fix(scripts): harden bash scripts — escape, compat, and error handling (#1869)

* fix(scripts): harden bash scripts with escape, compat, and cleanup fixes

- common.sh: complete RFC 8259 JSON escape (\b, \f, strip control chars)
- common.sh: distinguish python3 success-empty vs failure in resolve_template
- check-prerequisites.sh: escape doc names through json_escape in fallback path
- create-new-feature.sh: remove duplicate json_escape (already in common.sh)
- create-new-feature.sh: warn on stderr when spec template is not found
- update-agent-context.sh: move nested function to top-level for bash 3.2 compat

* fix(scripts): explicit resolve_template return code and best-effort agent updates

- common.sh: resolve_template now returns 1 when no template is found,
  making the "not found" case explicit instead of relying on empty stdout
- setup-plan.sh, create-new-feature.sh: add || true to resolve_template
  calls so set -e does not abort on missing templates (non-fatal)
- update-agent-context.sh: accumulate errors in update_all_existing_agents
  instead of silently discarding them — all agents are attempted and the
  composite result is returned, matching the PowerShell equivalent behavior

* style(scripts): add clarifying comment in resolve_template preset branch

* fix(scripts): wrap python3 call in if-condition to prevent set -e abort

Move the python3 command substitution in resolve_template into an
if-condition so that a non-zero exit (e.g. invalid .registry JSON)
does not abort the function under set -e. The fallback directory
scan now executes as intended regardless of caller errexit settings.

* fix(scripts): track agent file existence before update and avoid top-level globals

- _update_if_new now records the path and sets _found_agent before calling
  update_agent_file, so that failures do not cause duplicate attempts on
  aliased paths (AMP/KIRO/BOB -> AGENTS_FILE) or false "no agent files
  found" fallback triggers
- Remove top-level initialisation of _updated_paths and _found_agent;
  they are now created exclusively inside update_all_existing_agents,
  keeping the script side-effect free when sourced

scripts/bash/check-prerequisites.sh

@@ -168,7 +168,7 @@ if $JSON_MODE; then
         if [[ ${#docs[@]} -eq 0 ]]; then
             json_docs="[]"
         else
-            json_docs=$(printf '"%s",' "${docs[@]}")
+            json_docs=$(for d in "${docs[@]}"; do printf '"%s",' "$(json_escape "$d")"; done)
             json_docs="[${json_docs%,}]"
         fi
         printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$(json_escape "$FEATURE_DIR")" "$json_docs"

scripts/bash/common.sh

@@ -161,7 +161,7 @@ has_jq() {
 }
 
 # 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).
+# Handles backslash, double-quote, and JSON-required control character escapes (RFC 8259).
 json_escape() {
     local s="$1"
     s="${s//\\/\\\\}"
@@ -169,6 +169,10 @@ json_escape() {
     s="${s//$'\n'/\\n}"
     s="${s//$'\t'/\\t}"
     s="${s//$'\r'/\\r}"
+    s="${s//$'\b'/\\b}"
+    s="${s//$'\f'/\\f}"
+    # Strip remaining control characters (U+0000–U+001F) not individually escaped above
+    s=$(printf '%s' "$s" | tr -d '\000-\007\013\016-\037')
     printf '%s' "$s"
 }
 
@@ -194,9 +198,11 @@ resolve_template() {
     if [ -d "$presets_dir" ]; then
         local registry_file="$presets_dir/.registry"
         if [ -f "$registry_file" ] && command -v python3 >/dev/null 2>&1; then
-            # Read preset IDs sorted by priority (lower number = higher precedence)
+            # Read preset IDs sorted by priority (lower number = higher precedence).
-            local sorted_presets
+            # The python3 call is wrapped in an if-condition so that set -e does not
-            sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
+            # abort the function when python3 exits non-zero (e.g. invalid JSON).
+            local sorted_presets=""
+            if sorted_presets=$(SPECKIT_REGISTRY="$registry_file" python3 -c "
 import json, sys, os
 try:
     with open(os.environ['SPECKIT_REGISTRY']) as f:
@@ -206,14 +212,17 @@ try:
         print(pid)
 except Exception:
     sys.exit(1)
-" 2>/dev/null)
+" 2>/dev/null); then
-            if [ $? -eq 0 ] && [ -n "$sorted_presets" ]; then
+                if [ -n "$sorted_presets" ]; then
-                while IFS= read -r preset_id; do
+                    # python3 succeeded and returned preset IDs — search in priority order
-                    local candidate="$presets_dir/$preset_id/templates/${template_name}.md"
+                    while IFS= read -r preset_id; do
-                    [ -f "$candidate" ] && echo "$candidate" && return 0
+                        local candidate="$presets_dir/$preset_id/templates/${template_name}.md"
-                done <<< "$sorted_presets"
+                        [ -f "$candidate" ] && echo "$candidate" && return 0
+                    done <<< "$sorted_presets"
+                fi
+                # python3 succeeded but registry has no presets — nothing to search
             else
-                # python3 returned empty list — fall through to directory scan
+                # python3 failed (missing, or registry parse error) — fall back to unordered directory scan
                 for preset in "$presets_dir"/*/; do
                     [ -d "$preset" ] || continue
                     local candidate="$preset/templates/${template_name}.md"
@@ -246,8 +255,9 @@ except Exception:
     local core="$base/${template_name}.md"
     [ -f "$core" ] && echo "$core" && return 0
 
-    # Return success with empty output so callers using set -e don't abort;
+    # Template not found in any location.
-    # callers check [ -n "$TEMPLATE" ] to detect "not found".
+    # Return 1 so callers can distinguish "not found" from "found".
-    return 0
+    # Callers running under set -e should use: TEMPLATE=$(resolve_template ...) || true
+    return 1
 }
 

scripts/bash/create-new-feature.sh

@@ -162,17 +162,6 @@ 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.
@@ -308,9 +297,14 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
-TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT")
+TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
+if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
+    cp "$TEMPLATE" "$SPEC_FILE"
+else
+    echo "Warning: Spec template not found; created empty spec file" >&2
+    touch "$SPEC_FILE"
+fi
 
 # Inform the user how to persist the feature variable in their own shell
 printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2

scripts/bash/setup-plan.sh

@@ -39,7 +39,7 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 mkdir -p "$FEATURE_DIR"
 
 # Copy plan template if it exists
-TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT")
+TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
 if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
     cp "$TEMPLATE" "$IMPL_PLAN"
     echo "Copied plan template to $IMPL_PLAN"

scripts/bash/update-agent-context.sh

@@ -686,56 +686,67 @@ update_specific_agent() {
     esac
 }
 
+# Helper: skip non-existent files and files already updated (dedup by
+# realpath so that variables pointing to the same file — e.g. AMP_FILE,
+# KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
+# Uses a linear array instead of associative array for bash 3.2 compatibility.
+# Note: defined at top level because bash 3.2 does not support true
+# nested/local functions. _updated_paths, _found_agent, and _all_ok are
+# initialised exclusively inside update_all_existing_agents so that
+# sourcing this script has no side effects on the caller's environment.
+
+_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
+    # Record the file as seen before attempting the update so that:
+    # (a) aliases pointing to the same path are not retried on failure
+    # (b) _found_agent reflects file existence, not update success
+    _updated_paths+=("$real_path")
+    _found_agent=true
+    update_agent_file "$file" "$name"
+}
+
 update_all_existing_agents() {
-    local found_agent=false
+    _found_agent=false
-    local _updated_paths=()
+    _updated_paths=()
+    local _all_ok=true
 
-    # Helper: skip non-existent files and files already updated (dedup by
+    _update_if_new "$CLAUDE_FILE" "Claude Code"           || _all_ok=false
-    # realpath so that variables pointing to the same file — e.g. AMP_FILE,
+    _update_if_new "$GEMINI_FILE" "Gemini CLI"             || _all_ok=false
-    # KIRO_FILE, BOB_FILE all resolving to AGENTS_FILE — are only written once).
+    _update_if_new "$COPILOT_FILE" "GitHub Copilot"        || _all_ok=false
-    # Uses a linear array instead of associative array for bash 3.2 compatibility.
+    _update_if_new "$CURSOR_FILE" "Cursor IDE"             || _all_ok=false
-    update_if_new() {
+    _update_if_new "$QWEN_FILE" "Qwen Code"                || _all_ok=false
-        local file="$1" name="$2"
+    _update_if_new "$AGENTS_FILE" "Codex/opencode"         || _all_ok=false
-        [[ -f "$file" ]] || return 0
+    _update_if_new "$AMP_FILE" "Amp"                       || _all_ok=false
-        local real_path
+    _update_if_new "$KIRO_FILE" "Kiro CLI"                 || _all_ok=false
-        real_path=$(realpath "$file" 2>/dev/null || echo "$file")
+    _update_if_new "$BOB_FILE" "IBM Bob"                   || _all_ok=false
-        local p
+    _update_if_new "$WINDSURF_FILE" "Windsurf"             || _all_ok=false
-        if [[ ${#_updated_paths[@]} -gt 0 ]]; then
+    _update_if_new "$KILOCODE_FILE" "Kilo Code"            || _all_ok=false
-            for p in "${_updated_paths[@]}"; do
+    _update_if_new "$AUGGIE_FILE" "Auggie CLI"             || _all_ok=false
-                [[ "$p" == "$real_path" ]] && return 0
+    _update_if_new "$ROO_FILE" "Roo Code"                  || _all_ok=false
-            done
+    _update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"       || _all_ok=false
-        fi
+    _update_if_new "$SHAI_FILE" "SHAI"                     || _all_ok=false
-        update_agent_file "$file" "$name" || return 1
+    _update_if_new "$TABNINE_FILE" "Tabnine CLI"           || _all_ok=false
-        _updated_paths+=("$real_path")
+    _update_if_new "$QODER_FILE" "Qoder CLI"               || _all_ok=false
-        found_agent=true
+    _update_if_new "$AGY_FILE" "Antigravity"               || _all_ok=false
-    }
+    _update_if_new "$VIBE_FILE" "Mistral Vibe"             || _all_ok=false
-
+    _update_if_new "$KIMI_FILE" "Kimi Code"                || _all_ok=false
-    update_if_new "$CLAUDE_FILE" "Claude Code"
-    update_if_new "$GEMINI_FILE" "Gemini CLI"
-    update_if_new "$COPILOT_FILE" "GitHub Copilot"
-    update_if_new "$CURSOR_FILE" "Cursor IDE"
-    update_if_new "$QWEN_FILE" "Qwen Code"
-    update_if_new "$AGENTS_FILE" "Codex/opencode"
-    update_if_new "$AMP_FILE" "Amp"
-    update_if_new "$KIRO_FILE" "Kiro CLI"
-    update_if_new "$BOB_FILE" "IBM Bob"
-    update_if_new "$WINDSURF_FILE" "Windsurf"
-    update_if_new "$KILOCODE_FILE" "Kilo Code"
-    update_if_new "$AUGGIE_FILE" "Auggie CLI"
-    update_if_new "$ROO_FILE" "Roo Code"
-    update_if_new "$CODEBUDDY_FILE" "CodeBuddy CLI"
-    update_if_new "$SHAI_FILE" "SHAI"
-    update_if_new "$TABNINE_FILE" "Tabnine CLI"
-    update_if_new "$QODER_FILE" "Qoder CLI"
-    update_if_new "$AGY_FILE" "Antigravity"
-    update_if_new "$VIBE_FILE" "Mistral Vibe"
-    update_if_new "$KIMI_FILE" "Kimi Code"
 
     # If no agent files exist, create a default Claude file
-    if [[ "$found_agent" == false ]]; then
+    if [[ "$_found_agent" == false ]]; then
         log_info "No existing agent files found, creating default Claude file..."
         update_agent_file "$CLAUDE_FILE" "Claude Code" || return 1
     fi
+
+    [[ "$_all_ok" == true ]]
 }
 print_summary() {
     echo