Fix shared script command hints for integration separators (#2627)

* fix shared script command refs for integration separators

* Fix integration use shared infra refresh hint

* Clarify shared infrastructure force wording

---------

Co-authored-by: root <1647273252@qq.com>
Co-authored-by: root <kinsonnee@gmail.com>

scripts/bash/check-prerequisites.sh

@@ -117,20 +117,20 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 # Validate required directories and files
 if [[ ! -d "$FEATURE_DIR" ]]; then
     echo "ERROR: Feature directory not found: $FEATURE_DIR" >&2
-    echo "Run /speckit.specify first to create the feature structure." >&2
+    echo "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure." >&2
     exit 1
 fi
 
 if [[ ! -f "$IMPL_PLAN" ]]; then
     echo "ERROR: plan.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.plan first to create the implementation plan." >&2
+    echo "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan." >&2
     exit 1
 fi
 
 # Check for tasks.md if required
 if $REQUIRE_TASKS && [[ ! -f "$TASKS" ]]; then
     echo "ERROR: tasks.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.tasks first to create the task list." >&2
+    echo "Run __SPECKIT_COMMAND_TASKS__ first to create the task list." >&2
     exit 1
 fi
 

scripts/bash/common.sh

@@ -186,7 +186,7 @@ read_feature_json_feature_directory() {
 }
 
 # Returns 0 when .specify/feature.json lists feature_directory that exists as a directory
-# and matches the resolved active FEATURE_DIR (so /speckit.plan can skip git branch pattern checks).
+# and matches the resolved active FEATURE_DIR (so __SPECKIT_COMMAND_PLAN__ can skip git branch pattern checks).
 # Delegates parsing to read_feature_json_feature_directory, which is safe under `set -e`.
 feature_json_matches_feature_dir() {
     local repo_root="$1"
@@ -262,7 +262,7 @@ get_feature_paths() {
 
     # Resolve feature directory.  Priority:
     #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
-    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
+    #   2. .specify/feature.json "feature_directory" key (persisted by __SPECKIT_COMMAND_SPECIFY__)
     #   3. Branch-name-based prefix lookup (legacy fallback)
     local feature_dir
     if [[ -n "${SPECIFY_FEATURE_DIRECTORY:-}" ]]; then
@@ -642,4 +642,3 @@ except Exception:
     printf '%s' "$content"
     return 0
 }
-

scripts/bash/setup-tasks.sh

@@ -35,13 +35,13 @@ fi
 
 if [[ ! -f "$IMPL_PLAN" ]]; then
     echo "ERROR: plan.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.plan first to create the implementation plan." >&2
+    echo "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan." >&2
     exit 1
 fi
 
 if [[ ! -f "$FEATURE_SPEC" ]]; then
     echo "ERROR: spec.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.specify first to create the feature structure." >&2
+    echo "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure." >&2
     exit 1
 fi
 

scripts/powershell/check-prerequisites.ps1

@@ -89,20 +89,20 @@ if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GI
 # Validate required directories and files
 if (-not (Test-Path $paths.FEATURE_DIR -PathType Container)) {
     Write-Output "ERROR: Feature directory not found: $($paths.FEATURE_DIR)"
-    Write-Output "Run /speckit.specify first to create the feature structure."
+    Write-Output "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure."
     exit 1
 }
 
 if (-not (Test-Path $paths.IMPL_PLAN -PathType Leaf)) {
     Write-Output "ERROR: plan.md not found in $($paths.FEATURE_DIR)"
-    Write-Output "Run /speckit.plan first to create the implementation plan."
+    Write-Output "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan."
     exit 1
 }
 
 # Check for tasks.md if required
 if ($RequireTasks -and -not (Test-Path $paths.TASKS -PathType Leaf)) {
     Write-Output "ERROR: tasks.md not found in $($paths.FEATURE_DIR)"
-    Write-Output "Run /speckit.tasks first to create the task list."
+    Write-Output "Run __SPECKIT_COMMAND_TASKS__ first to create the task list."
     exit 1
 }
 

scripts/powershell/common.ps1

@@ -165,7 +165,7 @@ function Test-FeatureBranch {
 }
 
 # True when .specify/feature.json pins an existing feature directory that matches the
-# active FEATURE_DIR from Get-FeaturePathsEnv (so /speckit.plan can skip git branch pattern checks).
+# active FEATURE_DIR from Get-FeaturePathsEnv (so __SPECKIT_COMMAND_PLAN__ can skip git branch pattern checks).
 function Test-FeatureJsonMatchesFeatureDir {
     param(
         [Parameter(Mandatory = $true)][string]$RepoRoot,
@@ -288,7 +288,7 @@ function Get-FeaturePathsEnv {
 
     # Resolve feature directory.  Priority:
     #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
-    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
+    #   2. .specify/feature.json "feature_directory" key (persisted by __SPECKIT_COMMAND_SPECIFY__)
     #   3. Branch-name-based prefix lookup (same as scripts/bash/common.sh)
     $featureJson = Join-Path $repoRoot '.specify/feature.json'
     if ($env:SPECIFY_FEATURE_DIRECTORY) {
@@ -640,4 +640,4 @@ except Exception:
     }
 
     return $content
-}
+}

scripts/powershell/setup-tasks.ps1

@@ -28,13 +28,13 @@ if (-not (Test-FeatureJsonMatchesFeatureDir -RepoRoot $paths.REPO_ROOT -ActiveFe
 
 if (-not (Test-Path $paths.IMPL_PLAN -PathType Leaf)) {
     [Console]::Error.WriteLine("ERROR: plan.md not found in $($paths.FEATURE_DIR)")
-    [Console]::Error.WriteLine("Run /speckit.plan first to create the implementation plan.")
+    [Console]::Error.WriteLine("Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan.")
     exit 1
 }
 
 if (-not (Test-Path $paths.FEATURE_SPEC -PathType Leaf)) {
     [Console]::Error.WriteLine("ERROR: spec.md not found in $($paths.FEATURE_DIR)")
-    [Console]::Error.WriteLine("Run /speckit.specify first to create the feature structure.")
+    [Console]::Error.WriteLine("Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure.")
     exit 1
 }
 

src/specify_cli/__init__.py

@@ -161,9 +161,9 @@ def _install_shared_infra(
     ``bash`` when *script_type* is ``"sh"`` and ``powershell`` when it is
     ``"ps"``.  Tracks all installed files in ``speckit.manifest.json``.
 
-    Page templates are processed to resolve ``__SPECKIT_COMMAND_<NAME>__``
-    placeholders using *invoke_separator* (``"."`` for markdown agents,
-    ``"-"`` for skills agents).
+    Shared scripts and page templates are processed to resolve
+    ``__SPECKIT_COMMAND_<NAME>__`` placeholders using *invoke_separator*
+    (``"."`` for markdown agents, ``"-"`` for skills agents).
 
     Overwrite policy:
 
@@ -741,6 +741,7 @@ def _set_default_integration(
     parsed_options: dict[str, Any] | None = None,
     refresh_templates: bool = True,
     refresh_templates_force: bool = False,
+    refresh_hint: str | None = None,
 ) -> None:
     """Persist *key* as default and align active runtime metadata."""
     resolved_script = _resolve_integration_script_type(project_root, state, key, script_type)
@@ -755,16 +756,19 @@ def _set_default_integration(
 
     if refresh_templates:
         try:
-            _refresh_shared_templates(
+            _install_shared_infra(
                 project_root,
+                resolved_script,
                 invoke_separator=_invoke_separator_for_integration(
                     integration, {"integration_settings": settings}, key, parsed_options
                 ),
                 force=refresh_templates_force,
+                refresh_managed=True,
+                refresh_hint=refresh_hint,
             )
         except (ValueError, OSError) as exc:
             raise _SharedTemplateRefreshError(
-                f"Failed to refresh shared templates for '{key}': {exc}"
+                f"Failed to refresh shared infrastructure for '{key}': {exc}"
             ) from exc
 
     _write_integration_json(project_root, key, installed_keys, settings)
@@ -1115,7 +1119,7 @@ def _update_init_options_for_integration(
 @integration_app.command("use")
 def integration_use(
     key: str = typer.Argument(help="Installed integration key to make the default"),
-    force: bool = typer.Option(False, "--force", help="Overwrite managed shared templates while changing the default"),
+    force: bool = typer.Option(False, "--force", help="Overwrite existing shared infrastructure files, including customizations, while changing the default"),
 ):
     """Set the default integration without uninstalling other integrations."""
     from .integrations import get_integration
@@ -1146,6 +1150,10 @@ def integration_use(
         raw_options=raw_options,
         parsed_options=parsed_options,
         refresh_templates_force=force,
+        refresh_hint=(
+            "To overwrite customizations, re-run with "
+            f"[cyan]specify integration use {key} --force[/cyan]."
+        ),
     )
     console.print(f"[green]✓[/green] Default integration set to [bold]{key}[/bold].")
 
@@ -1315,7 +1323,7 @@ def integration_switch(
             )
             console.print(
                 f"\n[green]✓[/green] Default integration remains [bold]{target}[/bold]; "
-                "managed shared templates refreshed."
+                "shared infrastructure refreshed."
             )
             raise typer.Exit(0)
         console.print(f"[yellow]Integration '{target}' is already the default integration. Nothing to switch.[/yellow]")
@@ -1671,16 +1679,18 @@ def integration_upgrade(
         )
         if installed_key == key:
             try:
-                _refresh_shared_templates(
+                _install_shared_infra(
                     project_root,
+                    selected_script,
                     invoke_separator=_invoke_separator_for_integration(
                         integration, {"integration_settings": settings}, key, parsed_options
                     ),
                     force=force,
+                    refresh_managed=True,
                 )
             except (ValueError, OSError) as exc:
                 raise _SharedTemplateRefreshError(
-                    f"Failed to refresh shared templates for '{key}': {exc}"
+                    f"Failed to refresh shared infrastructure for '{key}': {exc}"
                 ) from exc
         new_manifest.save()
         _write_integration_json(project_root, installed_key, installed_keys, settings)

src/specify_cli/shared_infra.py

@@ -369,7 +369,16 @@ def install_shared_infra(
 
                         if not _ensure_or_bucket_dir(dst_path.parent):
                             continue
-                        planned_copies.append((dst_path, rel, src_path.read_bytes(), src_path.stat().st_mode & 0o777))
+                        content = src_path.read_text(encoding="utf-8")
+                        content = IntegrationBase.resolve_command_refs(content, invoke_separator)
+                        planned_copies.append(
+                            (
+                                dst_path,
+                                rel,
+                                content.encode("utf-8"),
+                                src_path.stat().st_mode & 0o777,
+                            )
+                        )
 
     templates_src = shared_templates_source(core_pack=core_pack, repo_root=repo_root)
     if templates_src.is_dir():

tests/integrations/test_cli.py

@@ -923,7 +923,23 @@ class TestGitExtensionAutoInstall:
 
 
 class TestSharedInfraCommandRefs:
-    """Verify _install_shared_infra resolves __SPECKIT_COMMAND_*__ in page templates."""
+    """Verify _install_shared_infra resolves __SPECKIT_COMMAND_*__ in shared infra."""
+
+    @staticmethod
+    def _combined_script_content(project, script_type):
+        script_dir = "bash" if script_type == "sh" else "powershell"
+        suffix = "sh" if script_type == "sh" else "ps1"
+        names = [
+            f"check-prerequisites.{suffix}",
+            f"common.{suffix}",
+            f"setup-tasks.{suffix}",
+        ]
+        return "\n".join(
+            (project / ".specify" / "scripts" / script_dir / name).read_text(
+                encoding="utf-8"
+            )
+            for name in names
+        )
 
     def test_dot_separator_in_page_templates(self, tmp_path):
         """Markdown agents get /speckit.<name> in page templates."""
@@ -968,6 +984,46 @@ class TestSharedInfraCommandRefs:
         assert "__SPECKIT_COMMAND_" not in content
         assert "/speckit-tasks" in content
 
+    @pytest.mark.parametrize("script_type", ["sh", "ps"])
+    def test_dot_separator_in_shared_scripts(self, tmp_path, script_type):
+        """Markdown agents get /speckit.<name> in shared script hints."""
+        from specify_cli import _install_shared_infra
+
+        project = tmp_path / f"dot-script-{script_type}"
+        project.mkdir()
+        (project / ".specify").mkdir()
+
+        _install_shared_infra(project, script_type, invoke_separator=".")
+
+        content = self._combined_script_content(project, script_type)
+        assert "__SPECKIT_COMMAND_" not in content
+        assert "/speckit.specify" in content
+        assert "/speckit.plan" in content
+        assert "/speckit.tasks" in content
+        assert "/speckit-specify" not in content
+        assert "/speckit-plan" not in content
+        assert "/speckit-tasks" not in content
+
+    @pytest.mark.parametrize("script_type", ["sh", "ps"])
+    def test_hyphen_separator_in_shared_scripts(self, tmp_path, script_type):
+        """Skills agents get /speckit-<name> in shared script hints."""
+        from specify_cli import _install_shared_infra
+
+        project = tmp_path / f"hyphen-script-{script_type}"
+        project.mkdir()
+        (project / ".specify").mkdir()
+
+        _install_shared_infra(project, script_type, invoke_separator="-")
+
+        content = self._combined_script_content(project, script_type)
+        assert "__SPECKIT_COMMAND_" not in content
+        assert "/speckit-specify" in content
+        assert "/speckit-plan" in content
+        assert "/speckit-tasks" in content
+        assert "/speckit.specify" not in content
+        assert "/speckit.plan" not in content
+        assert "/speckit.tasks" not in content
+
     def test_full_init_claude_resolves_page_templates(self, tmp_path):
         """Full CLI init with Claude (skills agent) produces hyphen refs in page templates."""
         from typer.testing import CliRunner
@@ -995,6 +1051,10 @@ class TestSharedInfraCommandRefs:
         assert "/speckit-plan" in content, "Claude (skills) should use /speckit-plan"
         assert "__SPECKIT_COMMAND_" not in content
 
+        script_content = self._combined_script_content(project, "sh")
+        assert "/speckit-specify" in script_content
+        assert "/speckit.specify" not in script_content
+
     def test_full_init_copilot_resolves_page_templates(self, tmp_path):
         """Full CLI init with Copilot (markdown agent) produces dot refs in page templates."""
         from typer.testing import CliRunner
@@ -1022,6 +1082,10 @@ class TestSharedInfraCommandRefs:
         assert "/speckit.plan" in content, "Copilot (markdown) should use /speckit.plan"
         assert "__SPECKIT_COMMAND_" not in content
 
+        script_content = self._combined_script_content(project, "sh")
+        assert "/speckit.specify" in script_content
+        assert "/speckit-specify" not in script_content
+
     def test_full_init_copilot_skills_resolves_page_templates(self, tmp_path):
         """Full CLI init with Copilot --skills produces hyphen refs in page templates."""
         from typer.testing import CliRunner
@@ -1051,6 +1115,10 @@ class TestSharedInfraCommandRefs:
         assert "/speckit.plan" not in content, "dot-notation leaked into Copilot skills page template"
         assert "__SPECKIT_COMMAND_" not in content
 
+        script_content = self._combined_script_content(project, "sh")
+        assert "/speckit-specify" in script_content
+        assert "/speckit.specify" not in script_content
+
 
 class TestIntegrationCatalogDiscoveryCLI:
     """End-to-end CLI tests for `integration search`, `info`, and `catalog …`.

tests/integrations/test_integration_subcommand.py

@@ -386,6 +386,10 @@ class TestIntegrationInstall:
         # Shared infrastructure should be present
         assert (project / ".specify" / "scripts").is_dir()
         assert (project / ".specify" / "templates").is_dir()
+        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+        script_content = script.read_text(encoding="utf-8")
+        assert "/speckit-specify" in script_content
+        assert "/speckit.specify" not in script_content
 
 
 # ── uninstall ────────────────────────────────────────────────────────
@@ -514,7 +518,9 @@ class TestIntegrationUninstall:
     def test_uninstall_default_refreshes_templates_for_fallback(self, tmp_path):
         project = _init_project(tmp_path, "gemini")
         template = project / ".specify" / "templates" / "plan-template.md"
+        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
+        assert "/speckit.plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -533,6 +539,7 @@ class TestIntegrationUninstall:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "claude"
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
+        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
     def test_uninstall_preserves_shared_infra(self, tmp_path):
         """Shared scripts and templates are not removed by integration uninstall."""
@@ -593,7 +600,9 @@ class TestIntegrationUse:
     def test_use_refreshes_shared_templates_between_command_styles(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         template = project / ".specify" / "templates" / "plan-template.md"
+        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
+        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -607,10 +616,14 @@ class TestIntegrationUse:
             use_gemini = runner.invoke(app, ["integration", "use", "gemini"], catch_exceptions=False)
             assert use_gemini.exit_code == 0, use_gemini.output
             assert "/speckit.plan" in template.read_text(encoding="utf-8")
+            assert "/speckit.plan" in script.read_text(encoding="utf-8")
+            assert "/speckit-plan" not in script.read_text(encoding="utf-8")
 
             use_claude = runner.invoke(app, ["integration", "use", "claude"], catch_exceptions=False)
             assert use_claude.exit_code == 0, use_claude.output
             assert "/speckit-plan" in template.read_text(encoding="utf-8")
+            assert "/speckit-plan" in script.read_text(encoding="utf-8")
+            assert "/speckit.plan" not in script.read_text(encoding="utf-8")
         finally:
             os.chdir(old_cwd)
 
@@ -630,6 +643,8 @@ class TestIntegrationUse:
 
             use_gemini = runner.invoke(app, ["integration", "use", "gemini"], catch_exceptions=False)
             assert use_gemini.exit_code == 0, use_gemini.output
+            normalized = " ".join(use_gemini.output.split())
+            assert "specify integration use gemini --force" in normalized
             assert template.read_text(encoding="utf-8") == "custom template with /speckit-plan\n"
 
             force_use = runner.invoke(app, [
@@ -644,8 +659,7 @@ class TestIntegrationUse:
         assert "/speckit.plan" in updated
         assert "custom template" not in updated
 
-    @pytest.mark.skipif(not hasattr(os, "symlink"), reason="symlinks are unavailable")
-    def test_use_does_not_persist_default_when_template_refresh_fails(self, tmp_path):
+    def test_use_does_not_persist_default_when_shared_infra_refresh_fails(self, tmp_path, monkeypatch):
         project = _init_project(tmp_path, "claude")
         int_json = project / ".specify" / "integration.json"
         init_options = project / ".specify" / "init-options.json"
@@ -661,12 +675,12 @@ class TestIntegrationUse:
 
             before_state = json.loads(int_json.read_text(encoding="utf-8"))
             before_options = json.loads(init_options.read_text(encoding="utf-8"))
+            import specify_cli
 
-            outside = tmp_path / "outside-template.md"
-            outside.write_text("# outside\n", encoding="utf-8")
-            template = project / ".specify" / "templates" / "plan-template.md"
-            template.unlink()
-            os.symlink(outside, template)
+            def fail_refresh(*args, **kwargs):
+                raise ValueError("refuse refresh")
+
+            monkeypatch.setattr(specify_cli, "_install_shared_infra", fail_refresh)
 
             result = runner.invoke(app, [
                 "integration", "use", "codex",
@@ -676,10 +690,9 @@ class TestIntegrationUse:
             os.chdir(old_cwd)
 
         assert result.exit_code != 0
-        assert "Failed to refresh shared templates" in result.output
+        assert "Failed to refresh shared infrastructure" in result.output
         assert json.loads(int_json.read_text(encoding="utf-8")) == before_state
         assert json.loads(init_options.read_text(encoding="utf-8")) == before_options
-        assert outside.read_text(encoding="utf-8") == "# outside\n"
 
 
 # ── switch ───────────────────────────────────────────────────────────
@@ -737,7 +750,9 @@ class TestIntegrationSwitch:
     def test_switch_same_force_refreshes_shared_templates(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         template = project / ".specify" / "templates" / "plan-template.md"
+        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         template.write_text("# custom shared template\n", encoding="utf-8")
+        script.write_text("# custom shared script\n", encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -749,8 +764,10 @@ class TestIntegrationSwitch:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0, result.output
-        assert "managed shared templates refreshed" in result.output
+        assert "shared infrastructure refreshed" in result.output
+        assert "managed shared infrastructure refreshed" not in result.output
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
+        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
     def test_switch_installed_target_rejects_integration_options(self, tmp_path):
         project = _init_project(tmp_path, "claude")
@@ -779,6 +796,8 @@ class TestIntegrationSwitch:
         project = _init_project(tmp_path, "claude")
         # Verify claude files exist (claude uses skills)
         assert (project / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        shared_script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+        assert "/speckit-specify" in shared_script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -797,6 +816,8 @@ class TestIntegrationSwitch:
 
         # New copilot files created
         assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
+        assert "/speckit.specify" in shared_script.read_text(encoding="utf-8")
+        assert "/speckit-specify" not in shared_script.read_text(encoding="utf-8")
 
         # integration.json updated
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
@@ -938,12 +959,13 @@ class TestIntegrationSwitch:
         assert "claude" not in git_meta["registered_commands"]
         assert "opencode" not in git_meta["registered_commands"]
 
-    def test_switch_preserves_shared_infra(self, tmp_path):
-        """Switching preserves shared scripts, templates, and memory."""
+    def test_switch_refreshes_managed_shared_script_refs(self, tmp_path):
+        """Switching refreshes managed shared scripts to the target command style."""
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
         assert shared_script.exists()
         shared_content = shared_script.read_text(encoding="utf-8")
+        assert "/speckit-plan" in shared_content
 
         old_cwd = os.getcwd()
         try:
@@ -956,9 +978,10 @@ class TestIntegrationSwitch:
             os.chdir(old_cwd)
         assert result.exit_code == 0
 
-        # Shared infra untouched
         assert shared_script.exists()
-        assert shared_script.read_text(encoding="utf-8") == shared_content
+        updated = shared_script.read_text(encoding="utf-8")
+        assert "/speckit.plan" in updated
+        assert "/speckit-plan" not in updated
 
     def test_switch_refreshes_stale_managed_shared_infra(self, tmp_path):
         """Regression for #2293: stale managed shared scripts get refreshed on switch."""
@@ -966,7 +989,7 @@ class TestIntegrationSwitch:
 
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
-        bundled_bytes = shared_script.read_bytes()
+        assert "/speckit-plan" in shared_script.read_text(encoding="utf-8")
 
         # Simulate a stale vendored script: write truncated content as bytes
         # (write_text would translate \n→\r\n on Windows and break the hash)
@@ -993,8 +1016,11 @@ class TestIntegrationSwitch:
             os.chdir(old_cwd)
         assert result.exit_code == 0
 
-        # Stale managed file should be replaced by the bundled version
-        assert shared_script.read_bytes() == bundled_bytes
+        # Stale managed file should be replaced by the target integration's rendered version.
+        updated = shared_script.read_text(encoding="utf-8")
+        assert "# stale vendored copy" not in updated
+        assert "/speckit.plan" in updated
+        assert "/speckit-plan" not in updated
 
     def test_switch_preserves_user_customized_shared_infra(self, tmp_path):
         """User customizations (hash divergence from manifest) survive switch without --refresh-shared-infra."""
@@ -1024,10 +1050,11 @@ class TestIntegrationSwitch:
         """--refresh-shared-infra explicitly overwrites user customizations on switch."""
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
-        bundled_bytes = shared_script.read_bytes()
+        assert "/speckit-plan" in shared_script.read_text(encoding="utf-8")
+        rendered_bytes = shared_script.read_bytes()
 
         # User customization (hash diverges from manifest)
-        custom_bytes = bundled_bytes + b"\n# user customization\n"
+        custom_bytes = rendered_bytes + b"\n# user customization\n"
         shared_script.write_bytes(custom_bytes)
 
         old_cwd = os.getcwd()
@@ -1041,8 +1068,11 @@ class TestIntegrationSwitch:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        # Customization is overwritten with the bundled version
-        assert shared_script.read_bytes() == bundled_bytes
+        # Customization is overwritten with the target integration's rendered version.
+        updated = shared_script.read_text(encoding="utf-8")
+        assert "# user customization" not in updated
+        assert "/speckit.plan" in updated
+        assert "/speckit-plan" not in updated
 
     def test_switch_skips_symlinked_parent_directory(self, tmp_path):
         """Regression: if .specify/scripts/bash is a symlink, switch must not write through it.
@@ -1222,7 +1252,7 @@ class TestIntegrationUpgrade:
         assert updated["ai"] == "gemini"
         assert updated["context_file"] == "GEMINI.md"
 
-    def test_upgrade_does_not_persist_state_when_template_refresh_fails(self, tmp_path, monkeypatch):
+    def test_upgrade_does_not_persist_state_when_shared_infra_refresh_fails(self, tmp_path, monkeypatch):
         project = _init_project(tmp_path, "claude")
         int_json = project / ".specify" / "integration.json"
         init_options = project / ".specify" / "init-options.json"
@@ -1234,10 +1264,16 @@ class TestIntegrationUpgrade:
 
         import specify_cli
 
-        def fail_refresh(*args, **kwargs):
-            raise ValueError("refuse refresh")
+        real_install_shared_infra = specify_cli._install_shared_infra
+        calls = {"count": 0}
 
-        monkeypatch.setattr(specify_cli, "_refresh_shared_templates", fail_refresh)
+        def fail_refresh(*args, **kwargs):
+            calls["count"] += 1
+            if calls["count"] == 2:
+                raise ValueError("refuse refresh")
+            return real_install_shared_infra(*args, **kwargs)
+
+        monkeypatch.setattr(specify_cli, "_install_shared_infra", fail_refresh)
 
         result = _run_in_project(project, [
             "integration", "upgrade", "claude",
@@ -1245,15 +1281,40 @@ class TestIntegrationUpgrade:
         ])
 
         assert result.exit_code != 0
-        assert "Failed to refresh shared templates" in result.output
+        assert "Failed to refresh shared infrastructure" in result.output
         assert json.loads(int_json.read_text(encoding="utf-8")) == before_state
         assert json.loads(init_options.read_text(encoding="utf-8")) == before_options
         assert manifest_path.read_text(encoding="utf-8") == before_manifest
 
+    def test_upgrade_default_refreshes_shared_script_refs_for_option_separator_change(self, tmp_path):
+        project = _init_project(tmp_path, "copilot")
+        template = project / ".specify" / "templates" / "plan-template.md"
+        managed_script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+        customized_script = project / ".specify" / "scripts" / "bash" / "setup-tasks.sh"
+
+        assert "/speckit.plan" in template.read_text(encoding="utf-8")
+        assert "/speckit.specify" in managed_script.read_text(encoding="utf-8")
+        customized_before = customized_script.read_text(encoding="utf-8") + "\n# user customization\n"
+        customized_script.write_text(customized_before, encoding="utf-8")
+
+        result = _run_in_project(project, [
+            "integration", "upgrade", "copilot",
+            "--integration-options", "--skills",
+        ])
+
+        assert result.exit_code == 0, result.output
+        assert "/speckit-plan" in template.read_text(encoding="utf-8")
+        managed_content = managed_script.read_text(encoding="utf-8")
+        assert "/speckit-specify" in managed_content
+        assert "/speckit.specify" not in managed_content
+        assert customized_script.read_text(encoding="utf-8") == customized_before
+
     def test_upgrade_non_default_keeps_default_template_invocations(self, tmp_path):
         project = _init_project(tmp_path, "gemini")
         template = project / ".specify" / "templates" / "plan-template.md"
+        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
+        assert "/speckit.plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -1276,6 +1337,8 @@ class TestIntegrationUpgrade:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "gemini"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
+        assert "/speckit.plan" in script.read_text(encoding="utf-8")
+        assert "/speckit-plan" not in script.read_text(encoding="utf-8")
 
     def test_upgrade_migrates_opencode_legacy_dir(self, tmp_path):
         """Upgrade moves OpenCode commands from .opencode/command/ to .opencode/commands/."""