fix(integration): refresh shared infra on integration switch

src/specify_cli/__init__.py

@@ -765,6 +765,8 @@ def _install_shared_infra(
     tracker: StepTracker | None = None,
     force: bool = False,
     invoke_separator: str = ".",
+    refresh_managed: bool = False,
+    refresh_hint: str | None = None,
 ) -> bool:
     """Install shared infrastructure files into *project_path*.
 
@@ -776,9 +778,23 @@ def _install_shared_infra(
     placeholders using *invoke_separator* (``"."`` for markdown agents,
     ``"-"`` for skills agents).
 
-    When *force* is ``True``, existing files are overwritten with the
-    latest bundled versions.  When ``False`` (default), only missing
-    files are added and existing ones are skipped.
+    Overwrite policy:
+
+    * ``force=True``  — overwrite every existing file (still skips symlinks
+      to avoid following links outside the project root).
+    * ``refresh_managed=True`` — overwrite only files whose on-disk hash
+      still matches the previously recorded manifest hash (i.e. unmodified
+      files installed by spec-kit). Files with diverging hashes are
+      treated as user customizations and preserved with a warning.
+    * Default — only add missing files; existing ones are skipped.
+
+    *refresh_hint* — caller-supplied rich-text fragment shown after the
+    "Preserved customized files" warning to tell the user which flag/command
+    they should re-run with to overwrite their customizations. Each caller
+    passes the flag that's actually valid in its CLI surface (e.g.
+    ``--refresh-shared-infra`` for ``integration switch``,
+    ``--force`` for ``init``/``integration upgrade``). When ``None``, no
+    remediation hint is printed for customizations.
 
     Returns ``True`` on success.
     """
@@ -791,6 +807,8 @@ def _install_shared_infra(
         console=console,
         force=force,
         invoke_separator=invoke_separator,
+        refresh_managed=refresh_managed,
+        refresh_hint=refresh_hint,
     )
 
 
@@ -800,6 +818,8 @@ def _install_shared_infra_or_exit(
     tracker: StepTracker | None = None,
     force: bool = False,
     invoke_separator: str = ".",
+    refresh_managed: bool = False,
+    refresh_hint: str | None = None,
 ) -> bool:
     try:
         return _install_shared_infra(
@@ -808,6 +828,8 @@ def _install_shared_infra_or_exit(
             tracker=tracker,
             force=force,
             invoke_separator=invoke_separator,
+            refresh_managed=refresh_managed,
+            refresh_hint=refresh_hint,
         )
     except (ValueError, OSError) as exc:
         console.print(f"[red]Error:[/red] Failed to install shared infrastructure: {exc}")
@@ -2578,7 +2600,8 @@ def integration_uninstall(
 def integration_switch(
     target: str = typer.Argument(help="Integration key to switch to"),
     script: str | None = typer.Option(None, "--script", help="Script type: sh or ps (default: from init-options.json or platform default)"),
-    force: bool = typer.Option(False, "--force", help="Force removal of modified files during uninstall"),
+    force: bool = typer.Option(False, "--force", help="Force removal of modified files during uninstall of the previous integration"),
+    refresh_shared_infra: bool = typer.Option(False, "--refresh-shared-infra", help="Also overwrite shared infrastructure files even if you customized them (otherwise customizations are preserved)"),
     integration_options: str | None = typer.Option(None, "--integration-options", help='Options for the target integration'),
 ):
     """Switch from the current integration to a different one."""
@@ -2749,14 +2772,27 @@ def integration_switch(
         target_integration, current, target, integration_options
     )
 
-    # Ensure shared infrastructure is present (safe to run unconditionally;
-    # _install_shared_infra merges missing files without overwriting).
+    # Refresh shared infrastructure to the current CLI version. Switching
+    # integrations is exactly when stale vendored shared scripts (e.g.
+    # update-agent-context.sh that pre-dates the target integration's
+    # supported-agent list) would silently break the new integration.
+    #
+    # Use refresh_managed=True so only files that match their previously
+    # recorded hash are overwritten — user customizations are detected via
+    # hash divergence and preserved with a warning. Pass
+    # --refresh-shared-infra to overwrite customizations as well. See #2293.
     _install_shared_infra_or_exit(
         project_root,
         selected_script,
+        force=refresh_shared_infra,
+        refresh_managed=True,
         invoke_separator=_invoke_separator_for_integration(
             target_integration, current, target, parsed_options
         ),
+        refresh_hint=(
+            "To overwrite customizations, re-run with "
+            "[cyan]specify integration switch ... --refresh-shared-infra[/cyan]."
+        ),
     )
     if os.name != "nt":
         ensure_executable_scripts(project_root)

src/specify_cli/shared_infra.py

@@ -11,6 +11,15 @@
 from .integrations.manifest import IntegrationManifest
 
 
+class SymlinkedSharedPathError(ValueError):
+    """Raised when a shared infrastructure path or ancestor is a symlink.
+
+    Distinct from other unsafe-path errors so callers can preserve symlinked
+    destinations as customizations while still letting genuine safety errors
+    (e.g. path escape, not-a-directory) propagate and abort the operation.
+    """
+
+
 def load_speckit_manifest(
     project_path: Path,
     *,
@@ -89,7 +98,7 @@ def _ensure_safe_shared_directory(project_path: Path, directory: Path, *, create
         current = current / part
         label = _shared_destination_label(project_path, current)
         if current.is_symlink():
-            raise ValueError(f"Refusing to use symlinked shared infrastructure directory: {label}")
+            raise SymlinkedSharedPathError(f"Refusing to use symlinked shared infrastructure directory: {label}")
         if current.exists():
             if not current.is_dir():
                 raise ValueError(f"Shared infrastructure directory path is not a directory: {label}")
@@ -102,7 +111,7 @@ def _ensure_safe_shared_directory(project_path: Path, directory: Path, *, create
             raise ValueError(f"Shared infrastructure directory does not exist: {label}")
         current.mkdir()
         if current.is_symlink():
-            raise ValueError(f"Refusing to use symlinked shared infrastructure directory: {label}")
+            raise SymlinkedSharedPathError(f"Refusing to use symlinked shared infrastructure directory: {label}")
         try:
             current.resolve().relative_to(root)
         except (OSError, ValueError):
@@ -119,7 +128,7 @@ def _validate_safe_shared_directory(project_path: Path, directory: Path) -> None
         current = current / part
         label = _shared_destination_label(project_path, current)
         if current.is_symlink():
-            raise ValueError(f"Refusing to use symlinked shared infrastructure directory: {label}")
+            raise SymlinkedSharedPathError(f"Refusing to use symlinked shared infrastructure directory: {label}")
         if not current.exists():
             continue
         if not current.is_dir():
@@ -145,7 +154,7 @@ def _ensure_safe_shared_destination(
         _validate_safe_shared_directory(project_path, dest.parent)
     label = _shared_destination_label(project_path, dest)
     if dest.is_symlink():
-        raise ValueError(f"Refusing to overwrite symlinked shared infrastructure path: {label}")
+        raise SymlinkedSharedPathError(f"Refusing to overwrite symlinked shared infrastructure path: {label}")
 
     if dest.exists():
         try:
@@ -242,58 +251,147 @@ def install_shared_infra(
     console: Any,
     force: bool = False,
     invoke_separator: str = ".",
+    refresh_managed: bool = False,
+    refresh_hint: str | None = None,
 ) -> bool:
-    """Install shared scripts and templates into *project_path*."""
+    """Install shared scripts and templates into *project_path*.
+
+    When ``refresh_managed`` is True, files whose on-disk hash still matches
+    the previously recorded manifest hash are overwritten with the bundled
+    version. Files whose hash diverges are treated as user customizations and
+    preserved with a warning. ``force=True`` overwrites every regular file
+    (symlinks and symlinked-parent destinations are always preserved with a
+    warning — the safe-destination check refuses to follow them so writes
+    cannot escape the project root). ``refresh_hint`` is shown after the
+    customization warning to tell the user which flag would overwrite their
+    customizations.
+    """
+    from .integrations.manifest import _sha256
+
     manifest = load_speckit_manifest(project_path, version=version, console=console)
+    prior_hashes = dict(manifest.files)
+
+    def _is_managed(rel: str, dst: Path) -> bool:
+        expected = prior_hashes.get(rel)
+        if not expected or not dst.is_file() or dst.is_symlink():
+            return False
+        try:
+            return _sha256(dst) == expected
+        except OSError:
+            return False
+
     skipped_files: list[str] = []
+    preserved_user_files: list[str] = []
+    symlinked_files: list[str] = []
     planned_copies: list[tuple[Path, str, bytes, int]] = []
     planned_templates: list[tuple[Path, str, str]] = []
 
+    def _decide_overwrite(rel: str, dst: Path) -> tuple[bool, str | None]:
+        """Return (write, bucket) where bucket is 'skip', 'preserved', or None."""
+        if not dst.exists():
+            return True, None
+        if force:
+            return True, None
+        if refresh_managed:
+            if _is_managed(rel, dst):
+                return True, None
+            if rel in prior_hashes:
+                return False, "preserved"
+            return False, "skip"
+        return False, "skip"
+
+    def _safe_dest_or_bucket(dst: Path, rel: str, *, parent_must_exist: bool = True) -> bool:
+        """Run the safe-destination check and bucket symlinked paths.
+
+        Returns True when the destination is safe to consider (write or skip).
+        Returns False (and records *rel* under ``symlinked_files``) when the
+        destination or any of its ancestors is a symlink — those paths can't
+        be written to safely, but they shouldn't abort the whole switch
+        either. They're surfaced as a separate "symlinked" warning bucket.
+
+        Other unsafe-path errors (e.g. path escape, parent-not-a-directory)
+        are NOT caught here: they re-raise so the operation aborts, since
+        treating them as "symlinked" would mask security-relevant failures.
+        """
+        try:
+            _ensure_safe_shared_destination(project_path, dst, parent_must_exist=parent_must_exist)
+        except SymlinkedSharedPathError:
+            symlinked_files.append(rel)
+            return False
+        return True
+
+    def _ensure_or_bucket_dir(directory: Path) -> bool:
+        """Create *directory* unless an ancestor is symlinked.
+
+        Returns True when the directory is safe to use. Returns False (and
+        records the path under ``symlinked_files``) when a symlink ancestor
+        forces us to skip the whole subtree. Other unsafe-path errors
+        (escape, not-a-directory) re-raise so the operation aborts.
+        """
+        try:
+            _ensure_safe_shared_directory(project_path, directory)
+        except SymlinkedSharedPathError:
+            symlinked_files.append(directory.relative_to(project_path).as_posix())
+            return False
+        return True
+
     scripts_src = shared_scripts_source(core_pack=core_pack, repo_root=repo_root)
     if scripts_src.is_dir():
         dest_scripts = project_path / ".specify" / "scripts"
-        _ensure_safe_shared_directory(project_path, dest_scripts)
-        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
-            _ensure_safe_shared_directory(project_path, dest_variant)
-            for src_path in variant_src.rglob("*"):
-                if not src_path.is_file():
-                    continue
-
-                rel_path = src_path.relative_to(variant_src)
-                dst_path = dest_variant / rel_path
-                _ensure_safe_shared_destination(project_path, dst_path, parent_must_exist=False)
-                if dst_path.exists() and not force:
-                    skipped_files.append(dst_path.relative_to(project_path).as_posix())
-                    continue
-
-                _ensure_safe_shared_directory(project_path, dst_path.parent)
-                rel = dst_path.relative_to(project_path).as_posix()
-                planned_copies.append((dst_path, rel, src_path.read_bytes(), src_path.stat().st_mode & 0o777))
+        if _ensure_or_bucket_dir(dest_scripts):
+            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
+                if _ensure_or_bucket_dir(dest_variant):
+                    for src_path in variant_src.rglob("*"):
+                        if not src_path.is_file():
+                            continue
+
+                        rel_path = src_path.relative_to(variant_src)
+                        dst_path = dest_variant / rel_path
+                        rel = dst_path.relative_to(project_path).as_posix()
+                        if not _safe_dest_or_bucket(dst_path, rel, parent_must_exist=False):
+                            continue
+                        write, bucket = _decide_overwrite(rel, dst_path)
+                        if not write:
+                            if bucket == "preserved":
+                                preserved_user_files.append(rel)
+                            else:
+                                skipped_files.append(rel)
+                            continue
+
+                        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))
 
     templates_src = shared_templates_source(core_pack=core_pack, repo_root=repo_root)
     if templates_src.is_dir():
         dest_templates = project_path / ".specify" / "templates"
-        _ensure_safe_shared_directory(project_path, dest_templates)
-        for src in templates_src.iterdir():
-            if not src.is_file() or src.name == "vscode-settings.json" or src.name.startswith("."):
-                continue
+        if _ensure_or_bucket_dir(dest_templates):
+            for src in templates_src.iterdir():
+                if not src.is_file() or src.name == "vscode-settings.json" or src.name.startswith("."):
+                    continue
 
-            dst = dest_templates / src.name
-            _ensure_safe_shared_destination(project_path, dst)
-            if dst.exists() and not force:
-                skipped_files.append(dst.relative_to(project_path).as_posix())
-                continue
+                dst = dest_templates / src.name
+                rel = dst.relative_to(project_path).as_posix()
+                if not _safe_dest_or_bucket(dst, rel):
+                    continue
+                write, bucket = _decide_overwrite(rel, dst)
+                if not write:
+                    if bucket == "preserved":
+                        preserved_user_files.append(rel)
+                    else:
+                        skipped_files.append(rel)
+                    continue
 
-            content = src.read_text(encoding="utf-8")
-            content = IntegrationBase.resolve_command_refs(content, invoke_separator)
-            rel = dst.relative_to(project_path).as_posix()
-            planned_templates.append((dst, rel, content))
+                content = src.read_text(encoding="utf-8")
+                content = IntegrationBase.resolve_command_refs(content, invoke_separator)
+                planned_templates.append((dst, rel, content))
 
     for dst_path, rel, content, mode in planned_copies:
-        _ensure_safe_shared_directory(project_path, dst_path.parent)
+        if not _ensure_or_bucket_dir(dst_path.parent):
+            continue
         _write_shared_bytes(project_path, dst_path, content, mode=mode)
         manifest.record_existing(rel)
 
@@ -313,5 +411,28 @@ def install_shared_infra(
             "[cyan]specify integration upgrade --force[/cyan]."
         )
 
+    if symlinked_files:
+        console.print(
+            f"[yellow]⚠[/yellow]  Skipped {len(symlinked_files)} symlinked shared "
+            "infrastructure file(s) — symlinks are never overwritten because they "
+            "may resolve outside the project root:"
+        )
+        for path in symlinked_files:
+            console.print(f"    {path}")
+        console.print(
+            "To restore the bundled version, remove or replace the symlink manually, "
+            "then re-run the command."
+        )
+
+    if preserved_user_files:
+        console.print(
+            f"[yellow]⚠[/yellow]  Preserved {len(preserved_user_files)} customized shared "
+            "infrastructure file(s) (hash differs from previous install):"
+        )
+        for path in preserved_user_files:
+            console.print(f"    {path}")
+        if refresh_hint:
+            console.print(refresh_hint)
+
     manifest.save()
     return True