Stage 3: Standard markdown integrations — 19 agents migrated to plugin architecture (#2038)

* Stage 3: Standard markdown integrations — 19 agents migrated to plugin architecture

Migrate all standard markdown integrations to self-contained subpackages
under integrations/. Each subclasses MarkdownIntegration with config-only
overrides (~10 lines per __init__.py).

Integrations migrated (19):
claude, qwen, opencode, junie, kilocode, auggie, roo, codebuddy,
qodercli, amp, shai, bob, trae, pi, iflow, kiro-cli, windsurf,
vibe, cursor-agent

Changes:
- Create integrations/<key>/ subpackage with __init__.py and scripts/
  (update-context.sh, update-context.ps1) for each integration
- Register all 19 in INTEGRATION_REGISTRY (20 total with copilot)
- MarkdownIntegration.setup() processes templates (replaces {SCRIPT},
  {ARGS}, __AGENT__; strips frontmatter blocks; rewrites paths)
- Extract install_scripts() to IntegrationBase; refactor copilot to use it
- Generalize --ai auto-promote from copilot-only to registry-driven:
  any integration registered in INTEGRATION_REGISTRY auto-promotes.
  Unregistered agents (gemini, tabnine, codex, kimi, agy, generic)
  continue through the legacy --ai path unchanged.
- Fix cursor/cursor-agent key mismatch in CommandRegistrar.AGENT_CONFIGS
- Add missing vibe entry to CommandRegistrar.AGENT_CONFIGS
- Update kiro alias test to reflect auto-promote behavior

Testing:
- Per-agent test files (test_integration_<agent>.py) with shared mixin
- 1316 tests passing, 0 failures
- Complete file inventory tests for both sh and ps variants
- Byte-for-byte validated against v0.4.3 release packages (684 files)

* Address PR review: fix repo root detection and no-op test

- Fix repo root fallback in all 20 update-context.sh scripts: walk up
  from script location to find .specify/ instead of falling back to pwd
- Fix repo root fallback in all 20 update-context.ps1 scripts: walk up
  from script location to find .specify/ instead of falling back to $PWD
- Add assertions to test_setup_writes_to_correct_directory: verify
  expected_dir exists and all command files reside under it

* Fix REPO_ROOT priority: prefer .specify walk-up over git root

In monorepos the git toplevel may differ from the project root that
contains .specify/. The previous fix still preferred git rev-parse
over the walk-up result.

Bash scripts (20): prefer the discovered _root when it contains
.specify/; only accept git root if it also contains .specify/.

PowerShell scripts (20): validate git root contains .specify/ before
using it; fall back to walking up from script directory otherwise.

* Guard git call with try/catch in PowerShell scripts

With $ErrorActionPreference = 'Stop', an unguarded git rev-parse
throws a terminating CommandNotFoundException when git is not
installed, preventing the .specify walk-up fallback from running.

Wrap the git call in try/catch across all 20 update-context.ps1
scripts so the fallback works reliably without git.

* Rename hyphenated package dirs to valid Python identifiers

Rename kiro-cli → kiro_cli and cursor-agent → cursor_agent so the
packages can be imported with normal Python syntax instead of
importlib.  The user-facing integration key (IntegrationBase.key)
stays hyphenated to match the actual CLI tool / binary name.

Also reorganize _register_builtins(): imports and registrations
are now grouped alphabetically with clear section comments.

* Reuse CommandRegistrar path rewriting in process_template()

Replace the duplicated regex-based path rewriting in
MarkdownIntegration.process_template() with a call to the shared
CommandRegistrar._rewrite_project_relative_paths() implementation.

This ensures extension-local paths are preserved and boundary rules
stay consistent across the codebase.

* Promote _rewrite_project_relative_paths to public API

Rename CommandRegistrar._rewrite_project_relative_paths() to
rewrite_project_relative_paths() (drop leading underscore) so
integrations can call it without reaching into a private method
across subsystem boundaries.

Addresses PR review feedback:
https://github.com/github/spec-kit/pull/2038#discussion_r3022105627

* Broaden TestRegistrarKeyAlignment to cover all integration keys

Parametrize across ALL_INTEGRATION_KEYS instead of only checking
cursor-agent and vibe.  Keeps a separate negative test for the
stale 'cursor' shorthand.

Addresses PR review feedback:
https://github.com/github/spec-kit/pull/2038#discussion_r3022269032

tests/integrations/test_registry.py

@@ -1,4 +1,4 @@
-"""Tests for INTEGRATION_REGISTRY."""
+"""Tests for INTEGRATION_REGISTRY — mechanics, completeness, and registrar alignment."""
 
 import pytest
 
@@ -11,6 +11,16 @@ from specify_cli.integrations.base import MarkdownIntegration
 from .conftest import StubIntegration
 
 
+# Every integration key that must be registered (Stage 2 + Stage 3).
+ALL_INTEGRATION_KEYS = [
+    "copilot",
+    # Stage 3 — standard markdown integrations
+    "claude", "qwen", "opencode", "junie", "kilocode", "auggie",
+    "roo", "codebuddy", "qodercli", "amp", "shai", "bob", "trae",
+    "pi", "iflow", "kiro-cli", "windsurf", "vibe", "cursor-agent",
+]
+
+
 class TestRegistry:
     def test_registry_is_dict(self):
         assert isinstance(INTEGRATION_REGISTRY, dict)
@@ -41,5 +51,26 @@ class TestRegistry:
         finally:
             INTEGRATION_REGISTRY.pop("stub", None)
 
-    def test_copilot_registered(self):
-        assert "copilot" in INTEGRATION_REGISTRY
+
+class TestRegistryCompleteness:
+    """Every expected integration must be registered."""
+
+    @pytest.mark.parametrize("key", ALL_INTEGRATION_KEYS)
+    def test_key_registered(self, key):
+        assert key in INTEGRATION_REGISTRY, f"{key} missing from registry"
+
+
+class TestRegistrarKeyAlignment:
+    """Every integration key must have a matching AGENT_CONFIGS entry."""
+
+    @pytest.mark.parametrize("key", ALL_INTEGRATION_KEYS)
+    def test_integration_key_in_registrar(self, key):
+        from specify_cli.agents import CommandRegistrar
+        assert key in CommandRegistrar.AGENT_CONFIGS, (
+            f"Integration '{key}' is registered but has no AGENT_CONFIGS entry"
+        )
+
+    def test_no_stale_cursor_shorthand(self):
+        """The old 'cursor' shorthand must not appear in AGENT_CONFIGS."""
+        from specify_cli.agents import CommandRegistrar
+        assert "cursor" not in CommandRegistrar.AGENT_CONFIGS