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)

Author: mnriem

src/specify_cli/__init__.py

@@ -1974,7 +1974,7 @@ def init(
         console.print("[yellow]Use:[/yellow] --integration for the new integration system, or --ai for the legacy path")
         raise typer.Exit(1)
 
-    # Auto-promote: --ai copilot → integration path with a nudge
+    # Auto-promote: --ai <key> → integration path with a nudge (if registered)
     use_integration = False
     if integration:
         from .integrations import INTEGRATION_REGISTRY, get_integration
@@ -1987,14 +1987,14 @@ def init(
         use_integration = True
         # Map integration key to the ai_assistant variable for downstream compatibility
         ai_assistant = integration
-    elif ai_assistant == "copilot":
+    elif ai_assistant:
         from .integrations import get_integration
-        resolved_integration = get_integration("copilot")
+        resolved_integration = get_integration(ai_assistant)
         if resolved_integration:
             use_integration = True
             console.print(
-                "[dim]Tip: Use [bold]--integration copilot[/bold] instead of "
-                "--ai copilot. The --ai flag will be deprecated in a future release.[/dim]"
+                f"[dim]Tip: Use [bold]--integration {ai_assistant}[/bold] instead of "
+                f"--ai {ai_assistant}. The --ai flag will be deprecated in a future release.[/dim]"
             )
 
     if project_name == ".":

src/specify_cli/agents.py

@@ -43,7 +43,7 @@ class CommandRegistrar:
             "args": "$ARGUMENTS",
             "extension": ".agent.md"
         },
-        "cursor": {
+        "cursor-agent": {
             "dir": ".cursor/commands",
             "format": "markdown",
             "args": "$ARGUMENTS",
@@ -162,6 +162,12 @@ class CommandRegistrar:
             "format": "markdown",
             "args": "$ARGUMENTS",
             "extension": ".md"
+        },
+        "vibe": {
+            "dir": ".vibe/prompts",
+            "format": "markdown",
+            "args": "$ARGUMENTS",
+            "extension": ".md"
         }
     }
 

src/specify_cli/integrations/__init__.py

@@ -42,5 +42,53 @@ def _register_builtins() -> None:
 
     _register(CopilotIntegration())
 
+    # Stage 3 — standard markdown integrations
+    from .claude import ClaudeIntegration
+    from .qwen import QwenIntegration
+    from .opencode import OpencodeIntegration
+    from .junie import JunieIntegration
+    from .kilocode import KilocodeIntegration
+    from .auggie import AuggieIntegration
+    from .roo import RooIntegration
+    from .codebuddy import CodebuddyIntegration
+    from .qodercli import QodercliIntegration
+    from .amp import AmpIntegration
+    from .shai import ShaiIntegration
+    from .bob import BobIntegration
+    from .trae import TraeIntegration
+    from .pi import PiIntegration
+    from .iflow import IflowIntegration
+
+    _register(ClaudeIntegration())
+    _register(QwenIntegration())
+    _register(OpencodeIntegration())
+    _register(JunieIntegration())
+    _register(KilocodeIntegration())
+    _register(AuggieIntegration())
+    _register(RooIntegration())
+    _register(CodebuddyIntegration())
+    _register(QodercliIntegration())
+    _register(AmpIntegration())
+    _register(ShaiIntegration())
+    _register(BobIntegration())
+    _register(TraeIntegration())
+    _register(PiIntegration())
+    _register(IflowIntegration())
+
+    # Hyphenated package names — use importlib for kiro-cli and cursor-agent
+    import importlib
+
+    kiro_mod = importlib.import_module(".kiro-cli", __package__)
+    _register(kiro_mod.KiroCliIntegration())
+
+    from .windsurf import WindsurfIntegration
+    from .vibe import VibeIntegration
+
+    _register(WindsurfIntegration())
+    _register(VibeIntegration())
+
+    cursor_mod = importlib.import_module(".cursor-agent", __package__)
+    _register(cursor_mod.CursorAgentIntegration())
+
 
 _register_builtins()

src/specify_cli/integrations/amp/__init__.py

@@ -0,0 +1,21 @@
+"""Amp CLI integration."""
+
+from ..base import MarkdownIntegration
+
+
+class AmpIntegration(MarkdownIntegration):
+    key = "amp"
+    config = {
+        "name": "Amp",
+        "folder": ".agents/",
+        "commands_subdir": "commands",
+        "install_url": "https://ampcode.com/manual#install",
+        "requires_cli": True,
+    }
+    registrar_config = {
+        "dir": ".agents/commands",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": ".md",
+    }
+    context_file = "AGENTS.md"

src/specify_cli/integrations/amp/scripts/update-context.ps1

@@ -0,0 +1,13 @@
+# update-context.ps1 — Amp integration: create/update AGENTS.md
+#
+# Thin wrapper that delegates to the shared update-agent-context script.
+# Activated in Stage 7 when the shared script uses integration.json dispatch.
+#
+# Until then, this delegates to the shared script as a subprocess.
+
+$ErrorActionPreference = 'Stop'
+
+$repoRoot = git rev-parse --show-toplevel 2>$null
+if (-not $repoRoot) { $repoRoot = $PWD.Path }
+
+& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType amp

src/specify_cli/integrations/amp/scripts/update-context.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+# update-context.sh — Amp integration: create/update AGENTS.md
+#
+# Thin wrapper that delegates to the shared update-agent-context script.
+# Activated in Stage 7 when the shared script uses integration.json dispatch.
+#
+# Until then, this delegates to the shared script as a subprocess.
+
+set -euo pipefail
+
+REPO_ROOT="${REPO_ROOT:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"
+
+exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" amp

src/specify_cli/integrations/auggie/__init__.py

@@ -0,0 +1,21 @@
+"""Auggie CLI integration."""
+
+from ..base import MarkdownIntegration
+
+
+class AuggieIntegration(MarkdownIntegration):
+    key = "auggie"
+    config = {
+        "name": "Auggie CLI",
+        "folder": ".augment/",
+        "commands_subdir": "commands",
+        "install_url": "https://docs.augmentcode.com/cli/setup-auggie/install-auggie-cli",
+        "requires_cli": True,
+    }
+    registrar_config = {
+        "dir": ".augment/commands",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": ".md",
+    }
+    context_file = ".augment/rules/specify-rules.md"

src/specify_cli/integrations/auggie/scripts/update-context.ps1

@@ -0,0 +1,13 @@
+# update-context.ps1 — Auggie CLI integration: create/update .augment/rules/specify-rules.md
+#
+# Thin wrapper that delegates to the shared update-agent-context script.
+# Activated in Stage 7 when the shared script uses integration.json dispatch.
+#
+# Until then, this delegates to the shared script as a subprocess.
+
+$ErrorActionPreference = 'Stop'
+
+$repoRoot = git rev-parse --show-toplevel 2>$null
+if (-not $repoRoot) { $repoRoot = $PWD.Path }
+
+& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType auggie

src/specify_cli/integrations/auggie/scripts/update-context.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+# update-context.sh — Auggie CLI integration: create/update .augment/rules/specify-rules.md
+#
+# Thin wrapper that delegates to the shared update-agent-context script.
+# Activated in Stage 7 when the shared script uses integration.json dispatch.
+#
+# Until then, this delegates to the shared script as a subprocess.
+
+set -euo pipefail
+
+REPO_ROOT="${REPO_ROOT:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"
+
+exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" auggie

src/specify_cli/integrations/base.py

@@ -206,6 +206,53 @@ def write_file_and_record(
         manifest.record_existing(rel)
         return dest
 
+    def integration_scripts_dir(self) -> Path | None:
+        """Return path to this integration's bundled ``scripts/`` directory.
+
+        Looks for a ``scripts/`` sibling of the module that defines the
+        concrete subclass (not ``IntegrationBase`` itself).
+        Returns ``None`` if the directory doesn't exist.
+        """
+        import inspect
+
+        cls_file = inspect.getfile(type(self))
+        scripts = Path(cls_file).resolve().parent / "scripts"
+        return scripts if scripts.is_dir() else None
+
+    def install_scripts(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+    ) -> list[Path]:
+        """Copy integration-specific scripts into the project.
+
+        Copies files from this integration's ``scripts/`` directory to
+        ``.specify/integrations/<key>/scripts/`` in the project.  Shell
+        scripts are made executable.  All copied files are recorded in
+        *manifest*.
+
+        Returns the list of files created.
+        """
+        scripts_src = self.integration_scripts_dir()
+        if not scripts_src:
+            return []
+
+        created: list[Path] = []
+        scripts_dest = project_root / ".specify" / "integrations" / self.key / "scripts"
+        scripts_dest.mkdir(parents=True, exist_ok=True)
+
+        for src_script in sorted(scripts_src.iterdir()):
+            if not src_script.is_file():
+                continue
+            dst_script = scripts_dest / src_script.name
+            shutil.copy2(src_script, dst_script)
+            if dst_script.suffix == ".sh":
+                dst_script.chmod(dst_script.stat().st_mode | 0o111)
+            self.record_file_in_manifest(dst_script, project_root, manifest)
+            created.append(dst_script)
+
+        return created
+
     @staticmethod
     def process_template(
         content: str,
@@ -405,11 +452,51 @@ class MarkdownIntegration(IntegrationBase):
     Subclasses only need to set ``key``, ``config``, ``registrar_config``
     (and optionally ``context_file``).  Everything else is inherited.
 
-    The default ``setup()`` from ``IntegrationBase`` copies templates
-    into the agent's commands directory — which is correct for the
-    standard Markdown case.
+    ``setup()`` processes command templates (replacing ``{SCRIPT}``,
+    ``{ARGS}``, ``__AGENT__``, rewriting paths) and installs
+    integration-specific scripts (``update-context.sh`` / ``.ps1``).
     """
 
-    # MarkdownIntegration inherits IntegrationBase.setup() as-is.
-    # Future stages may add markdown-specific path rewriting here.
-    pass
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        templates = self.list_command_templates()
+        if not templates:
+            return []
+
+        project_root_resolved = project_root.resolve()
+        if manifest.project_root != project_root_resolved:
+            raise ValueError(
+                f"manifest.project_root ({manifest.project_root}) does not match "
+                f"project_root ({project_root_resolved})"
+            )
+
+        dest = self.commands_dest(project_root).resolve()
+        try:
+            dest.relative_to(project_root_resolved)
+        except ValueError as exc:
+            raise ValueError(
+                f"Integration destination {dest} escapes "
+                f"project root {project_root_resolved}"
+            ) from exc
+        dest.mkdir(parents=True, exist_ok=True)
+
+        script_type = opts.get("script_type", "sh")
+        arg_placeholder = self.registrar_config.get("args", "$ARGUMENTS") if self.registrar_config else "$ARGUMENTS"
+        created: list[Path] = []
+
+        for src_file in templates:
+            raw = src_file.read_text(encoding="utf-8")
+            processed = self.process_template(raw, self.key, script_type, arg_placeholder)
+            dst_name = self.command_filename(src_file.stem)
+            dst_file = self.write_file_and_record(
+                processed, dest / dst_name, project_root, manifest
+            )
+            created.append(dst_file)
+
+        created.extend(self.install_scripts(project_root, manifest))
+        return created