diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index f528535a6..e53d7f18e 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1197,6 +1197,84 @@ def _locate_release_script() -> tuple[Path, str]:
     raise FileNotFoundError(f"Release script '{name}' not found in core_pack or source checkout")
 
 
+def _install_shared_infra(
+    project_path: Path,
+    script_type: str,
+    tracker: StepTracker | None = None,
+) -> bool:
+    """Install shared infrastructure files into *project_path*.
+
+    Copies ``.specify/scripts/`` and ``.specify/templates/`` from the
+    bundled core_pack or source checkout.  Tracks all installed files
+    in ``speckit.manifest.json``.
+    Returns ``True`` on success.
+    """
+    from .integrations.manifest import IntegrationManifest
+
+    core = _locate_core_pack()
+    manifest = IntegrationManifest("speckit", project_path, version=get_speckit_version())
+
+    # Scripts
+    if core and (core / "scripts").is_dir():
+        scripts_src = core / "scripts"
+    else:
+        repo_root = Path(__file__).parent.parent.parent
+        scripts_src = repo_root / "scripts"
+
+    skipped_files: list[str] = []
+
+    if scripts_src.is_dir():
+        dest_scripts = project_path / ".specify" / "scripts"
+        dest_scripts.mkdir(parents=True, exist_ok=True)
+        variant_dir = "bash" if script_type == "sh" else "powershell"
+        variant_src = scripts_src / variant_dir
+        if variant_src.is_dir():
+            dest_variant = dest_scripts / variant_dir
+            dest_variant.mkdir(parents=True, exist_ok=True)
+            # Merge without overwriting — only add files that don't exist yet
+            for src_path in variant_src.rglob("*"):
+                if src_path.is_file():
+                    rel_path = src_path.relative_to(variant_src)
+                    dst_path = dest_variant / rel_path
+                    if dst_path.exists():
+                        skipped_files.append(str(dst_path.relative_to(project_path)))
+                    else:
+                        dst_path.parent.mkdir(parents=True, exist_ok=True)
+                        shutil.copy2(src_path, dst_path)
+                        rel = dst_path.relative_to(project_path).as_posix()
+                        manifest.record_existing(rel)
+
+    # Page templates (not command templates, not vscode-settings.json)
+    if core and (core / "templates").is_dir():
+        templates_src = core / "templates"
+    else:
+        repo_root = Path(__file__).parent.parent.parent
+        templates_src = repo_root / "templates"
+
+    if templates_src.is_dir():
+        dest_templates = project_path / ".specify" / "templates"
+        dest_templates.mkdir(parents=True, exist_ok=True)
+        for f in templates_src.iterdir():
+            if f.is_file() and f.name != "vscode-settings.json" and not f.name.startswith("."):
+                dst = dest_templates / f.name
+                if dst.exists():
+                    skipped_files.append(str(dst.relative_to(project_path)))
+                else:
+                    shutil.copy2(f, dst)
+                    rel = dst.relative_to(project_path).as_posix()
+                    manifest.record_existing(rel)
+
+    if skipped_files:
+        import logging
+        logging.getLogger(__name__).warning(
+            "The following shared files already exist and were not overwritten:\n%s",
+            "\n".join(f"  {f}" for f in skipped_files),
+        )
+
+    manifest.save()
+    return True
+
+
 def scaffold_from_core_pack(
     project_path: Path,
     ai_assistant: str,
@@ -1828,6 +1906,7 @@ def init(
     offline: bool = typer.Option(False, "--offline", help="Use assets bundled in the specify-cli package instead of downloading from GitHub (no network access required). Bundled assets will become the default in v0.6.0 and this flag will be removed."),
     preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
     branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),
+    integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
 ):
     """
     Initialize a new Specify project.
@@ -1889,6 +1968,35 @@ def init(
     if ai_assistant:
         ai_assistant = AI_ASSISTANT_ALIASES.get(ai_assistant, ai_assistant)
 
+    # --integration and --ai are mutually exclusive
+    if integration and ai_assistant:
+        console.print("[red]Error:[/red] --integration and --ai are mutually exclusive")
+        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
+    use_integration = False
+    if integration:
+        from .integrations import INTEGRATION_REGISTRY, get_integration
+        resolved_integration = get_integration(integration)
+        if not resolved_integration:
+            console.print(f"[red]Error:[/red] Unknown integration: '{integration}'")
+            available = ", ".join(sorted(INTEGRATION_REGISTRY))
+            console.print(f"[yellow]Available integrations:[/yellow] {available}")
+            raise typer.Exit(1)
+        use_integration = True
+        # Map integration key to the ai_assistant variable for downstream compatibility
+        ai_assistant = integration
+    elif ai_assistant == "copilot":
+        from .integrations import get_integration
+        resolved_integration = get_integration("copilot")
+        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]"
+            )
+
     if project_name == ".":
         here = True
         project_name = None  # Clear project_name to use existing validation logic
@@ -2057,7 +2165,10 @@ def init(
             "This will become the default in v0.6.0."
         )
 
-    if use_github:
+    if use_integration:
+        tracker.add("integration", "Install integration")
+        tracker.add("shared-infra", "Install shared infrastructure")
+    elif use_github:
         for key, label in [
             ("fetch", "Fetch latest release"),
             ("download", "Download template"),
@@ -2092,7 +2203,39 @@ def init(
             verify = not skip_tls
             local_ssl_context = ssl_context if verify else False
 
-            if use_github:
+            if use_integration:
+                # Integration-based scaffolding (new path)
+                from .integrations.manifest import IntegrationManifest
+                tracker.start("integration")
+                manifest = IntegrationManifest(
+                    resolved_integration.key, project_path, version=get_speckit_version()
+                )
+                resolved_integration.setup(
+                    project_path, manifest,
+                    script_type=selected_script,
+                )
+                manifest.save()
+
+                # Write .specify/integration.json
+                script_ext = "sh" if selected_script == "sh" else "ps1"
+                integration_json = project_path / ".specify" / "integration.json"
+                integration_json.parent.mkdir(parents=True, exist_ok=True)
+                integration_json.write_text(json.dumps({
+                    "integration": resolved_integration.key,
+                    "version": get_speckit_version(),
+                    "scripts": {
+                        "update-context": f".specify/integrations/{resolved_integration.key}/scripts/update-context.{script_ext}",
+                    },
+                }, indent=2) + "\n", encoding="utf-8")
+
+                tracker.complete("integration", resolved_integration.config.get("name", resolved_integration.key))
+
+                # Install shared infrastructure (scripts, templates)
+                tracker.start("shared-infra")
+                _install_shared_infra(project_path, selected_script, tracker=tracker)
+                tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
+
+            elif use_github:
                 with httpx.Client(verify=local_ssl_context) as local_client:
                     download_and_extract_template(
                         project_path,
@@ -2227,7 +2370,7 @@ def init(
             # Persist the CLI options so later operations (e.g. preset add)
             # can adapt their behaviour without re-scanning the filesystem.
             # Must be saved BEFORE preset install so _get_skills_dir() works.
-            save_init_options(project_path, {
+            init_opts = {
                 "ai": selected_ai,
                 "ai_skills": ai_skills,
                 "ai_commands_dir": ai_commands_dir,
@@ -2237,7 +2380,10 @@ def init(
                 "offline": offline,
                 "script": selected_script,
                 "speckit_version": get_speckit_version(),
-            })
+            }
+            if use_integration:
+                init_opts["integration"] = resolved_integration.key
+            save_init_options(project_path, init_opts)
 
             # Install preset if specified
             if preset:
diff --git a/src/specify_cli/integrations/__init__.py b/src/specify_cli/integrations/__init__.py
index 18292633f..e5ddc5c5a 100644
--- a/src/specify_cli/integrations/__init__.py
+++ b/src/specify_cli/integrations/__init__.py
@@ -32,3 +32,15 @@ def _register(integration: IntegrationBase) -> None:
 def get_integration(key: str) -> IntegrationBase | None:
     """Return the integration for *key*, or ``None`` if not registered."""
     return INTEGRATION_REGISTRY.get(key)
+
+
+# -- Register built-in integrations --------------------------------------
+
+def _register_builtins() -> None:
+    """Register all built-in integrations."""
+    from .copilot import CopilotIntegration
+
+    _register(CopilotIntegration())
+
+
+_register_builtins()
diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index 73e51ae7f..012b45c4c 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -9,6 +9,7 @@ Provides:
 
 from __future__ import annotations
 
+import re
 import shutil
 from abc import ABC
 from dataclasses import dataclass
@@ -84,35 +85,65 @@ class IntegrationBase(ABC):
         """Return options this integration accepts. Default: none."""
         return []
 
-    def templates_dir(self) -> Path:
-        """Return the path to this integration's bundled templates.
+    # -- Primitives — building blocks for setup() -------------------------
 
-        By convention, templates live in a ``templates/`` subdirectory
-        next to the file where the integration class is defined.
+    def shared_commands_dir(self) -> Path | None:
+        """Return path to the shared command templates directory.
+
+        Checks ``core_pack/commands/`` (wheel install) first, then
+        ``templates/commands/`` (source checkout).  Returns ``None``
+        if neither exists.
         """
         import inspect
 
-        module_file = inspect.getfile(type(self))
-        return Path(module_file).resolve().parent / "templates"
+        pkg_dir = Path(inspect.getfile(IntegrationBase)).resolve().parent.parent
+        for candidate in [
+            pkg_dir / "core_pack" / "commands",
+            pkg_dir.parent.parent / "templates" / "commands",
+        ]:
+            if candidate.is_dir():
+                return candidate
+        return None
 
-    def setup(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        parsed_options: dict[str, Any] | None = None,
-        **opts: Any,
-    ) -> list[Path]:
-        """Install integration files into *project_root*.
+    def shared_templates_dir(self) -> Path | None:
+        """Return path to the shared page templates directory.
 
-        Returns the list of files created.  The default implementation
-        copies every file from ``templates_dir()`` into the commands
-        directory derived from ``config``, recording each in *manifest*.
+        Contains ``vscode-settings.json``, ``spec-template.md``, etc.
+        Checks ``core_pack/templates/`` then ``templates/``.
         """
-        created: list[Path] = []
-        tpl_dir = self.templates_dir()
-        if not tpl_dir.is_dir():
-            return created
+        import inspect
 
+        pkg_dir = Path(inspect.getfile(IntegrationBase)).resolve().parent.parent
+        for candidate in [
+            pkg_dir / "core_pack" / "templates",
+            pkg_dir.parent.parent / "templates",
+        ]:
+            if candidate.is_dir():
+                return candidate
+        return None
+
+    def list_command_templates(self) -> list[Path]:
+        """Return sorted list of command template files from the shared directory."""
+        cmd_dir = self.shared_commands_dir()
+        if not cmd_dir or not cmd_dir.is_dir():
+            return []
+        return sorted(f for f in cmd_dir.iterdir() if f.is_file() and f.suffix == ".md")
+
+    def command_filename(self, template_name: str) -> str:
+        """Return the destination filename for a command template.
+
+        *template_name* is the stem of the source file (e.g. ``"plan"``).
+        Default: ``speckit.{template_name}.md``.  Subclasses override
+        to change the extension or naming convention.
+        """
+        return f"speckit.{template_name}.md"
+
+    def commands_dest(self, project_root: Path) -> Path:
+        """Return the absolute path to the commands output directory.
+
+        Derived from ``config["folder"]`` and ``config["commands_subdir"]``.
+        Raises ``ValueError`` if ``config`` or ``folder`` is missing.
+        """
         if not self.config:
             raise ValueError(
                 f"{type(self).__name__}.config is not set; integration "
@@ -123,6 +154,179 @@ class IntegrationBase(ABC):
             raise ValueError(
                 f"{type(self).__name__}.config is missing required 'folder' entry."
             )
+        subdir = self.config.get("commands_subdir", "commands")
+        return project_root / folder / subdir
+
+    # -- File operations — granular primitives for setup() ----------------
+
+    @staticmethod
+    def copy_command_to_directory(
+        src: Path,
+        dest_dir: Path,
+        filename: str,
+    ) -> Path:
+        """Copy a command template to *dest_dir* with the given *filename*.
+
+        Creates *dest_dir* if needed.  Returns the absolute path of the
+        written file.  The caller can post-process the file before
+        recording it in the manifest.
+        """
+        dest_dir.mkdir(parents=True, exist_ok=True)
+        dst = dest_dir / filename
+        shutil.copy2(src, dst)
+        return dst
+
+    @staticmethod
+    def record_file_in_manifest(
+        file_path: Path,
+        project_root: Path,
+        manifest: IntegrationManifest,
+    ) -> None:
+        """Hash *file_path* and record it in *manifest*.
+
+        *file_path* must be inside *project_root*.
+        """
+        rel = file_path.resolve().relative_to(project_root.resolve())
+        manifest.record_existing(rel)
+
+    @staticmethod
+    def write_file_and_record(
+        content: str,
+        dest: Path,
+        project_root: Path,
+        manifest: IntegrationManifest,
+    ) -> Path:
+        """Write *content* to *dest*, hash it, and record in *manifest*.
+
+        Creates parent directories as needed.  Returns *dest*.
+        """
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        dest.write_text(content, encoding="utf-8")
+        rel = dest.resolve().relative_to(project_root.resolve())
+        manifest.record_existing(rel)
+        return dest
+
+    @staticmethod
+    def process_template(
+        content: str,
+        agent_name: str,
+        script_type: str,
+        arg_placeholder: str = "$ARGUMENTS",
+    ) -> str:
+        """Process a raw command template into agent-ready content.
+
+        Performs the same transformations as the release script:
+        1. Extract ``scripts.<script_type>`` value from YAML frontmatter
+        2. Replace ``{SCRIPT}`` with the extracted script command
+        3. Extract ``agent_scripts.<script_type>`` and replace ``{AGENT_SCRIPT}``
+        4. Strip ``scripts:`` and ``agent_scripts:`` sections from frontmatter
+        5. Replace ``{ARGS}`` with *arg_placeholder*
+        6. Replace ``__AGENT__`` with *agent_name*
+        7. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
+        """
+        # 1. Extract script command from frontmatter
+        script_command = ""
+        script_pattern = re.compile(
+            rf"^\s*{re.escape(script_type)}:\s*(.+)$", re.MULTILINE
+        )
+        # Find the scripts: block
+        in_scripts = False
+        for line in content.splitlines():
+            if line.strip() == "scripts:":
+                in_scripts = True
+                continue
+            if in_scripts and line and not line[0].isspace():
+                in_scripts = False
+            if in_scripts:
+                m = script_pattern.match(line)
+                if m:
+                    script_command = m.group(1).strip()
+                    break
+
+        # 2. Replace {SCRIPT}
+        if script_command:
+            content = content.replace("{SCRIPT}", script_command)
+
+        # 3. Extract agent_script command
+        agent_script_command = ""
+        in_agent_scripts = False
+        for line in content.splitlines():
+            if line.strip() == "agent_scripts:":
+                in_agent_scripts = True
+                continue
+            if in_agent_scripts and line and not line[0].isspace():
+                in_agent_scripts = False
+            if in_agent_scripts:
+                m = script_pattern.match(line)
+                if m:
+                    agent_script_command = m.group(1).strip()
+                    break
+
+        if agent_script_command:
+            content = content.replace("{AGENT_SCRIPT}", agent_script_command)
+
+        # 4. Strip scripts: and agent_scripts: sections from frontmatter
+        lines = content.splitlines(keepends=True)
+        output_lines: list[str] = []
+        in_frontmatter = False
+        skip_section = False
+        dash_count = 0
+        for line in lines:
+            stripped = line.rstrip("\n\r")
+            if stripped == "---":
+                dash_count += 1
+                if dash_count == 1:
+                    in_frontmatter = True
+                else:
+                    in_frontmatter = False
+                skip_section = False
+                output_lines.append(line)
+                continue
+            if in_frontmatter:
+                if stripped in ("scripts:", "agent_scripts:"):
+                    skip_section = True
+                    continue
+                if skip_section:
+                    if line[0:1].isspace():
+                        continue  # skip indented content under scripts/agent_scripts
+                    skip_section = False
+            output_lines.append(line)
+        content = "".join(output_lines)
+
+        # 5. Replace {ARGS}
+        content = content.replace("{ARGS}", arg_placeholder)
+
+        # 6. Replace __AGENT__
+        content = content.replace("__AGENT__", agent_name)
+
+        # 7. Rewrite paths (matches release script's rewrite_paths())
+        content = re.sub(r"(/?)memory/", r".specify/memory/", content)
+        content = re.sub(r"(/?)scripts/", r".specify/scripts/", content)
+        content = re.sub(r"(/?)templates/", r".specify/templates/", content)
+        # Fix double-prefix (same as release script's .specify.specify/ fix)
+        content = content.replace(".specify.specify/", ".specify/")
+        content = content.replace(".specify/.specify/", ".specify/")
+
+        return content
+
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        """Install integration command files into *project_root*.
+
+        Returns the list of files created.  Copies raw templates without
+        processing.  Integrations that need placeholder replacement
+        (e.g. ``{SCRIPT}``, ``__AGENT__``) should override ``setup()``
+        and call ``process_template()`` in their own loop — see
+        ``CopilotIntegration`` for an example.
+        """
+        templates = self.list_command_templates()
+        if not templates:
+            return []
 
         project_root_resolved = project_root.resolve()
         if manifest.project_root != project_root_resolved:
@@ -130,9 +334,8 @@ class IntegrationBase(ABC):
                 f"manifest.project_root ({manifest.project_root}) does not match "
                 f"project_root ({project_root_resolved})"
             )
-        subdir = self.config.get("commands_subdir", "commands")
-        dest = (project_root / folder / subdir).resolve()
-        # Ensure destination stays within the project root
+
+        dest = self.commands_dest(project_root).resolve()
         try:
             dest.relative_to(project_root_resolved)
         except ValueError as exc:
@@ -141,16 +344,13 @@ class IntegrationBase(ABC):
                 f"project root {project_root_resolved}"
             ) from exc
 
-        dest.mkdir(parents=True, exist_ok=True)
+        created: list[Path] = []
 
-        for src_file in sorted(tpl_dir.iterdir()):
-            if src_file.is_file():
-                dst_file = dest / src_file.name
-                dst_resolved = dst_file.resolve()
-                rel = dst_resolved.relative_to(project_root_resolved)
-                shutil.copy2(src_file, dst_file)
-                manifest.record_existing(rel)
-                created.append(dst_file)
+        for src_file in templates:
+            dst_name = self.command_filename(src_file.stem)
+            dst_file = self.copy_command_to_directory(src_file, dest, dst_name)
+            self.record_file_in_manifest(dst_file, project_root, manifest)
+            created.append(dst_file)
 
         return created
 
diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
new file mode 100644
index 000000000..0c5354d53
--- /dev/null
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -0,0 +1,197 @@
+"""Copilot integration — GitHub Copilot in VS Code.
+
+Copilot has several unique behaviors compared to standard markdown agents:
+- Commands use ``.agent.md`` extension (not ``.md``)
+- Each command gets a companion ``.prompt.md`` file in ``.github/prompts/``
+- Installs ``.vscode/settings.json`` with prompt file recommendations
+- Context file lives at ``.github/copilot-instructions.md``
+"""
+
+from __future__ import annotations
+
+import json
+import shutil
+from pathlib import Path
+from typing import Any
+
+from ..base import IntegrationBase
+from ..manifest import IntegrationManifest
+
+
+class CopilotIntegration(IntegrationBase):
+    """Integration for GitHub Copilot in VS Code."""
+
+    key = "copilot"
+    config = {
+        "name": "GitHub Copilot",
+        "folder": ".github/",
+        "commands_subdir": "agents",
+        "install_url": None,
+        "requires_cli": False,
+    }
+    registrar_config = {
+        "dir": ".github/agents",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": ".agent.md",
+    }
+    context_file = ".github/copilot-instructions.md"
+
+    def command_filename(self, template_name: str) -> str:
+        """Copilot commands use ``.agent.md`` extension."""
+        return f"speckit.{template_name}.agent.md"
+
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        """Install copilot commands, companion prompts, and VS Code settings.
+
+        Uses base class primitives to: read templates, process them
+        (replace placeholders, strip script blocks, rewrite paths),
+        write as ``.agent.md``, then add companion prompts and VS Code settings.
+        """
+        project_root_resolved = project_root.resolve()
+        if manifest.project_root != project_root_resolved:
+            raise ValueError(
+                f"manifest.project_root ({manifest.project_root}) does not match "
+                f"project_root ({project_root_resolved})"
+            )
+
+        templates = self.list_command_templates()
+        if not templates:
+            return []
+
+        dest = self.commands_dest(project_root)
+        dest_resolved = dest.resolve()
+        try:
+            dest_resolved.relative_to(project_root_resolved)
+        except ValueError as exc:
+            raise ValueError(
+                f"Integration destination {dest_resolved} escapes "
+                f"project root {project_root_resolved}"
+            ) from exc
+        dest.mkdir(parents=True, exist_ok=True)
+        created: list[Path] = []
+
+        script_type = opts.get("script_type", "sh")
+        arg_placeholder = self.registrar_config.get("args", "$ARGUMENTS")
+
+        # 1. Process and write command files as .agent.md
+        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)
+
+        # 2. Generate companion .prompt.md files from the templates we just wrote
+        prompts_dir = project_root / ".github" / "prompts"
+        for src_file in templates:
+            cmd_name = f"speckit.{src_file.stem}"
+            prompt_content = f"---\nagent: {cmd_name}\n---\n"
+            prompt_file = self.write_file_and_record(
+                prompt_content,
+                prompts_dir / f"{cmd_name}.prompt.md",
+                project_root,
+                manifest,
+            )
+            created.append(prompt_file)
+
+        # Write .vscode/settings.json
+        settings_src = self._vscode_settings_path()
+        if settings_src and settings_src.is_file():
+            dst_settings = project_root / ".vscode" / "settings.json"
+            dst_settings.parent.mkdir(parents=True, exist_ok=True)
+            if dst_settings.exists():
+                # Merge into existing — don't track since we can't safely
+                # remove the user's settings file on uninstall.
+                self._merge_vscode_settings(settings_src, dst_settings)
+            else:
+                shutil.copy2(settings_src, dst_settings)
+                self.record_file_in_manifest(dst_settings, project_root, manifest)
+                created.append(dst_settings)
+
+        # 4. Install integration-specific update-context scripts
+        scripts_src = Path(__file__).resolve().parent / "scripts"
+        if scripts_src.is_dir():
+            scripts_dest = project_root / ".specify" / "integrations" / "copilot" / "scripts"
+            scripts_dest.mkdir(parents=True, exist_ok=True)
+            for src_script in sorted(scripts_src.iterdir()):
+                if src_script.is_file():
+                    dst_script = scripts_dest / src_script.name
+                    shutil.copy2(src_script, dst_script)
+                    # Make shell scripts executable
+                    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
+
+    def _vscode_settings_path(self) -> Path | None:
+        """Return path to the bundled vscode-settings.json template."""
+        tpl_dir = self.shared_templates_dir()
+        if tpl_dir:
+            candidate = tpl_dir / "vscode-settings.json"
+            if candidate.is_file():
+                return candidate
+        return None
+
+    @staticmethod
+    def _merge_vscode_settings(src: Path, dst: Path) -> None:
+        """Merge settings from *src* into existing *dst* JSON file.
+
+        Top-level keys from *src* are added only if missing in *dst*.
+        For dict-valued keys, sub-keys are merged the same way.
+
+        If *dst* cannot be parsed (e.g. JSONC with comments), the merge
+        is skipped to avoid overwriting user settings.
+        """
+        try:
+            existing = json.loads(dst.read_text(encoding="utf-8"))
+        except (json.JSONDecodeError, OSError):
+            # Cannot parse existing file (likely JSONC with comments).
+            # Skip merge to preserve the user's settings, but show
+            # what they should add manually.
+            import logging
+            template_content = src.read_text(encoding="utf-8")
+            logging.getLogger(__name__).warning(
+                "Could not parse %s (may contain JSONC comments). "
+                "Skipping settings merge to preserve existing file.\n"
+                "Please add the following settings manually:\n%s",
+                dst, template_content,
+            )
+            return
+
+        new_settings = json.loads(src.read_text(encoding="utf-8"))
+
+        if not isinstance(existing, dict) or not isinstance(new_settings, dict):
+            import logging
+            logging.getLogger(__name__).warning(
+                "Skipping settings merge: %s or template is not a JSON object.", dst
+            )
+            return
+
+        changed = False
+        for key, value in new_settings.items():
+            if key not in existing:
+                existing[key] = value
+                changed = True
+            elif isinstance(existing[key], dict) and isinstance(value, dict):
+                for sub_key, sub_value in value.items():
+                    if sub_key not in existing[key]:
+                        existing[key][sub_key] = sub_value
+                        changed = True
+
+        if not changed:
+            return
+
+        dst.write_text(
+            json.dumps(existing, indent=4) + "\n", encoding="utf-8"
+        )
diff --git a/src/specify_cli/integrations/copilot/scripts/update-context.ps1 b/src/specify_cli/integrations/copilot/scripts/update-context.ps1
new file mode 100644
index 000000000..c6f9845a3
--- /dev/null
+++ b/src/specify_cli/integrations/copilot/scripts/update-context.ps1
@@ -0,0 +1,22 @@
+# update-context.ps1 — Copilot integration: create/update .github/copilot-instructions.md
+#
+# This is the copilot-specific implementation that produces the GitHub
+# Copilot instructions file. The shared dispatcher reads
+# .specify/integration.json and calls this script.
+#
+# NOTE: This script is not yet active. It will be activated in Stage 7
+# when the shared update-agent-context.ps1 replaces its switch statement
+# with integration.json-based dispatch. The shared script must also be
+# refactored to support SPECKIT_SOURCE_ONLY (guard the Main call) before
+# dot-sourcing will work.
+#
+# 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 = $PWD.Path }
+
+# Invoke shared update-agent-context script as a separate process.
+# Dot-sourcing is unsafe until that script guards its Main call.
+& "$repoRoot/.specify/scripts/powershell/update-agent-context.ps1" -AgentType copilot
diff --git a/src/specify_cli/integrations/copilot/scripts/update-context.sh b/src/specify_cli/integrations/copilot/scripts/update-context.sh
new file mode 100644
index 000000000..84c86422e
--- /dev/null
+++ b/src/specify_cli/integrations/copilot/scripts/update-context.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# update-context.sh — Copilot integration: create/update .github/copilot-instructions.md
+#
+# This is the copilot-specific implementation that produces the GitHub
+# Copilot instructions file. The shared dispatcher reads
+# .specify/integration.json and calls this script.
+#
+# NOTE: This script is not yet active. It will be activated in Stage 7
+# when the shared update-agent-context.sh replaces its case statement
+# with integration.json-based dispatch. The shared script must also be
+# refactored to support SPECKIT_SOURCE_ONLY (guard the main logic)
+# before sourcing will work.
+#
+# 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)}"
+
+# Invoke shared update-agent-context script as a separate process.
+# Sourcing is unsafe until that script guards its main logic.
+exec "$REPO_ROOT/.specify/scripts/bash/update-agent-context.sh" copilot
diff --git a/tests/integrations/__init__.py b/tests/integrations/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/integrations/conftest.py b/tests/integrations/conftest.py
new file mode 100644
index 000000000..54f59e23a
--- /dev/null
+++ b/tests/integrations/conftest.py
@@ -0,0 +1,23 @@
+"""Shared test helpers for integration tests."""
+
+from specify_cli.integrations.base import MarkdownIntegration
+
+
+class StubIntegration(MarkdownIntegration):
+    """Minimal concrete integration for testing."""
+
+    key = "stub"
+    config = {
+        "name": "Stub Agent",
+        "folder": ".stub/",
+        "commands_subdir": "commands",
+        "install_url": None,
+        "requires_cli": False,
+    }
+    registrar_config = {
+        "dir": ".stub/commands",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": ".md",
+    }
+    context_file = "STUB.md"
diff --git a/tests/integrations/test_base.py b/tests/integrations/test_base.py
new file mode 100644
index 000000000..03b5eb306
--- /dev/null
+++ b/tests/integrations/test_base.py
@@ -0,0 +1,169 @@
+"""Tests for IntegrationOption, IntegrationBase, MarkdownIntegration, and primitives."""
+
+import pytest
+
+from specify_cli.integrations.base import (
+    IntegrationBase,
+    IntegrationOption,
+    MarkdownIntegration,
+)
+from specify_cli.integrations.manifest import IntegrationManifest
+from .conftest import StubIntegration
+
+
+class TestIntegrationOption:
+    def test_defaults(self):
+        opt = IntegrationOption(name="--flag")
+        assert opt.name == "--flag"
+        assert opt.is_flag is False
+        assert opt.required is False
+        assert opt.default is None
+        assert opt.help == ""
+
+    def test_flag_option(self):
+        opt = IntegrationOption(name="--skills", is_flag=True, default=True, help="Enable skills")
+        assert opt.is_flag is True
+        assert opt.default is True
+        assert opt.help == "Enable skills"
+
+    def test_required_option(self):
+        opt = IntegrationOption(name="--commands-dir", required=True, help="Dir path")
+        assert opt.required is True
+
+    def test_frozen(self):
+        opt = IntegrationOption(name="--x")
+        with pytest.raises(AttributeError):
+            opt.name = "--y"  # type: ignore[misc]
+
+
+class TestIntegrationBase:
+    def test_key_and_config(self):
+        i = StubIntegration()
+        assert i.key == "stub"
+        assert i.config["name"] == "Stub Agent"
+        assert i.registrar_config["format"] == "markdown"
+        assert i.context_file == "STUB.md"
+
+    def test_options_default_empty(self):
+        assert StubIntegration.options() == []
+
+    def test_shared_commands_dir(self):
+        i = StubIntegration()
+        cmd_dir = i.shared_commands_dir()
+        assert cmd_dir is not None
+        assert cmd_dir.is_dir()
+
+    def test_setup_uses_shared_templates(self, tmp_path):
+        i = StubIntegration()
+        manifest = IntegrationManifest("stub", tmp_path)
+        created = i.setup(tmp_path, manifest)
+        assert len(created) > 0
+        for f in created:
+            assert f.parent == tmp_path / ".stub" / "commands"
+            assert f.name.startswith("speckit.")
+            assert f.name.endswith(".md")
+
+    def test_setup_copies_templates(self, tmp_path, monkeypatch):
+        tpl = tmp_path / "_templates"
+        tpl.mkdir()
+        (tpl / "plan.md").write_text("plan content", encoding="utf-8")
+        (tpl / "specify.md").write_text("spec content", encoding="utf-8")
+
+        i = StubIntegration()
+        monkeypatch.setattr(type(i), "list_command_templates", lambda self: sorted(tpl.glob("*.md")))
+
+        project = tmp_path / "project"
+        project.mkdir()
+        created = i.setup(project, IntegrationManifest("stub", project))
+        assert len(created) == 2
+        assert (project / ".stub" / "commands" / "speckit.plan.md").exists()
+        assert (project / ".stub" / "commands" / "speckit.specify.md").exists()
+
+    def test_install_delegates_to_setup(self, tmp_path):
+        i = StubIntegration()
+        manifest = IntegrationManifest("stub", tmp_path)
+        result = i.install(tmp_path, manifest)
+        assert len(result) > 0
+
+    def test_uninstall_delegates_to_teardown(self, tmp_path):
+        i = StubIntegration()
+        manifest = IntegrationManifest("stub", tmp_path)
+        removed, skipped = i.uninstall(tmp_path, manifest)
+        assert removed == []
+        assert skipped == []
+
+
+class TestMarkdownIntegration:
+    def test_is_subclass_of_base(self):
+        assert issubclass(MarkdownIntegration, IntegrationBase)
+
+    def test_stub_is_markdown(self):
+        assert isinstance(StubIntegration(), MarkdownIntegration)
+
+
+class TestBasePrimitives:
+    def test_shared_commands_dir_returns_path(self):
+        i = StubIntegration()
+        cmd_dir = i.shared_commands_dir()
+        assert cmd_dir is not None
+        assert cmd_dir.is_dir()
+
+    def test_shared_templates_dir_returns_path(self):
+        i = StubIntegration()
+        tpl_dir = i.shared_templates_dir()
+        assert tpl_dir is not None
+        assert tpl_dir.is_dir()
+
+    def test_list_command_templates_returns_md_files(self):
+        i = StubIntegration()
+        templates = i.list_command_templates()
+        assert len(templates) > 0
+        assert all(t.suffix == ".md" for t in templates)
+
+    def test_command_filename_default(self):
+        i = StubIntegration()
+        assert i.command_filename("plan") == "speckit.plan.md"
+
+    def test_commands_dest(self, tmp_path):
+        i = StubIntegration()
+        dest = i.commands_dest(tmp_path)
+        assert dest == tmp_path / ".stub" / "commands"
+
+    def test_commands_dest_no_config_raises(self, tmp_path):
+        class NoConfig(MarkdownIntegration):
+            key = "noconfig"
+        with pytest.raises(ValueError, match="config is not set"):
+            NoConfig().commands_dest(tmp_path)
+
+    def test_copy_command_to_directory(self, tmp_path):
+        src = tmp_path / "source.md"
+        src.write_text("content", encoding="utf-8")
+        dest_dir = tmp_path / "output"
+        result = IntegrationBase.copy_command_to_directory(src, dest_dir, "speckit.plan.md")
+        assert result == dest_dir / "speckit.plan.md"
+        assert result.read_text(encoding="utf-8") == "content"
+
+    def test_record_file_in_manifest(self, tmp_path):
+        f = tmp_path / "f.txt"
+        f.write_text("hello", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        IntegrationBase.record_file_in_manifest(f, tmp_path, m)
+        assert "f.txt" in m.files
+
+    def test_write_file_and_record(self, tmp_path):
+        m = IntegrationManifest("test", tmp_path)
+        dest = tmp_path / "sub" / "f.txt"
+        result = IntegrationBase.write_file_and_record("content", dest, tmp_path, m)
+        assert result == dest
+        assert dest.read_text(encoding="utf-8") == "content"
+        assert "sub/f.txt" in m.files
+
+    def test_setup_copies_shared_templates(self, tmp_path):
+        i = StubIntegration()
+        m = IntegrationManifest("stub", tmp_path)
+        created = i.setup(tmp_path, m)
+        assert len(created) > 0
+        for f in created:
+            assert f.parent.name == "commands"
+            assert f.name.startswith("speckit.")
+            assert f.name.endswith(".md")
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
new file mode 100644
index 000000000..03b0e1186
--- /dev/null
+++ b/tests/integrations/test_cli.py
@@ -0,0 +1,122 @@
+"""Tests for --integration flag on specify init (CLI-level)."""
+
+import json
+import os
+
+import pytest
+
+
+class TestInitIntegrationFlag:
+    def test_integration_and_ai_mutually_exclusive(self):
+        from typer.testing import CliRunner
+        from specify_cli import app
+        runner = CliRunner()
+        result = runner.invoke(app, [
+            "init", "test-project", "--ai", "claude", "--integration", "copilot",
+        ])
+        assert result.exit_code != 0
+        assert "mutually exclusive" in result.output
+
+    def test_unknown_integration_rejected(self):
+        from typer.testing import CliRunner
+        from specify_cli import app
+        runner = CliRunner()
+        result = runner.invoke(app, [
+            "init", "test-project", "--integration", "nonexistent",
+        ])
+        assert result.exit_code != 0
+        assert "Unknown integration" in result.output
+
+    def test_integration_copilot_creates_files(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+        runner = CliRunner()
+        project = tmp_path / "int-test"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = runner.invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
+        assert (project / ".github" / "prompts" / "speckit.plan.prompt.md").exists()
+        assert (project / ".specify" / "scripts" / "bash" / "common.sh").exists()
+
+        data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
+        assert data["integration"] == "copilot"
+        assert "scripts" in data
+        assert "update-context" in data["scripts"]
+
+        opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
+        assert opts["integration"] == "copilot"
+
+        assert (project / ".specify" / "integrations" / "copilot.manifest.json").exists()
+        assert (project / ".specify" / "integrations" / "copilot" / "scripts" / "update-context.sh").exists()
+
+        shared_manifest = project / ".specify" / "integrations" / "speckit.manifest.json"
+        assert shared_manifest.exists()
+
+    def test_ai_copilot_auto_promotes(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+        project = tmp_path / "promote-test"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--ai", "copilot", "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        assert "--integration copilot" in result.output
+        assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
+
+    def test_shared_infra_skips_existing_files(self, tmp_path):
+        """Pre-existing shared files are not overwritten by _install_shared_infra."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "skip-test"
+        project.mkdir()
+
+        # Pre-create a shared script with custom content
+        scripts_dir = project / ".specify" / "scripts" / "bash"
+        scripts_dir.mkdir(parents=True)
+        custom_content = "# user-modified common.sh\n"
+        (scripts_dir / "common.sh").write_text(custom_content, encoding="utf-8")
+
+        # Pre-create a shared template with custom content
+        templates_dir = project / ".specify" / "templates"
+        templates_dir.mkdir(parents=True)
+        custom_template = "# user-modified spec-template\n"
+        (templates_dir / "spec-template.md").write_text(custom_template, encoding="utf-8")
+
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(app, [
+                "init", "--here", "--force",
+                "--integration", "copilot",
+                "--script", "sh",
+                "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0
+
+        # User's files should be preserved
+        assert (scripts_dir / "common.sh").read_text(encoding="utf-8") == custom_content
+        assert (templates_dir / "spec-template.md").read_text(encoding="utf-8") == custom_template
+
+        # Other shared files should still be installed
+        assert (scripts_dir / "setup-plan.sh").exists()
+        assert (templates_dir / "plan-template.md").exists()
diff --git a/tests/integrations/test_copilot.py b/tests/integrations/test_copilot.py
new file mode 100644
index 000000000..5db0155bd
--- /dev/null
+++ b/tests/integrations/test_copilot.py
@@ -0,0 +1,266 @@
+"""Tests for CopilotIntegration."""
+
+import json
+import os
+
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.manifest import IntegrationManifest
+
+
+class TestCopilotIntegration:
+    def test_copilot_key_and_config(self):
+        copilot = get_integration("copilot")
+        assert copilot is not None
+        assert copilot.key == "copilot"
+        assert copilot.config["folder"] == ".github/"
+        assert copilot.config["commands_subdir"] == "agents"
+        assert copilot.registrar_config["extension"] == ".agent.md"
+        assert copilot.context_file == ".github/copilot-instructions.md"
+
+    def test_command_filename_agent_md(self):
+        copilot = get_integration("copilot")
+        assert copilot.command_filename("plan") == "speckit.plan.agent.md"
+
+    def test_setup_creates_agent_md_files(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        assert len(created) > 0
+        agent_files = [f for f in created if ".agent." in f.name]
+        assert len(agent_files) > 0
+        for f in agent_files:
+            assert f.parent == tmp_path / ".github" / "agents"
+            assert f.name.endswith(".agent.md")
+
+    def test_setup_creates_companion_prompts(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        prompt_files = [f for f in created if f.parent.name == "prompts"]
+        assert len(prompt_files) > 0
+        for f in prompt_files:
+            assert f.name.endswith(".prompt.md")
+            content = f.read_text(encoding="utf-8")
+            assert content.startswith("---\nagent: speckit.")
+
+    def test_agent_and_prompt_counts_match(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        agents = [f for f in created if ".agent.md" in f.name]
+        prompts = [f for f in created if ".prompt.md" in f.name]
+        assert len(agents) == len(prompts)
+
+    def test_setup_creates_vscode_settings_new(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        assert copilot._vscode_settings_path() is not None
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        settings = tmp_path / ".vscode" / "settings.json"
+        assert settings.exists()
+        assert settings in created
+        assert any("settings.json" in k for k in m.files)
+
+    def test_setup_merges_existing_vscode_settings(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        vscode_dir = tmp_path / ".vscode"
+        vscode_dir.mkdir(parents=True)
+        existing = {"editor.fontSize": 14, "custom.setting": True}
+        (vscode_dir / "settings.json").write_text(json.dumps(existing, indent=4), encoding="utf-8")
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        settings = tmp_path / ".vscode" / "settings.json"
+        data = json.loads(settings.read_text(encoding="utf-8"))
+        assert data["editor.fontSize"] == 14
+        assert data["custom.setting"] is True
+        assert settings not in created
+        assert not any("settings.json" in k for k in m.files)
+
+    def test_all_created_files_tracked_in_manifest(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.setup(tmp_path, m)
+        for f in created:
+            rel = f.resolve().relative_to(tmp_path.resolve()).as_posix()
+            assert rel in m.files, f"Created file {rel} not tracked in manifest"
+
+    def test_install_uninstall_roundtrip(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.install(tmp_path, m)
+        assert len(created) > 0
+        m.save()
+        for f in created:
+            assert f.exists()
+        removed, skipped = copilot.uninstall(tmp_path, m)
+        assert len(removed) == len(created)
+        assert skipped == []
+
+    def test_modified_file_survives_uninstall(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        created = copilot.install(tmp_path, m)
+        m.save()
+        modified_file = created[0]
+        modified_file.write_text("user modified this", encoding="utf-8")
+        removed, skipped = copilot.uninstall(tmp_path, m)
+        assert modified_file.exists()
+        assert modified_file in skipped
+
+    def test_directory_structure(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        copilot.setup(tmp_path, m)
+        agents_dir = tmp_path / ".github" / "agents"
+        assert agents_dir.is_dir()
+        agent_files = sorted(agents_dir.glob("speckit.*.agent.md"))
+        assert len(agent_files) == 9
+        expected_commands = {
+            "analyze", "checklist", "clarify", "constitution",
+            "implement", "plan", "specify", "tasks", "taskstoissues",
+        }
+        actual_commands = {f.name.removeprefix("speckit.").removesuffix(".agent.md") for f in agent_files}
+        assert actual_commands == expected_commands
+
+    def test_templates_are_processed(self, tmp_path):
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        copilot.setup(tmp_path, m)
+        agents_dir = tmp_path / ".github" / "agents"
+        for agent_file in agents_dir.glob("speckit.*.agent.md"):
+            content = agent_file.read_text(encoding="utf-8")
+            assert "{SCRIPT}" not in content, f"{agent_file.name} has unprocessed {{SCRIPT}}"
+            assert "__AGENT__" not in content, f"{agent_file.name} has unprocessed __AGENT__"
+            assert "{ARGS}" not in content, f"{agent_file.name} has unprocessed {{ARGS}}"
+            assert "\nscripts:\n" not in content
+            assert "\nagent_scripts:\n" not in content
+
+    def test_complete_file_inventory_sh(self, tmp_path):
+        """Every file produced by specify init --integration copilot --script sh."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        project = tmp_path / "inventory-sh"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
+        expected = sorted([
+            ".github/agents/speckit.analyze.agent.md",
+            ".github/agents/speckit.checklist.agent.md",
+            ".github/agents/speckit.clarify.agent.md",
+            ".github/agents/speckit.constitution.agent.md",
+            ".github/agents/speckit.implement.agent.md",
+            ".github/agents/speckit.plan.agent.md",
+            ".github/agents/speckit.specify.agent.md",
+            ".github/agents/speckit.tasks.agent.md",
+            ".github/agents/speckit.taskstoissues.agent.md",
+            ".github/prompts/speckit.analyze.prompt.md",
+            ".github/prompts/speckit.checklist.prompt.md",
+            ".github/prompts/speckit.clarify.prompt.md",
+            ".github/prompts/speckit.constitution.prompt.md",
+            ".github/prompts/speckit.implement.prompt.md",
+            ".github/prompts/speckit.plan.prompt.md",
+            ".github/prompts/speckit.specify.prompt.md",
+            ".github/prompts/speckit.tasks.prompt.md",
+            ".github/prompts/speckit.taskstoissues.prompt.md",
+            ".vscode/settings.json",
+            ".specify/integration.json",
+            ".specify/init-options.json",
+            ".specify/integrations/copilot.manifest.json",
+            ".specify/integrations/speckit.manifest.json",
+            ".specify/integrations/copilot/scripts/update-context.ps1",
+            ".specify/integrations/copilot/scripts/update-context.sh",
+            ".specify/scripts/bash/check-prerequisites.sh",
+            ".specify/scripts/bash/common.sh",
+            ".specify/scripts/bash/create-new-feature.sh",
+            ".specify/scripts/bash/setup-plan.sh",
+            ".specify/scripts/bash/update-agent-context.sh",
+            ".specify/templates/agent-file-template.md",
+            ".specify/templates/checklist-template.md",
+            ".specify/templates/constitution-template.md",
+            ".specify/templates/plan-template.md",
+            ".specify/templates/spec-template.md",
+            ".specify/templates/tasks-template.md",
+            ".specify/memory/constitution.md",
+        ])
+        assert actual == expected, (
+            f"Missing: {sorted(set(expected) - set(actual))}\n"
+            f"Extra: {sorted(set(actual) - set(expected))}"
+        )
+
+    def test_complete_file_inventory_ps(self, tmp_path):
+        """Every file produced by specify init --integration copilot --script ps."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        project = tmp_path / "inventory-ps"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "ps", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
+        expected = sorted([
+            ".github/agents/speckit.analyze.agent.md",
+            ".github/agents/speckit.checklist.agent.md",
+            ".github/agents/speckit.clarify.agent.md",
+            ".github/agents/speckit.constitution.agent.md",
+            ".github/agents/speckit.implement.agent.md",
+            ".github/agents/speckit.plan.agent.md",
+            ".github/agents/speckit.specify.agent.md",
+            ".github/agents/speckit.tasks.agent.md",
+            ".github/agents/speckit.taskstoissues.agent.md",
+            ".github/prompts/speckit.analyze.prompt.md",
+            ".github/prompts/speckit.checklist.prompt.md",
+            ".github/prompts/speckit.clarify.prompt.md",
+            ".github/prompts/speckit.constitution.prompt.md",
+            ".github/prompts/speckit.implement.prompt.md",
+            ".github/prompts/speckit.plan.prompt.md",
+            ".github/prompts/speckit.specify.prompt.md",
+            ".github/prompts/speckit.tasks.prompt.md",
+            ".github/prompts/speckit.taskstoissues.prompt.md",
+            ".vscode/settings.json",
+            ".specify/integration.json",
+            ".specify/init-options.json",
+            ".specify/integrations/copilot.manifest.json",
+            ".specify/integrations/speckit.manifest.json",
+            ".specify/integrations/copilot/scripts/update-context.ps1",
+            ".specify/integrations/copilot/scripts/update-context.sh",
+            ".specify/scripts/powershell/check-prerequisites.ps1",
+            ".specify/scripts/powershell/common.ps1",
+            ".specify/scripts/powershell/create-new-feature.ps1",
+            ".specify/scripts/powershell/setup-plan.ps1",
+            ".specify/scripts/powershell/update-agent-context.ps1",
+            ".specify/templates/agent-file-template.md",
+            ".specify/templates/checklist-template.md",
+            ".specify/templates/constitution-template.md",
+            ".specify/templates/plan-template.md",
+            ".specify/templates/spec-template.md",
+            ".specify/templates/tasks-template.md",
+            ".specify/memory/constitution.md",
+        ])
+        assert actual == expected, (
+            f"Missing: {sorted(set(expected) - set(actual))}\n"
+            f"Extra: {sorted(set(actual) - set(expected))}"
+        )
diff --git a/tests/test_integrations.py b/tests/integrations/test_manifest.py
similarity index 52%
rename from tests/test_integrations.py
rename to tests/integrations/test_manifest.py
index aeb17ae99..b5d5bc39f 100644
--- a/tests/test_integrations.py
+++ b/tests/integrations/test_manifest.py
@@ -1,164 +1,18 @@
-"""Tests for the integrations foundation (Stage 1).
-
-Covers:
-- IntegrationOption dataclass
-- IntegrationBase ABC and MarkdownIntegration base class
-- IntegrationManifest — record, hash, save, load, uninstall, modified detection
-- INTEGRATION_REGISTRY basics
-"""
+"""Tests for IntegrationManifest — record, hash, save, load, uninstall, modified detection."""
 
 import hashlib
 import json
 
 import pytest
 
-from specify_cli.integrations import (
-    INTEGRATION_REGISTRY,
-    _register,
-    get_integration,
-)
-from specify_cli.integrations.base import (
-    IntegrationBase,
-    IntegrationOption,
-    MarkdownIntegration,
-)
 from specify_cli.integrations.manifest import IntegrationManifest, _sha256
 
 
-# ── helpers ──────────────────────────────────────────────────────────────────
-
-
-class _StubIntegration(MarkdownIntegration):
-    """Minimal concrete integration for testing."""
-
-    key = "stub"
-    config = {
-        "name": "Stub Agent",
-        "folder": ".stub/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": False,
-    }
-    registrar_config = {
-        "dir": ".stub/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".md",
-    }
-    context_file = "STUB.md"
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationOption
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestIntegrationOption:
-    def test_defaults(self):
-        opt = IntegrationOption(name="--flag")
-        assert opt.name == "--flag"
-        assert opt.is_flag is False
-        assert opt.required is False
-        assert opt.default is None
-        assert opt.help == ""
-
-    def test_flag_option(self):
-        opt = IntegrationOption(name="--skills", is_flag=True, default=True, help="Enable skills")
-        assert opt.is_flag is True
-        assert opt.default is True
-        assert opt.help == "Enable skills"
-
-    def test_required_option(self):
-        opt = IntegrationOption(name="--commands-dir", required=True, help="Dir path")
-        assert opt.required is True
-
-    def test_frozen(self):
-        opt = IntegrationOption(name="--x")
-        with pytest.raises(AttributeError):
-            opt.name = "--y"  # type: ignore[misc]
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationBase / MarkdownIntegration
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestIntegrationBase:
-    def test_key_and_config(self):
-        i = _StubIntegration()
-        assert i.key == "stub"
-        assert i.config["name"] == "Stub Agent"
-        assert i.registrar_config["format"] == "markdown"
-        assert i.context_file == "STUB.md"
-
-    def test_options_default_empty(self):
-        assert _StubIntegration.options() == []
-
-    def test_templates_dir(self):
-        i = _StubIntegration()
-        td = i.templates_dir()
-        # Should point to a templates/ dir next to this test module.
-        # It won't exist, but the path should be well-formed.
-        assert td.name == "templates"
-
-    def test_setup_no_templates_returns_empty(self, tmp_path):
-        """setup() gracefully returns empty list when templates dir is missing."""
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        created = i.setup(tmp_path, manifest)
-        assert created == []
-
-    def test_setup_copies_templates(self, tmp_path, monkeypatch):
-        """setup() copies template files and records them in the manifest."""
-        # Create templates under tmp_path so we don't mutate the source tree
-        tpl = tmp_path / "_templates"
-        tpl.mkdir()
-        (tpl / "speckit.plan.md").write_text("plan content", encoding="utf-8")
-        (tpl / "speckit.specify.md").write_text("spec content", encoding="utf-8")
-
-        i = _StubIntegration()
-        monkeypatch.setattr(type(i), "templates_dir", lambda self: tpl)
-
-        project = tmp_path / "project"
-        project.mkdir()
-        created = i.setup(project, IntegrationManifest("stub", project))
-        assert len(created) == 2
-        assert (project / ".stub" / "commands" / "speckit.plan.md").exists()
-        assert (project / ".stub" / "commands" / "speckit.specify.md").exists()
-
-    def test_install_delegates_to_setup(self, tmp_path):
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        result = i.install(tmp_path, manifest)
-        assert result == []  # no templates dir → empty
-
-    def test_uninstall_delegates_to_teardown(self, tmp_path):
-        i = _StubIntegration()
-        manifest = IntegrationManifest("stub", tmp_path)
-        removed, skipped = i.uninstall(tmp_path, manifest)
-        assert removed == []
-        assert skipped == []
-
-
-class TestMarkdownIntegration:
-    def test_is_subclass_of_base(self):
-        assert issubclass(MarkdownIntegration, IntegrationBase)
-
-    def test_stub_is_markdown(self):
-        assert isinstance(_StubIntegration(), MarkdownIntegration)
-
-
-# ═══════════════════════════════════════════════════════════════════════════
-# IntegrationManifest
-# ═══════════════════════════════════════════════════════════════════════════
-
-
 class TestManifestRecordFile:
     def test_record_file_writes_and_hashes(self, tmp_path):
         m = IntegrationManifest("test", tmp_path)
         content = "hello world"
         abs_path = m.record_file("a/b.txt", content)
-
         assert abs_path == tmp_path / "a" / "b.txt"
         assert abs_path.read_text(encoding="utf-8") == content
         expected_hash = hashlib.sha256(content.encode()).hexdigest()
@@ -191,7 +45,6 @@ class TestManifestPathTraversal:
             m.record_file("/tmp/escape.txt", "bad")
 
     def test_record_existing_rejects_parent_traversal(self, tmp_path):
-        # Create a file outside the project root
         escape = tmp_path.parent / "escape.txt"
         escape.write_text("evil", encoding="utf-8")
         try:
@@ -202,15 +55,11 @@ class TestManifestPathTraversal:
             escape.unlink(missing_ok=True)
 
     def test_uninstall_skips_traversal_paths(self, tmp_path):
-        """If a manifest is corrupted with traversal paths, uninstall ignores them."""
         m = IntegrationManifest("test", tmp_path)
         m.record_file("safe.txt", "good")
-        # Manually inject a traversal path into the manifest
         m._files["../outside.txt"] = "fakehash"
         m.save()
-
         removed, skipped = m.uninstall()
-        # Only the safe file should have been removed
         assert len(removed) == 1
         assert removed[0].name == "safe.txt"
 
@@ -234,7 +83,6 @@ class TestManifestCheckModified:
         assert m.check_modified() == []
 
     def test_symlink_treated_as_modified(self, tmp_path):
-        """A tracked file replaced with a symlink is reported as modified."""
         m = IntegrationManifest("test", tmp_path)
         m.record_file("f.txt", "original")
         target = tmp_path / "target.txt"
@@ -249,11 +97,9 @@ class TestManifestUninstall:
         m = IntegrationManifest("test", tmp_path)
         m.record_file("d/f.txt", "content")
         m.save()
-
         removed, skipped = m.uninstall()
         assert len(removed) == 1
         assert not (tmp_path / "d" / "f.txt").exists()
-        # Parent dir cleaned up because empty
         assert not (tmp_path / "d").exists()
         assert skipped == []
 
@@ -262,7 +108,6 @@ class TestManifestUninstall:
         m.record_file("f.txt", "original")
         m.save()
         (tmp_path / "f.txt").write_text("modified", encoding="utf-8")
-
         removed, skipped = m.uninstall()
         assert removed == []
         assert len(skipped) == 1
@@ -273,18 +118,15 @@ class TestManifestUninstall:
         m.record_file("f.txt", "original")
         m.save()
         (tmp_path / "f.txt").write_text("modified", encoding="utf-8")
-
         removed, skipped = m.uninstall(force=True)
         assert len(removed) == 1
         assert skipped == []
-        assert not (tmp_path / "f.txt").exists()
 
     def test_already_deleted_file(self, tmp_path):
         m = IntegrationManifest("test", tmp_path)
         m.record_file("f.txt", "content")
         m.save()
         (tmp_path / "f.txt").unlink()
-
         removed, skipped = m.uninstall()
         assert removed == []
         assert skipped == []
@@ -294,7 +136,6 @@ class TestManifestUninstall:
         m.record_file("f.txt", "content")
         m.save()
         assert m.manifest_path.exists()
-
         m.uninstall()
         assert not m.manifest_path.exists()
 
@@ -302,26 +143,19 @@ class TestManifestUninstall:
         m = IntegrationManifest("test", tmp_path)
         m.record_file("a/b/c/f.txt", "content")
         m.save()
-
         m.uninstall()
-        assert not (tmp_path / "a" / "b" / "c").exists()
-        assert not (tmp_path / "a" / "b").exists()
         assert not (tmp_path / "a").exists()
 
     def test_preserves_nonempty_parent_dirs(self, tmp_path):
         m = IntegrationManifest("test", tmp_path)
         m.record_file("a/b/tracked.txt", "content")
-        # Create an untracked sibling
         (tmp_path / "a" / "b" / "other.txt").write_text("keep", encoding="utf-8")
         m.save()
-
         m.uninstall()
         assert not (tmp_path / "a" / "b" / "tracked.txt").exists()
         assert (tmp_path / "a" / "b" / "other.txt").exists()
-        assert (tmp_path / "a" / "b").is_dir()
 
     def test_symlink_skipped_without_force(self, tmp_path):
-        """A tracked file replaced with a symlink is skipped unless force."""
         m = IntegrationManifest("test", tmp_path)
         m.record_file("f.txt", "original")
         m.save()
@@ -329,14 +163,11 @@ class TestManifestUninstall:
         target.write_text("target", encoding="utf-8")
         (tmp_path / "f.txt").unlink()
         (tmp_path / "f.txt").symlink_to(target)
-
         removed, skipped = m.uninstall()
         assert removed == []
         assert len(skipped) == 1
-        assert (tmp_path / "f.txt").is_symlink()  # still there
 
     def test_symlink_removed_with_force(self, tmp_path):
-        """A tracked file replaced with a symlink is removed with force."""
         m = IntegrationManifest("test", tmp_path)
         m.record_file("f.txt", "original")
         m.save()
@@ -344,11 +175,9 @@ class TestManifestUninstall:
         target.write_text("target", encoding="utf-8")
         (tmp_path / "f.txt").unlink()
         (tmp_path / "f.txt").symlink_to(target)
-
         removed, skipped = m.uninstall(force=True)
         assert len(removed) == 1
-        assert not (tmp_path / "f.txt").exists()
-        assert target.exists()  # target not deleted
+        assert target.exists()
 
 
 class TestManifestPersistence:
@@ -356,12 +185,10 @@ class TestManifestPersistence:
         m = IntegrationManifest("myagent", tmp_path, version="2.0.1")
         m.record_file("dir/file.md", "# Hello")
         m.save()
-
         loaded = IntegrationManifest.load("myagent", tmp_path)
         assert loaded.key == "myagent"
         assert loaded.version == "2.0.1"
         assert loaded.files == m.files
-        assert loaded._installed_at == m._installed_at
 
     def test_manifest_path(self, tmp_path):
         m = IntegrationManifest("copilot", tmp_path)
@@ -378,58 +205,16 @@ class TestManifestPersistence:
         assert path.exists()
         data = json.loads(path.read_text(encoding="utf-8"))
         assert data["integration"] == "test"
-        assert "installed_at" in data
-        assert "f.txt" in data["files"]
 
     def test_save_preserves_installed_at(self, tmp_path):
         m = IntegrationManifest("test", tmp_path)
         m.record_file("f.txt", "content")
         m.save()
         first_ts = m._installed_at
-
-        # Save again — timestamp should not change
         m.save()
         assert m._installed_at == first_ts
 
 
-# ═══════════════════════════════════════════════════════════════════════════
-# Registry
-# ═══════════════════════════════════════════════════════════════════════════
-
-
-class TestRegistry:
-    def test_registry_starts_empty(self):
-        # Registry may have been populated by other tests; at minimum
-        # it should be a dict.
-        assert isinstance(INTEGRATION_REGISTRY, dict)
-
-    def test_register_and_get(self):
-        stub = _StubIntegration()
-        _register(stub)
-        try:
-            assert get_integration("stub") is stub
-        finally:
-            INTEGRATION_REGISTRY.pop("stub", None)
-
-    def test_get_missing_returns_none(self):
-        assert get_integration("nonexistent-xyz") is None
-
-    def test_register_empty_key_raises(self):
-        class EmptyKey(MarkdownIntegration):
-            key = ""
-        with pytest.raises(ValueError, match="empty key"):
-            _register(EmptyKey())
-
-    def test_register_duplicate_raises(self):
-        stub = _StubIntegration()
-        _register(stub)
-        try:
-            with pytest.raises(KeyError, match="already registered"):
-                _register(_StubIntegration())
-        finally:
-            INTEGRATION_REGISTRY.pop("stub", None)
-
-
 class TestManifestLoadValidation:
     def test_load_non_dict_raises(self, tmp_path):
         path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
diff --git a/tests/integrations/test_registry.py b/tests/integrations/test_registry.py
new file mode 100644
index 000000000..8fb5ef066
--- /dev/null
+++ b/tests/integrations/test_registry.py
@@ -0,0 +1,45 @@
+"""Tests for INTEGRATION_REGISTRY."""
+
+import pytest
+
+from specify_cli.integrations import (
+    INTEGRATION_REGISTRY,
+    _register,
+    get_integration,
+)
+from specify_cli.integrations.base import MarkdownIntegration
+from .conftest import StubIntegration
+
+
+class TestRegistry:
+    def test_registry_is_dict(self):
+        assert isinstance(INTEGRATION_REGISTRY, dict)
+
+    def test_register_and_get(self):
+        stub = StubIntegration()
+        _register(stub)
+        try:
+            assert get_integration("stub") is stub
+        finally:
+            INTEGRATION_REGISTRY.pop("stub", None)
+
+    def test_get_missing_returns_none(self):
+        assert get_integration("nonexistent-xyz") is None
+
+    def test_register_empty_key_raises(self):
+        class EmptyKey(MarkdownIntegration):
+            key = ""
+        with pytest.raises(ValueError, match="empty key"):
+            _register(EmptyKey())
+
+    def test_register_duplicate_raises(self):
+        stub = StubIntegration()
+        _register(stub)
+        try:
+            with pytest.raises(KeyError, match="already registered"):
+                _register(StubIntegration())
+        finally:
+            INTEGRATION_REGISTRY.pop("stub", None)
+
+    def test_copilot_registered(self):
+        assert "copilot" in INTEGRATION_REGISTRY