The spec-kit pin is 1.2.6

.claude/skills/speckit-specify/SKILL.md

@@ -94,9 +94,9 @@ Given that feature description, do this:
       - If `branch_numbering` was used (and `feature_numbering` was absent), emit a one-line warning: "⚠️ `branch_numbering` in init-options.json is deprecated. Rename to `feature_numbering`."
 
    **Create the directory and spec file**:
+   - Run `.specify/scripts/bash/resolve-template.sh spec-template --json` from the repository root and parse `TEMPLATE_CONTENT` as the active `spec-template`. The shared resolver composes project overrides, preset layers, and extension layers over the core template, including `append`, `prepend`, and `wrap` strategies. If it fails, stop and report the resolution error; do not continue with only one contributing template layer.
    - `mkdir -p SPECIFY_FEATURE_DIRECTORY`
-   - Resolve the active `spec-template` through the Spec Kit preset/template resolution stack (equivalent to `specify preset resolve spec-template`)
-   - Copy the resolved `spec-template` file to `SPECIFY_FEATURE_DIRECTORY/spec.md` as the starting point
+   - Write `TEMPLATE_CONTENT` to `SPECIFY_FEATURE_DIRECTORY/spec.md` as the starting point. Do not copy a template file from disk instead: when a preset composes `spec-template`, no single file holds the full template.
    - Set `SPEC_FILE` to `SPECIFY_FEATURE_DIRECTORY/spec.md`
    - Persist the resolved path to `.specify/feature.json`:
      ```json
@@ -112,7 +112,7 @@ Given that feature description, do this:
    - The spec directory name and the git branch name are independent — they may be the same but that is the user's choice
    - The spec directory and file are always created by this command, never by the hook
 
-4. Load the resolved active `spec-template` file to understand required sections.
+4. Use `TEMPLATE_CONTENT` to understand required sections.
 
 5. **IF EXISTS**: Load `.specify/memory/constitution.md` for project principles and governance constraints.
 

.claude/skills/speckit-taskstoissues/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: "speckit-taskstoissues"
-description: "Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts."
+description: "Deprecated: Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts."
 argument-hint: "Optional filter or label for GitHub issues"
 compatibility: "Requires spec-kit project structure with .specify/ directory"
 metadata:
@@ -11,6 +11,14 @@ disable-model-invocation: false
 ---
 
 
+## Deprecation Notice
+
+You **MUST display the following concise warning first**, as the first step of this command and before the User Input and Pre-Execution Checks sections below:
+
+> ⚠️ `/speckit-taskstoissues` is deprecated and will be removed in a future minor release. Use the bundled `github` extension instead: run `specify extension add github`, then invoke `/speckit-github-taskstoissues`.
+
+Continue with the existing workflow unchanged. Do not install or enable the extension automatically, do not stop, and do not run the replacement command.
+
 ## User Input
 
 ```text

.specify/.gitignore

@@ -7,3 +7,8 @@ feature.json
 
 # Per-machine extension config overrides.
 extensions/*/local-config.yml
+
+# Executable adapter packages and their per-checkout provenance registry.
+# Execution consent is stored separately in the user's local trust registry.
+integrations/packages/
+integrations/packages.json

.specify/init-options.json

@@ -1,9 +1,10 @@
 {
   "ai": "claude",
   "ai_skills": true,
+  "allow_symlinks": false,
   "feature_numbering": "sequential",
   "here": true,
   "integration": "claude",
   "script": "sh",
-  "speckit_version": "1.0.10"
+  "speckit_version": "1.2.6"
 }

.specify/integration.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.10",
+  "version": "1.2.6",
   "integration_state_schema": 1,
   "installed_integrations": [
     "claude"

.specify/integrations/claude.manifest.json

@@ -1,7 +1,7 @@
 {
   "integration": "claude",
-  "version": "1.0.10",
-  "installed_at": "2026-09-23T04:46:11.261794+00:00",
+  "version": "1.2.6",
+  "installed_at": "2026-11-03T05:57:00.821508+00:00",
   "files": {
     ".claude/skills/speckit-analyze/SKILL.md": "3237cd827194efaf6bb06ba05ef9bc1a703a223d362f5e34d0558c5a38ae34d0",
     ".claude/skills/speckit-clarify/SKILL.md": "164f49ef87cb2e922585316f5281b455a8e1940b1efd25317d517a567acae472",
@@ -10,8 +10,8 @@
     ".claude/skills/speckit-converge/SKILL.md": "9f93c1d573592f146670202210128ed24a9d75c92133951b19a2bb0e34eac13b",
     ".claude/skills/speckit-plan/SKILL.md": "9e97fc0b4ce895c70a1ea720dc0377618c23e27c83ecf4d87b6e0f6c323790a4",
     ".claude/skills/speckit-checklist/SKILL.md": "5dc436df0c727e9078bf182dd385e5cb1b60ee67ebe644d3f659ec12e3b78abb",
-    ".claude/skills/speckit-specify/SKILL.md": "d4d93f2444355136e78bb533988aa2dd560dc4b258f4923f67b1a437e7de38f8",
+    ".claude/skills/speckit-specify/SKILL.md": "044bfaa8d053f1bb4006f318fdf691fabf7da71e1f0ec4908527d5c8eddc61d5",
     ".claude/skills/speckit-tasks/SKILL.md": "d148aeda1011260c4465c5f105fa1e045a0b0224ccb3e6e0c1ec32c732cae1ae",
-    ".claude/skills/speckit-taskstoissues/SKILL.md": "464bbaf464a28ffa371b0452599c18e7cb5799630148d9f945e6a4d7066a1234"
+    ".claude/skills/speckit-taskstoissues/SKILL.md": "471edc95cb41acdc18d4ab3c0f024334bbc4bac9936f955dde30fc3cb9d77473"
   }
 }

.specify/integrations/speckit.manifest.json

@@ -1,19 +1,19 @@
 {
   "integration": "speckit",
-  "version": "1.0.10",
+  "version": "1.2.6",
   "installed_at": "2026-07-09T09:52:36.384815+00:00",
   "files": {
-    ".specify/scripts/bash/common.sh": "ff7ab71ddcf3db2ee85564a3fd66b4d2a26390150a8540c62109541e5ae607a0",
-    ".specify/scripts/bash/setup-plan.sh": "d0bd298c026446f3c63167130d65e49e4aa4485de6bef18bcdfd57b19aa0de96",
+    ".specify/scripts/bash/common.sh": "53cb1c23e349db4586c272436ce35c6e2f36a9c0b5351a85e0b216d9887a26b7",
+    ".specify/scripts/bash/setup-plan.sh": "d378ec66ba20d2da01c71dad8935062c1c27f0bba890be9a6d3dda52ea056a4e",
     ".specify/scripts/bash/setup-tasks.sh": "4a33dd1e6c32ddc7d570f4b538572c54069192573eed0ec654d9fb826e31a4fe",
-    ".specify/scripts/bash/check-prerequisites.sh": "daa377146db4fb69912f42611a7b91c5d55873b3e3e27ed33bd8d67505826344",
-    ".specify/scripts/bash/create-new-feature.sh": "f4244c6cf95025e5726669938e9152d4a557cc7c1e8b027a43cb4de72677da16",
+    ".specify/scripts/bash/check-prerequisites.sh": "e127735bbc5ac42181e2a3c773a2d639979f865f18e74a1a977cdf53392a0a7d",
+    ".specify/scripts/bash/create-new-feature.sh": "972f03ed8ca5ee17b7baad6d56d821d46269d77abc337496beafb0fe85a725f2",
     ".specify/templates/constitution-template.md": "ce7549540fa45543cca797a150201d868e64495fdff39dc38246fb17bd4024b3",
     ".specify/templates/checklist-template.md": "856532b3cb66171c662cc16f16b31a5856e4655a8666aad1e545bbfc7f603ca1",
     ".specify/templates/tasks-template.md": "fc29a233f6f5a27ca31f1aa46b596af6500c627441c6e62b2bc4a1d721525842",
     ".specify/templates/spec-template.md": "3945437fc35cd30a5b2bf7beea680337c3516826d3efa5a6b92c4a7eca1ba28e",
     ".specify/templates/plan-template.md": "7e637502d41eccf0ca672496636365691fdca62ef37b27ec07fcb412dbfa90d4",
     ".specify/scripts/bash/resolve-template.sh": "829e227096abc8bf0889889ec9f792f503ca5d395b7836a8a7eb739ee75214e7",
-    ".specify/.gitignore": "8c908410d177a1ef3d0dee16d7ad55f2ac3333df3104c4d4adee1c9b82f1dbc1"
+    ".specify/.gitignore": "0a61c5378b0bb2e0f85babff99c8b166f2170a2c12378cd17d929aa19296ec88"
   }
 }

.specify/scripts/bash/check-prerequisites.sh

@@ -148,6 +148,12 @@ if [[ ! -f "$IMPL_PLAN" ]]; then
     exit 1
 fi
 
+if [[ ! -s "$IMPL_PLAN" ]]; then
+    echo "ERROR: plan.md is empty in $FEATURE_DIR" >&2
+    echo "Populate it, or remove the empty file and rerun /speckit-plan with a valid plan template." >&2
+    exit 1
+fi
+
 # Check for spec.md if required
 if $REQUIRE_SPEC && [[ ! -f "$FEATURE_SPEC" ]]; then
     echo "ERROR: spec.md not found in $FEATURE_DIR" >&2

.specify/scripts/bash/common.sh

@@ -112,7 +112,7 @@ read_feature_json_feature_directory() {
     fi
     if [[ -z "$_fd" ]] && command -v python3 >/dev/null 2>&1; then
         # Use Python so pretty-printed/multi-line JSON still parses correctly.
-        if ! _fd=$(python3 -c "import json,sys; d=json.load(open(sys.argv[1])); v=d.get('feature_directory'); print(v if v else '')" "$fj" 2>/dev/null); then
+        if ! _fd=$(python3 -c "import json,sys; d=json.load(open(sys.argv[1], encoding='utf-8')); v=d.get('feature_directory'); print(v if v else '')" "$fj" 2>/dev/null); then
             _fd=''
         fi
     fi
@@ -169,6 +169,13 @@ get_feature_paths() {
         no_persist=true
         shift
     fi
+    # SPECIFY_FEATURE_NO_PERSIST is the environment-level equivalent of --no-persist,
+    # letting an orchestrator (multi-agent runner, CI matrix) guarantee that no
+    # script invocation in the process tree writes .specify/feature.json, even
+    # scripts that don't pass --no-persist themselves (#4128).
+    if [[ "${SPECIFY_FEATURE_NO_PERSIST:-}" == "1" || "${SPECIFY_FEATURE_NO_PERSIST:-}" == "true" ]]; then
+        no_persist=true
+    fi
 
     # Split decl/assignment so a SPECIFY_INIT_DIR validation failure in
     # get_repo_root propagates as a hard error instead of being masked by `local`.
@@ -399,26 +406,35 @@ check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 check_dir() { [[ -d "$1" && -n $(ls -A "$1" 2>/dev/null) ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
 
 _python3_command() {
-    if command -v python3 >/dev/null 2>&1 &&
+    # SPECKIT_PYTHON_EXECUTABLE is the canonical override; SPECKIT_PYTHON is
+    # kept as a deprecated fallback (still used by update-agent-context.sh).
+    local override="${SPECKIT_PYTHON_EXECUTABLE:-${SPECKIT_PYTHON:-}}"
+    if [[ -n "$override" ]] && command -v "$override" >/dev/null 2>&1 &&
+        "$override" -c 'import sys; raise SystemExit(sys.version_info.major != 3)' >/dev/null 2>&1 &&
+        "$override" -c 'import yaml' >/dev/null 2>&1; then
+        printf '%s\n' "$override"
+    elif command -v python3 >/dev/null 2>&1 &&
         python3 -c 'import sys; raise SystemExit(sys.version_info.major != 3)' >/dev/null 2>&1; then
         printf '%s\n' "python3"
     elif command -v python >/dev/null 2>&1 &&
         python -c 'import sys; raise SystemExit(sys.version_info.major != 3)' >/dev/null 2>&1; then
         printf '%s\n' "python"
     elif command -v py >/dev/null 2>&1 &&
         py -3 -c 'import sys' >/dev/null 2>&1; then
-        printf '%s\n' "py -3"
+        printf '%s\n' "py" "-3"
     else
         return 1
     fi
 }
 
 _sorted_extension_ids() {
     local ext_dir="$1"
-    local python_spec
-    if python_spec=$(_python3_command); then
-        local -a python_cmd
-        read -r -a python_cmd <<< "$python_spec"
+    local -a python_cmd=()
+    local _python_cmd_line
+    while IFS= read -r _python_cmd_line; do
+        python_cmd+=("$_python_cmd_line")
+    done < <(_python3_command)
+    if [ "${#python_cmd[@]}" -gt 0 ]; then
         local py_stderr sorted_ids
         py_stderr=$(mktemp)
         if sorted_ids=$(SPECKIT_EXTENSIONS="$ext_dir" "${python_cmd[@]}" -c "
@@ -513,11 +529,11 @@ resolve_template() {
     local presets_dir="$repo_root/.specify/presets"
     if [ -d "$presets_dir" ]; then
         local registry_file="$presets_dir/.registry"
-        local python_spec=""
         local -a python_cmd=()
-        if python_spec=$(_python3_command); then
-            read -r -a python_cmd <<< "$python_spec"
-        fi
+        local _python_cmd_line
+        while IFS= read -r _python_cmd_line; do
+            python_cmd+=("$_python_cmd_line")
+        done < <(_python3_command)
         if [ -f "$registry_file" ] && [ "${#python_cmd[@]}" -gt 0 ]; then
             # Read preset IDs sorted by priority (lower number = higher precedence).
             # The python3 call is wrapped in an if-condition so that set -e does not
@@ -636,11 +652,11 @@ resolve_template_content() {
         local registry_file="$presets_dir/.registry"
         local sorted_presets=""
         local registry_parsed=false
-        local python_spec=""
         local -a python_cmd=()
-        if python_spec=$(_python3_command); then
-            read -r -a python_cmd <<< "$python_spec"
-        fi
+        local _python_cmd_line
+        while IFS= read -r _python_cmd_line; do
+            python_cmd+=("$_python_cmd_line")
+        done < <(_python3_command)
         if [ -f "$registry_file" ] && [ "${#python_cmd[@]}" -gt 0 ]; then
             if sorted_presets=$(SPECKIT_REGISTRY="$registry_file" "${python_cmd[@]}" -c "
 import json, re, sys, os