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>

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():