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

src/specify_cli/integrations/__init__.py

@@ -37,10 +37,57 @@ def get_integration(key: str) -> IntegrationBase | None:
 # -- Register built-in integrations --------------------------------------
 
 def _register_builtins() -> None:
-    """Register all built-in integrations."""
-    from .copilot import CopilotIntegration
+    """Register all built-in integrations.
 
+    Package directories use Python-safe identifiers (e.g. ``kiro_cli``,
+    ``cursor_agent``).  The user-facing integration key stored in
+    ``IntegrationBase.key`` stays hyphenated (``"kiro-cli"``,
+    ``"cursor-agent"``) to match the actual CLI tool / binary name that
+    users install and invoke.
+    """
+    # -- Imports (alphabetical) -------------------------------------------
+    from .amp import AmpIntegration
+    from .auggie import AuggieIntegration
+    from .bob import BobIntegration
+    from .claude import ClaudeIntegration
+    from .codebuddy import CodebuddyIntegration
+    from .copilot import CopilotIntegration
+    from .cursor_agent import CursorAgentIntegration
+    from .iflow import IflowIntegration
+    from .junie import JunieIntegration
+    from .kilocode import KilocodeIntegration
+    from .kiro_cli import KiroCliIntegration
+    from .opencode import OpencodeIntegration
+    from .pi import PiIntegration
+    from .qodercli import QodercliIntegration
+    from .qwen import QwenIntegration
+    from .roo import RooIntegration
+    from .shai import ShaiIntegration
+    from .trae import TraeIntegration
+    from .vibe import VibeIntegration
+    from .windsurf import WindsurfIntegration
+
+    # -- Registration (alphabetical) --------------------------------------
+    _register(AmpIntegration())
+    _register(AuggieIntegration())
+    _register(BobIntegration())
+    _register(ClaudeIntegration())
+    _register(CodebuddyIntegration())
     _register(CopilotIntegration())
+    _register(CursorAgentIntegration())
+    _register(IflowIntegration())
+    _register(JunieIntegration())
+    _register(KilocodeIntegration())
+    _register(KiroCliIntegration())
+    _register(OpencodeIntegration())
+    _register(PiIntegration())
+    _register(QodercliIntegration())
+    _register(QwenIntegration())
+    _register(RooIntegration())
+    _register(ShaiIntegration())
+    _register(TraeIntegration())
+    _register(VibeIntegration())
+    _register(WindsurfIntegration())
 
 
 _register_builtins()