'FEATURE_DIR=%q\n' "$feature_dir"
-IMPL_PLAN='$feature_dir/plan.md'
+    printf 'FEATURE_SPEC=%q\n' "$feature_dir/spec.md"
-TASKS='$feature_dir/tasks.md'
+    printf 'IMPL_PLAN=%q\n' "$feature_dir/plan.md"
-RESEARCH='$feature_dir/research.md'
+    printf 'TASKS=%q\n' "$feature_dir/tasks.md"
-DATA_MODEL='$feature_dir/data-model.md'
+    printf 'RESEARCH=%q\n' "$feature_dir/research.md"
-QUICKSTART='$feature_dir/quickstart.md'
+    printf 'DATA_MODEL=%q\n' "$feature_dir/data-model.md"
-CONTRACTS_DIR='$feature_dir/contracts'
+    printf 'QUICKSTART=%q\n' "$feature_dir/quickstart.md"
-EOF
+    printf 'CONTRACTS_DIR=%q\n' "$feature_dir/contracts"
+}
+
+# Check if jq is available for safe JSON construction
+has_jq() {
+    command -v jq >/dev/null 2>&1
+}
+
+# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
+# Handles backslash, double-quote, and control characters (newline, tab, carriage return).
+json_escape() {
+    local s="$1"
+    s="${s//\\/\\\\}"
+    s="${s//\"/\\\"}"
+    s="${s//$'\n'/\\n}"
+    s="${s//$'\t'/\\t}"
+    s="${s//$'\r'/\\r}"
+    printf '%s' "$s"
 }
 
 check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }

scripts/bash/create-new-feature.sh

@@ -162,6 +162,17 @@ clean_branch_name() {
     echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }
 
+# Escape a string for safe embedding in a JSON value (fallback when jq is unavailable).
+json_escape() {
+    local s="$1"
+    s="${s//\\/\\\\}"
+    s="${s//\"/\\\"}"
+    s="${s//$'\n'/\\n}"
+    s="${s//$'\t'/\\t}"
+    s="${s//$'\r'/\\r}"
+    printf '%s' "$s"
+}
+
 # Resolve repository root. Prefer git information when available, but fall back
 # to searching for repository markers so the workflow still functions in repositories that
 # were initialised with --no-git.
@@ -300,14 +311,22 @@ TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
 SPEC_FILE="$FEATURE_DIR/spec.md"
 if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
 
-# Set the SPECIFY_FEATURE environment variable for the current session
+# Inform the user how to persist the feature variable in their own shell
-export SPECIFY_FEATURE="$BRANCH_NAME"
+printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2
 
 if $JSON_MODE; then
-    printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$BRANCH_NAME" "$SPEC_FILE" "$FEATURE_NUM"
+    if command -v jq >/dev/null 2>&1; then
+        jq -cn \
+            --arg branch_name "$BRANCH_NAME" \
+            --arg spec_file "$SPEC_FILE" \
+            --arg feature_num "$FEATURE_NUM" \
+            '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num}'
+    else
+        printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$(json_escape "$BRANCH_NAME")" "$(json_escape "$SPEC_FILE")" "$(json_escape "$FEATURE_NUM")"
+    fi
 else
     echo "BRANCH_NAME: $BRANCH_NAME"
     echo "SPEC_FILE: $SPEC_FILE"
     echo "FEATURE_NUM: $FEATURE_NUM"
-    echo "SPECIFY_FEATURE environment variable set to: $BRANCH_NAME"
+    printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
 fi

scripts/bash/setup-plan.sh

@@ -28,7 +28,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 
 # Check if we're on a proper feature branch (only for git repos)
 check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
@@ -49,8 +51,18 @@ fi
 
 # Output results
 if $JSON_MODE; then
+    if has_jq; then
+        jq -cn \
+            --arg feature_spec "$FEATURE_SPEC" \
+            --arg impl_plan "$IMPL_PLAN" \
+            --arg specs_dir "$FEATURE_DIR" \
+            --arg branch "$CURRENT_BRANCH" \
+            --arg has_git "$HAS_GIT" \
+            '{FEATURE_SPEC:$feature_spec,IMPL_PLAN:$impl_plan,SPECS_DIR:$specs_dir,BRANCH:$branch,HAS_GIT:$has_git}'
+    else
         printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
-        "$FEATURE_SPEC" "$IMPL_PLAN" "$FEATURE_DIR" "$CURRENT_BRANCH" "$HAS_GIT"
+            "$(json_escape "$FEATURE_SPEC")" "$(json_escape "$IMPL_PLAN")" "$(json_escape "$FEATURE_DIR")" "$(json_escape "$CURRENT_BRANCH")" "$(json_escape "$HAS_GIT")"
+    fi
 else
     echo "FEATURE_SPEC: $FEATURE_SPEC"
     echo "IMPL_PLAN: $IMPL_PLAN" 

scripts/bash/update-agent-context.sh

@@ -53,7 +53,9 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get all paths and variables from common functions
-eval $(get_feature_paths)
+_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+eval "$_paths_output"
+unset _paths_output
 
 NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
 AGENT_TYPE="${1:-}"
@@ -71,12 +73,14 @@ AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
 ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
 CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
 QODER_FILE="$REPO_ROOT/QODER.md"
-AMP_FILE="$REPO_ROOT/AGENTS.md"
+# AMP, Kiro CLI, and IBM Bob all share AGENTS.md — use AGENTS_FILE to avoid
+# updating the same file multiple times.
+AMP_FILE="$AGENTS_FILE"
 SHAI_FILE="$REPO_ROOT/SHAI.md"
 TABNINE_FILE="$REPO_ROOT/TABNINE.md"
-KIRO_FILE="$REPO_ROOT/AGENTS.md"
+KIRO_FILE="$AGENTS_FILE"
 AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
-BOB_FILE="$REPO_ROOT/AGENTS.md"
+BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
 
@@ -112,6 +116,8 @@ log_warning() {
 # Cleanup function for temporary files
 cleanup() {
     local exit_code=$?
+    # Disarm traps to prevent re-entrant loop
+    trap - EXIT INT TERM
     rm -f /tmp/agent_update_*_$$
     rm -f /tmp/manual_additions_$$
     exit $exit_code
@@ -607,67 +613,67 @@ update_specific_agent() {
     
     case "$agent_type" in
         claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code"
+            update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
             ;;
         gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI"
+            update_agent_file "$GEMINI_FILE" "Gemini CLI" || return 1
             ;;
         copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot"
+            update_agent_file "$COPILOT_FILE" "GitHub Copilot" || return 1
             ;;
         cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE"
+            update_agent_file "$CURSOR_FILE" "Cursor IDE" || return 1
             ;;
         qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code"
+            update_agent_file "$QWEN_FILE" "Qwen Code" || return 1
             ;;
         opencode)
-            update_agent_file "$AGENTS_FILE" "opencode"
+            update_agent_file "$AGENTS_FILE" "opencode" || return 1
             ;;
         codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI"
+            update_agent_file "$AGENTS_FILE" "Codex CLI" || return 1
             ;;
         windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf"
+            update_agent_file "$WINDSURF_FILE" "Windsurf" || return 1
             ;;
         kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code"
+            update_agent_file "$KILOCODE_FILE" "Kilo Code" || return 1
             ;;
         auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI"
+            update_agent_file "$AUGGIE_FILE" "Auggie CLI" || return 1
             ;;
         roo)
-            update_agent_file "$ROO_FILE" "Roo Code"
+            update_agent_file "$ROO_FILE" "Roo Code" || return 1
             ;;
         codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
+            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI" || return 1
             ;;
         qodercli)
-            update_agent_file "$QODER_FILE" "Qoder CLI"
+            update_agent_file "$QODER_FILE" "Qoder CLI" || return 1
             ;;
         amp)
-            update_agent_file "$AMP_FILE" "Amp"
+            update_agent_file "$AMP_FILE" "Amp" || return 1
             ;;
         shai)
-            update_agent_file "$SHAI_FILE" "SHAI"
+            update_agent_file "$SHAI_FILE" "SHAI" || return 1
             ;;
         tabnine)
-            update_agent_file "$TABNINE_FILE" "Tabnine CLI"
+            update_agent_file "$TABNINE_FILE" "Tabnine CLI" || return 1
             ;;
         kiro-cli)
-            update_agent_file "$KIRO_FILE" "Kiro CLI"
+            update_agent_file "$KIRO_FILE" "Kiro CLI" || return 1
             ;;
         agy)
-            update_agent_file "$AGY_FILE" "Antigravity"
+            update_agent_file "$AGY_FILE" "Antigravity" || return 1
             ;;
         bob)
-            update_agent_file "$BOB_FILE" "IBM Bob"
+            update_agent_file "$BOB_FILE" "IBM Bob" || return 1
             ;;
         vibe)
-            update_agent_file "$VIBE_FILE" "Mistral Vibe"
+            update_agent_file "$VIBE_FILE" "Mistral Vibe" || return 1
             ;;
         kimi)
-            update_agent_file "$KIMI_FILE" "Kimi Code"
+            update_agent_file "$KIMI_FILE" "Kimi Code" || return 1
             ;;
         generic)
             log_info "Generic agent: no predefined context file. Use the agent-specific update script for your agent."
@@ -682,106 +688,53 @@ update_specific_agent() {
 
 update_all_existing_agents() {
     local found_agent=false
+    local _updated_paths=()
 
-    # Check each possible agent file and update if it exists
+    # Helper: skip non-existent files and files already updated (dedup by
-    if [[ -f "$CLAUDE_FILE" ]]; then
+    # realpath so that variables pointing to the same file — e.g. AMP_FILE,
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
+    # KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
-        found_agent=true
+    # Uses a linear array instead of associative array for bash 3.2 compatibility.
+    update_if_new() {
+        local file="$1" name="$2"
+        [[ -f "$file" ]] || return 0
+        local real_path
+        real_path=$(realpath "$file" 2>/dev/null || echo "$file")
+        local p
+        if [[ ${#_updated_paths[@]} -gt 0 ]]; then
+            for p in "${_updated_paths[@]}"; do
+                [[ "$p" == "$real_path" ]] && return 0
+            done
         fi
+        update_agent_file "$file" "$name" || return 1
+        _updated_paths+=("$real_path")
+        found_agent=true
+    }
 
-    if [[ -f "$GEMINI_FILE" ]]; then
+    update_if_new "$CLAUDE_FILE" "Claude Code"
-        update_agent_file "$GEMINI_FILE" "Gemini CLI"
+    update_if_new "$GEMINI_FILE" "Gemini CLI"
-        found_agent=true
+    update_if_new "$COPILOT_FILE" "GitHub Copilot"
-    fi
+    update_if_new "$CURSOR_FILE" "Cursor IDE"
-    
+    update_if_new "$QWEN_FILE" "Qwen Code"
-    if [[ -f "$COPILOT_FILE" ]]; then
+    update_if_new "$AGENTS_FILE" "Codex/opencode"
-        update_agent_file "$COPILOT_FILE" "GitHub Copilot"
+    update_if_new "$AMP_FILE" "Amp"
-        found_agent=true
+    update_if_new "$KIRO_FILE" "Kiro CLI"
-    fi
+    update_if_new "$BOB_FILE" "IBM Bob"
-    
+    update_if_new "$WINDSURF_FILE" "Windsurf"
-    if [[ -f "$CURSOR_FILE" ]]; then
+    update_if_new "$KILOCODE_FILE" "Kilo Code"
-        update_agent_file "$CURSOR_FILE" "Cursor IDE"
+    update_if_new "$AUGGIE_FILE" "Auggie CLI"
-        found_agent=true
+    update_if_new "$ROO_FILE" "Roo Code"
-    fi
+    update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"
-    
+    update_if_new "$SHAI_FILE" "SHAI"
-    if [[ -f "$QWEN_FILE" ]]; then
+    update_if_new "$TABNINE_FILE" "Tabnine CLI"
-        update_agent_file "$QWEN_FILE" "Qwen Code"
+    update_if_new "$QODER_FILE" "Qoder CLI"
-        found_agent=true
+    update_if_new "$AGY_FILE" "Antigravity"
-    fi
+    update_if_new "$VIBE_FILE" "Mistral Vibe"
-    
+    update_if_new "$KIMI_FILE" "Kimi Code"
-    if [[ -f "$AGENTS_FILE" ]]; then
-        update_agent_file "$AGENTS_FILE" "Codex/opencode"
-        found_agent=true
-    fi
-    
-    if [[ -f "$WINDSURF_FILE" ]]; then
-        update_agent_file "$WINDSURF_FILE" "Windsurf"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KILOCODE_FILE" ]]; then
-        update_agent_file "$KILOCODE_FILE" "Kilo Code"
-        found_agent=true
-    fi
-
-    if [[ -f "$AUGGIE_FILE" ]]; then
-        update_agent_file "$AUGGIE_FILE" "Auggie CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$ROO_FILE" ]]; then
-        update_agent_file "$ROO_FILE" "Roo Code"
-        found_agent=true
-    fi
-
-    if [[ -f "$CODEBUDDY_FILE" ]]; then
-        update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$SHAI_FILE" ]]; then
-        update_agent_file "$SHAI_FILE" "SHAI"
-        found_agent=true
-    fi
-
-    if [[ -f "$TABNINE_FILE" ]]; then
-        update_agent_file "$TABNINE_FILE" "Tabnine CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$QODER_FILE" ]]; then
-        update_agent_file "$QODER_FILE" "Qoder CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$KIRO_FILE" ]]; then
-        update_agent_file "$KIRO_FILE" "Kiro CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$AGY_FILE" ]]; then
-        update_agent_file "$AGY_FILE" "Antigravity"
-        found_agent=true
-    fi
-    if [[ -f "$BOB_FILE" ]]; then
-        update_agent_file "$BOB_FILE" "IBM Bob"
-        found_agent=true
-    fi
-
-    if [[ -f "$VIBE_FILE" ]]; then
-        update_agent_file "$VIBE_FILE" "Mistral Vibe"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KIMI_FILE" ]]; then
-        update_agent_file "$KIMI_FILE" "Kimi Code"
-        found_agent=true
-    fi
 
     # If no agent files exist, create a default Claude file
     if [[ "$found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
+        update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
     fi
 }
 print_summary() {