chore: bump version to 0.12.9

.github/workflows/lint.yml

@@ -37,7 +37,7 @@ jobs:
           fi
 
       - name: Run markdownlint-cli2
-        uses: DavidAnson/markdownlint-cli2-action@8de2aa07cae85fd17c0b35642db70cf5495f1d25 # v24.0.0
+        uses: DavidAnson/markdownlint-cli2-action@ded1f9488f68a970bc66ea5619e13e9b52e601cd # v23
         with:
           globs: |
             '**/*.md'

.github/workflows/publish-pypi.yml

@@ -32,7 +32,7 @@ jobs:
           ref: refs/tags/${{ inputs.tag }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -74,7 +74,7 @@ jobs:
           path: dist/
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Publish to PyPI
         run: uv publish

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -37,7 +37,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6

CHANGELOG.md

@@ -2,21 +2,6 @@
 
 <!-- insert new changelog below this comment -->
 
-## [0.12.10] - 2026-07-10
-
-### Changed
-
-- chore(deps): bump astral-sh/setup-uv from 8.2.0 to 8.3.2 (#3439)
-- chore(deps): bump DavidAnson/markdownlint-cli2-action (#3438)
-- fix(templates): correct phase numbering in plan.md (#3416)
-- fix(git-ext): honor explicit -Number 0 in PowerShell branch creation (#3412)
-- docs: add 'spectatui' entry to friends.md (#3362)
-- test: pin interpreter probe so py-template render test passes on Windows (#3428)
-- feat(workflows): make shell step timeout configurable (#3404)
-- fix: find plans in nested spec directories (#3405)
-- feat(templates): add py: lines to command templates' scripts frontmatter (#3403)
-- chore: release 0.12.9, begin 0.12.10.dev0 development (#3426)
-
 ## [0.12.9] - 2026-07-09
 
 ### Changed

docs/community/friends.md

@@ -14,5 +14,3 @@ Community projects that extend, visualize, or build on Spec Kit:
 - **[SpecKit Companion](https://marketplace.visualstudio.com/items?itemName=alfredoperez.speckit-companion)** — A VS Code extension that brings a visual GUI to Spec Kit. Browse specs in a rich markdown viewer with clickable file references, create specifications with image attachments, comment and refine each step inline (GitHub-style review), track your progress through the SDD workflow with a visual phase stepper, and manage steering documents like constitutions and templates.
 
 - **[cc-spec-kit](https://github.com/speckit-community/cc-spec-kit)** — Community-maintained plugin for Claude Code and GitHub Copilot CLI that installs Spec Kit skills via the plugin marketplace.
-
-- **[spectatui](https://github.com/tinesoft/spectatui)** — A terminal UI (TUI) dashboard for Spec Kit that lets you track features, manage specifications, integrations, presets, workflows, and extensions, and monitor AI agent workflows. Attach to existing AI sessions or launch new ones from your terminal. Keyboard and mouse support. Light/dark theme support. Customizable and performance-oriented. Requires the `specify` CLI in your PATH.

extensions/agent-context/commands/speckit.agent-context.update.md

@@ -15,7 +15,7 @@ The script reads the agent-context extension config at
 - `context_files` — optional project-relative paths for multiple coding agent context files. When non-empty, the script updates each listed file and the list takes precedence over `context_file`.
 - `context_markers.start` / `.end` — the delimiters surrounding the managed section. Defaults to `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` when the field is missing.
 
-It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/**/plan.md`, any depth).
+It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/<feature>/plan.md`).
 
 If `context_files` and `context_file` are empty, the command reports nothing to do and exits successfully. Context file paths must stay project-relative; absolute paths, Windows drive paths, backslash separators, and `..` path segments are rejected.
 
@@ -24,4 +24,4 @@ If `context_files` and `context_file` are empty, the command reports nothing to
 - **Bash**: `.specify/extensions/agent-context/scripts/bash/update-agent-context.sh [plan_path]`
 - **PowerShell**: `.specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1 [plan_path]`
 
-When `plan_path` is omitted, the script auto-detects the most recently modified `specs/**/plan.md` (any depth, so scoped layouts like `specs/<scope>/<feature>/plan.md` are found).
+When `plan_path` is omitted, the script auto-detects the most recently modified `specs/*/plan.md`.

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 set -euo pipefail
 
@@ -307,14 +307,14 @@ import sys
 from pathlib import Path
 root = Path(sys.argv[1]).resolve()
 specs = root / "specs"
-plan = max(
-    specs.glob("**/plan.md"),
+plans = sorted(
+    specs.glob("*/plan.md"),
     key=lambda p: p.stat().st_mtime,
-    default=None,
+    reverse=True,
 )
-if plan:
+if plans:
     try:
-        print(plan.relative_to(root).as_posix())
+        print(plans[0].relative_to(root).as_posix())
     except ValueError:
         print("")
 else:

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 [CmdletBinding()]
 param(
@@ -426,7 +426,9 @@ if (-not $PlanPath) {
     if (-not $PlanPath) {
         try {
             $specsDir = Join-Path $ProjectRoot 'specs'
-            $candidate = Get-ChildItem -Path $specsDir -Recurse -File -Filter 'plan.md' -ErrorAction SilentlyContinue |
+            $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
+                ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
+                Where-Object { $_ } |
                 Sort-Object LastWriteTime -Descending |
                 Select-Object -First 1
             if ($candidate) {

extensions/git/scripts/powershell/create-new-feature-branch.ps1

@@ -446,10 +446,7 @@ if ($env:GIT_BRANCH_NAME) {
         $branchSuffix = Get-BranchName -Description $featureDesc
     }
 
-    # Warn if -Number and -Timestamp are both specified. Use ContainsKey (not
-    # `-ne 0`) so an explicit `-Number 0` is also detected, matching the bash twin's
-    # `[ -n "$BRANCH_NUMBER" ]` check.
-    if ($Timestamp -and $PSBoundParameters.ContainsKey('Number')) {
+    if ($Timestamp -and $Number -ne 0) {
         Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
         $Number = 0
     }
@@ -459,10 +456,7 @@ if ($env:GIT_BRANCH_NAME) {
         $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
     } else {
         $branchScopePrefix = Get-BranchScopePrefix -Template $branchTemplate -BranchSuffix $branchSuffix
-        # Auto-detect the next number only when -Number was not supplied; an
-        # explicit value (including 0) is honored, matching the bash twin's
-        # `[ -z "$BRANCH_NUMBER" ]` check.
-        if (-not $PSBoundParameters.ContainsKey('Number')) {
+        if ($Number -eq 0) {
             if ($DryRun -and $hasGit) {
                 $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch -ScopePrefix $branchScopePrefix
             } elseif ($DryRun) {

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.10"
+version = "0.12.9"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 readme = "README.md"
 requires-python = ">=3.11"

src/specify_cli/__init__.py

@@ -141,9 +141,8 @@ def _install_shared_infra(
 
     Copies ``.specify/scripts/<variant>/`` and ``.specify/templates/`` from
     the bundled core_pack or source checkout, where ``<variant>`` is
-    ``bash`` when *script_type* is ``"sh"``, ``python`` when it is ``"py"``,
-    and ``powershell`` when it is ``"ps"``.  Tracks all installed files in
-    ``speckit.manifest.json``.
+    ``bash`` when *script_type* is ``"sh"`` and ``powershell`` when it is
+    ``"ps"``.  Tracks all installed files in ``speckit.manifest.json``.
 
     Shared scripts and page templates are processed to resolve
     ``__SPECKIT_COMMAND_<NAME>__`` placeholders using *invoke_separator*

src/specify_cli/shared_infra.py

@@ -403,7 +403,7 @@ def install_shared_infra(
     # manifest entries the core no longer ships (stale-script cleanup, #3076).
     seen_rels: set[str] = set()
     scripts_scanned = False
-    variant_dir = {"sh": "bash", "py": "python"}.get(script_type, "powershell")
+    variant_dir = "bash" if script_type == "sh" else "powershell"
 
     def _decide_overwrite(rel: str, dst: Path) -> tuple[bool, str | None]:
         """Return (write, bucket) where bucket is 'skip', 'preserved', or None."""
@@ -465,10 +465,6 @@ def install_shared_infra(
                     for src_path in variant_src.rglob("*"):
                         if not src_path.is_file():
                             continue
-                        # Python bytecode caches are local artifacts, not
-                        # workflow scripts — never install them.
-                        if "__pycache__" in src_path.parts:
-                            continue
                         # Mark scanned only once a real source file is seen. An
                         # empty (or symlink-skipped) variant keeps this False, so
                         # stale-cleanup is skipped — otherwise it would treat every

src/specify_cli/workflows/steps/shell/__init__.py

@@ -25,14 +25,6 @@ class ShellStep(StepBase):
         run_cmd = str(run_cmd)
 
         cwd = context.project_root or "."
-        # Defensive: the engine does not auto-validate step config, so an
-        # invalid ``timeout`` (string, None, ...) would otherwise raise a
-        # TypeError from subprocess.run() and crash the whole run.  Mirror
-        # the engine's handling of unvalidated ``continue_on_error`` by
-        # only honoring well-formed values and falling back to the default.
-        timeout = config.get("timeout", 300)
-        if isinstance(timeout, bool) or not isinstance(timeout, int) or timeout <= 0:
-            timeout = 300
 
         # NOTE: shell=True is required to support pipes, redirects, and
         # multi-command expressions in workflow YAML.  Workflow authors
@@ -45,7 +37,7 @@ class ShellStep(StepBase):
                 capture_output=True,
                 text=True,
                 cwd=cwd,
-                timeout=timeout,
+                timeout=300,
             )
             output = {
                 "exit_code": proc.returncode,
@@ -82,7 +74,7 @@ class ShellStep(StepBase):
         except subprocess.TimeoutExpired:
             return StepResult(
                 status=StepStatus.FAILED,
-                error=f"Shell command timed out after {timeout} seconds.",
+                error="Shell command timed out after 300 seconds.",
                 output={"exit_code": -1, "stdout": "", "stderr": "timeout"},
             )
         except OSError as exc:
@@ -114,16 +106,4 @@ class ShellStep(StepBase):
                 f"Shell step {config.get('id', '?')!r}: 'output_format' must "
                 f"be 'json' when present, got {output_format!r}."
             )
-        if "timeout" in config:
-            timeout = config["timeout"]
-            # bool is an int subclass, so reject it explicitly.
-            if (
-                isinstance(timeout, bool)
-                or not isinstance(timeout, int)
-                or timeout <= 0
-            ):
-                errors.append(
-                    f"Shell step {config.get('id', '?')!r}: 'timeout' must be a "
-                    f"positive integer (seconds) when present, got {timeout!r}."
-                )
         return errors

templates/commands/analyze.md

@@ -3,7 +3,6 @@ description: Perform a non-destructive cross-artifact consistency and quality an
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/checklist.md

@@ -3,7 +3,6 @@ description: Generate a custom checklist for the current feature based on user r
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json
   ps: scripts/powershell/check-prerequisites.ps1 -Json
-  py: scripts/python/check_prerequisites.py --json
 ---
 
 ## Checklist Purpose: "Unit Tests for English"

templates/commands/clarify.md

@@ -7,7 +7,6 @@ handoffs:
 scripts:
    sh: scripts/bash/check-prerequisites.sh --json --paths-only
    ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly
-   py: scripts/python/check_prerequisites.py --json --paths-only
 ---
 
 ## User Input

templates/commands/converge.md

@@ -3,7 +3,6 @@ description: Assess the current codebase against the feature's spec, plan, and t
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/implement.md

@@ -3,7 +3,6 @@ description: Execute the implementation plan by processing and executing all tas
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/plan.md

@@ -68,6 +68,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Evaluate gates (ERROR if violations unjustified)
    - Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
    - Phase 1: Generate data-model.md, contracts/, quickstart.md
+   - Phase 1: Update agent context by running the agent script
    - Re-evaluate Constitution Check post-design
 
 ## Mandatory Post-Execution Hooks
@@ -106,7 +107,7 @@ Check if `.specify/extensions.yml` exists in the project root.
 
 ## Completion Report
 
-Command ends after Phase 1 design. Report branch, IMPL_PLAN path, and generated artifacts.
+Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
 
 ## Phases
 

templates/commands/taskstoissues.md

@@ -4,7 +4,6 @@ tools: ['github/github-mcp-server/list_issues', 'github/github-mcp-server/issue_
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

tests/extensions/git/test_git_extension.py

@@ -638,21 +638,6 @@ class TestCreateFeatureBash:
         assert result.returncode != 0
         assert "requires updated Spec Kit core scripts" in result.stderr
 
-    def test_explicit_number_zero_is_honored(self, tmp_path: Path):
-        """An explicit --number 0 is honored (yields 000), not treated as
-        'auto-detect'. Pins the canonical behavior the PowerShell twin must
-        mirror; the empty-string check (`[ -z "$BRANCH_NUMBER" ]`) already
-        distinguishes an unset flag from a supplied 0."""
-        project = _setup_project(tmp_path)
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--number", "0", "--short-name", "zero", "Zero feature",
-        )
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "000-zero"
-        assert data["FEATURE_NUM"] == "000"
-
 
 @pytest.mark.skipif(not HAS_PWSH, reason="pwsh not available")
 class TestCreateFeaturePowerShell:
@@ -957,23 +942,6 @@ class TestCreateFeaturePowerShell:
         assert result.returncode != 0
         assert "requires updated Spec Kit core scripts" in result.stderr
 
-    def test_explicit_number_zero_is_honored(self, tmp_path: Path):
-        """An explicit -Number 0 is honored (yields 000), matching the bash twin's
-        --number 0. Regression guard: -Number defaults to 0, so a bare `-eq 0`
-        check cannot tell an unset flag from a supplied 0 and would silently
-        auto-detect instead. Uses PSBoundParameters.ContainsKey('Number')."""
-        project = _setup_project(tmp_path)
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-Number", "0", "-ShortName", "zero", "Zero feature",
-        )
-        assert result.returncode == 0, result.stderr
-        json_line = [ln for ln in result.stdout.splitlines() if ln.strip().startswith("{")]
-        assert json_line, f"No JSON in output: {result.stdout}"
-        data = json.loads(json_line[-1])
-        assert data["BRANCH_NAME"] == "000-zero"
-        assert data["FEATURE_NUM"] == "000"
-
 
 # ── auto-commit.sh Tests ─────────────────────────────────────────────────────
 

tests/extensions/test_extension_agent_context.py

@@ -688,62 +688,6 @@ class TestExtensionSelfSeed:
 _MDC_CONTEXT_FILE = ".cursor/rules/specify-rules.mdc"
 
 
-class TestPlanDiscovery:
-    """Mtime fallback must find plans in nested spec layouts (#3024).
-
-    Repos using SPECIFY_FEATURE_DIRECTORY place plans at
-    ``specs/<scope>/<feature>/plan.md``; a one-level ``specs/*/plan.md``
-    glob never matches those.
-    """
-
-    @staticmethod
-    def _make_plans(project: Path) -> Path:
-        # Older flat plan plus a newer nested plan: recursive discovery
-        # must pick the nested one by mtime.
-        flat = project / "specs" / "old-feature" / "plan.md"
-        flat.parent.mkdir(parents=True)
-        flat.write_text("flat plan\n", encoding="utf-8")
-        os.utime(flat, (1_000_000_000, 1_000_000_000))
-        nested = project / "specs" / "scope" / "new-feature" / "plan.md"
-        nested.parent.mkdir(parents=True)
-        nested.write_text("nested plan\n", encoding="utf-8")
-        return nested
-
-    @requires_bash
-    def test_bash_script_finds_nested_plan(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md"],
-        )
-        self._make_plans(project)
-
-        result = _run_bash_agent_context_script(project)
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        content = (project / "AGENTS.md").read_text(encoding="utf-8")
-        assert "specs/scope/new-feature/plan.md" in content
-
-    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
-    def test_powershell_script_finds_nested_plan(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md"],
-        )
-        self._make_plans(project)
-
-        result = _run_powershell_agent_context_script(project)
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        content = (project / "AGENTS.md").read_text(encoding="utf-8")
-        assert "specs/scope/new-feature/plan.md" in content
-
-
 class TestMdcFrontmatter:
     """Cursor-style ``.mdc`` targets must carry ``alwaysApply: true`` frontmatter
     so the rule file is auto-loaded; non-``.mdc`` targets must not gain any."""

tests/test_command_template_py_scripts.py

@@ -1,107 +0,0 @@
-"""Command templates with a py: script line must render for --script py.
-
-Covers #3283: ``py:`` lines in the ``scripts:`` frontmatter of
-``templates/commands/*.md`` reference Python scripts that exist in the repo,
-and ``process_template`` turns them into a valid Python invocation
-(interpreter-prefixed, path rewritten to the ``.specify`` tree).
-
-``plan.md`` and ``tasks.md`` gain their ``py:`` lines together with
-``setup_plan.py``/``setup_tasks.py`` in the core-scripts port (#3280); the
-existence check below enforces that ordering.
-"""
-
-import re
-from pathlib import Path
-
-import pytest
-
-from specify_cli.integrations.base import IntegrationBase
-
-REPO_ROOT = Path(__file__).parent.parent
-TEMPLATES_DIR = REPO_ROOT / "templates" / "commands"
-
-_PY_LINE = re.compile(r"^\s*py: (scripts/python/\S+\.py)", re.MULTILINE)
-
-
-def _py_script(name: str) -> str | None:
-    match = _PY_LINE.search((TEMPLATES_DIR / name).read_text(encoding="utf-8"))
-    return match.group(1) if match else None
-
-
-PY_TEMPLATES = sorted(
-    p.name for p in TEMPLATES_DIR.glob("*.md") if _py_script(p.name)
-)
-
-
-@pytest.fixture(autouse=True)
-def _pin_interpreter(monkeypatch):
-    monkeypatch.setattr(
-        "specify_cli.integrations.base.shutil.which",
-        lambda name: "/usr/bin/python3" if name == "python3" else None,
-    )
-    # On Windows, ``resolve_python_interpreter`` guards the ``which`` result
-    # with a real ``_interpreter_runs`` subprocess probe (#3304). The mocked
-    # ``/usr/bin/python3`` path does not exist on a Windows runner, so the
-    # probe would fail and the resolver would fall back to ``sys.executable``
-    # (a ``...python.exe`` path), breaking the ``python3``-anchored assertion.
-    # Pin the probe to True so the interpreter token stays ``python3`` on all
-    # platforms.
-    monkeypatch.setattr(
-        "specify_cli.integrations.base.IntegrationBase._interpreter_runs",
-        staticmethod(lambda path: True),
-    )
-
-
-def test_py_templates_discovered():
-    # Guard: the glob must find the known py-scripted templates, otherwise
-    # the parametrized tests below would silently pass on an empty set.
-    assert "implement.md" in PY_TEMPLATES
-    assert "clarify.md" in PY_TEMPLATES
-
-
-@pytest.mark.parametrize("name", PY_TEMPLATES)
-def test_referenced_python_script_exists(name: str):
-    # A py: line must never point at a script the repo does not ship —
-    # rendering would produce a broken invocation at runtime.
-    script = _py_script(name)
-    assert (REPO_ROOT / script).is_file(), f"{name} references missing {script}"
-
-
-@pytest.mark.parametrize("name", PY_TEMPLATES)
-def test_template_renders_python_invocation(name: str):
-    content = (TEMPLATES_DIR / name).read_text(encoding="utf-8")
-    result = IntegrationBase.process_template(content, "agent", "py")
-    assert "{SCRIPT}" not in result
-    assert re.search(
-        r"python3 \.specify/scripts/python/\w+\.py(?: --[\w-]+)*", result
-    ), f"{name} did not render a Python invocation"
-
-
-@pytest.mark.parametrize("name", PY_TEMPLATES)
-def test_sh_rendering_unchanged(name: str):
-    # Negative: adding py: lines must not leak into sh rendering.
-    content = (TEMPLATES_DIR / name).read_text(encoding="utf-8")
-    result = IntegrationBase.process_template(content, "agent", "sh")
-    assert "{SCRIPT}" not in result
-    assert "scripts/python" not in result
-
-
-def test_install_shared_infra_copies_python_scripts(tmp_path):
-    # --script py must install scripts/python/ into .specify/scripts/python/
-    # so the rendered invocations point at files that exist.
-    from rich.console import Console
-
-    from specify_cli.shared_infra import install_shared_infra
-
-    install_shared_infra(
-        tmp_path,
-        "py",
-        version="0.0.0",
-        core_pack=None,
-        repo_root=REPO_ROOT,
-        console=Console(quiet=True),
-        force=False,
-    )
-    dest = tmp_path / ".specify" / "scripts" / "python"
-    assert (dest / "check_prerequisites.py").is_file()
-    assert not (tmp_path / ".specify" / "scripts" / "powershell").exists()

tests/test_workflows.py

@@ -1353,106 +1353,6 @@ class TestShellStep:
         assert step.validate({"id": "s", "run": "echo hi"}) == []
         assert step.validate({"id": "s", "run": "{{ steps.x.output }}"}) == []
 
-    def test_timeout_is_configurable(self, monkeypatch):
-        """A 'timeout' field overrides the 300s default (#3327)."""
-        import subprocess as sp
-
-        from specify_cli.workflows.steps.shell import ShellStep
-        from specify_cli.workflows.base import StepContext, StepStatus
-
-        seen = {}
-        real_run = sp.run
-
-        def spy_run(*args, **kwargs):
-            seen["timeout"] = kwargs.get("timeout")
-            return real_run(*args, **kwargs)
-
-        monkeypatch.setattr(
-            "specify_cli.workflows.steps.shell.subprocess.run", spy_run
-        )
-        step = ShellStep()
-        result = step.execute(
-            {"id": "t", "run": "echo hi", "timeout": 1800}, StepContext()
-        )
-        assert result.status == StepStatus.COMPLETED
-        assert seen["timeout"] == 1800
-
-    def test_timeout_defaults_to_300(self, monkeypatch):
-        import subprocess as sp
-
-        from specify_cli.workflows.steps.shell import ShellStep
-        from specify_cli.workflows.base import StepContext, StepStatus
-
-        seen = {}
-        real_run = sp.run
-
-        def spy_run(*args, **kwargs):
-            seen["timeout"] = kwargs.get("timeout")
-            return real_run(*args, **kwargs)
-
-        monkeypatch.setattr(
-            "specify_cli.workflows.steps.shell.subprocess.run", spy_run
-        )
-        result = ShellStep().execute({"id": "t", "run": "echo hi"}, StepContext())
-        assert result.status == StepStatus.COMPLETED
-        assert seen["timeout"] == 300
-
-    def test_timeout_error_reports_configured_value(self, monkeypatch):
-        import subprocess as sp
-
-        from specify_cli.workflows.steps.shell import ShellStep
-        from specify_cli.workflows.base import StepContext, StepStatus
-
-        def raise_timeout(*args, **kwargs):
-            raise sp.TimeoutExpired(cmd="x", timeout=kwargs.get("timeout"))
-
-        monkeypatch.setattr(
-            "specify_cli.workflows.steps.shell.subprocess.run", raise_timeout
-        )
-        result = ShellStep().execute(
-            {"id": "t", "run": "sleep 999", "timeout": 7}, StepContext()
-        )
-        assert result.status == StepStatus.FAILED
-        assert "7 seconds" in result.error
-
-    @pytest.mark.parametrize("bad", [0, -5, "600", 1.5, None, True])
-    def test_execute_ignores_unvalidated_bad_timeout(self, bad, monkeypatch):
-        """execute() falls back to 300 when config skipped validation (#3327)."""
-        import subprocess as sp
-
-        from specify_cli.workflows.steps.shell import ShellStep
-        from specify_cli.workflows.base import StepContext, StepStatus
-
-        seen = {}
-        real_run = sp.run
-
-        def spy_run(*args, **kwargs):
-            seen["timeout"] = kwargs.get("timeout")
-            return real_run(*args, **kwargs)
-
-        monkeypatch.setattr(
-            "specify_cli.workflows.steps.shell.subprocess.run", spy_run
-        )
-        result = ShellStep().execute(
-            {"id": "t", "run": "echo hi", "timeout": bad}, StepContext()
-        )
-        assert result.status == StepStatus.COMPLETED
-        assert seen["timeout"] == 300
-
-    @pytest.mark.parametrize("bad", [0, -5, "600", 1.5, None, True])
-    def test_validate_rejects_bad_timeout(self, bad):
-        from specify_cli.workflows.steps.shell import ShellStep
-
-        errors = ShellStep().validate({"id": "s", "run": "echo hi", "timeout": bad})
-        assert any("'timeout'" in e for e in errors)
-
-    def test_validate_accepts_positive_int_timeout(self):
-        from specify_cli.workflows.steps.shell import ShellStep
-
-        assert (
-            ShellStep().validate({"id": "s", "run": "echo hi", "timeout": 1800}) == []
-        )
-
 
     def test_output_format_json_exposes_data(self, tmp_path):
         from specify_cli.workflows.steps.shell import ShellStep