fix(shared-infra): refresh_shared_templates preserves recovered user files (#3378)

* fix(shared-infra): refresh_shared_templates preserves recovered user files

refresh_shared_templates skipped a shared template only when it was
untracked or modified, ignoring the manifest's is_recovered marker that
install_shared_infra already honors. So a pre-existing user template
(adopted via record_existing(recovered=True), hence tracked and
hash-unmodified) was silently overwritten with bundled content on
refresh — the exact data-loss class that #2918 fixed for
install_shared_infra. Add the is_recovered check to the skip predicate.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(shared-infra): include recovered files in refresh skip warning

The skip predicate now also skips recovered (pre-existing user) files,
so the warning saying only 'modified or untracked' could mislead a user
into thinking they edited a file that was simply recorded as recovered.
Reword to 'modified, untracked, or preserved (recovered)'.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/specify_cli/shared_infra.py

@@ -328,7 +328,10 @@ def refresh_shared_templates(
         _ensure_safe_shared_destination(project_path, dst)
         rel = dst.relative_to(project_path).as_posix()
         if dst.exists() and not force:
-            if rel not in tracked_files or rel in modified:
+            if rel not in tracked_files or rel in modified or manifest.is_recovered(rel):
+                # Never overwrite a recovered (pre-existing user) file without
+                # --force, matching install_shared_infra's is_recovered gate
+                # (#2918). Without this, refresh clobbers user content.
                 skipped_files.append(rel)
                 continue
 
@@ -344,7 +347,7 @@ def refresh_shared_templates(
 
     if skipped_files:
         console.print(
-            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified or untracked shared template file(s) were not updated:"
+            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified, untracked, or preserved (recovered) shared template file(s) were not updated:"
         )
         for rel in skipped_files:
             console.print(f"    {rel}")

tests/integrations/test_cli.py

@@ -2073,3 +2073,44 @@ class TestIntegrationCatalogDiscoveryCLI:
         assert listing.exit_code == 0, listing.output
         assert "default" in listing.output
         assert "community" in listing.output
+
+
+def test_refresh_shared_templates_preserves_recovered_user_file(tmp_path):
+    """refresh_shared_templates must not overwrite a recovered (pre-existing
+    user) template without --force, matching install_shared_infra's gate (#2918).
+    """
+    from specify_cli.shared_infra import (
+        load_speckit_manifest,
+        refresh_shared_templates,
+    )
+
+    project = tmp_path / "proj"
+    templates_dir = project / ".specify" / "templates"
+    templates_dir.mkdir(parents=True)
+    user_file = templates_dir / "spec-template.md"
+    user_file.write_text("# USER CUSTOM CONTENT\n", encoding="utf-8")
+
+    # Record the pre-existing file as recovered (its hash was adopted, not written).
+    manifest = load_speckit_manifest(project, version="test", console=_NoopConsole())
+    rel = ".specify/templates/spec-template.md"
+    manifest.record_existing(rel, recovered=True)
+    manifest.save()
+
+    # Bundled source ships a different body for the same template.
+    core_pack = tmp_path / "core-pack"
+    src = core_pack / "templates"
+    src.mkdir(parents=True)
+    (src / "spec-template.md").write_text("# BUNDLED CONTENT v2\n", encoding="utf-8")
+
+    refresh_shared_templates(
+        project,
+        version="test",
+        core_pack=core_pack,
+        repo_root=tmp_path / "unused",
+        console=_NoopConsole(),
+        invoke_separator=".",
+        force=False,
+    )
+
+    # Recovered user content must survive (fail-before: replaced by bundled body).
+    assert user_file.read_text(encoding="utf-8") == "# USER CUSTOM CONTENT\n"