fix(extensions): preserve keep-config leftover on reinstall (data loss)

remove(keep_config=True) intentionally leaves the top-level *-config.yml /
*-config.local.yml in place and drops the registry entry. A subsequent
install_from_directory is not a --force removal (did_remove is False), so
the unconditional 'if dest_dir.exists(): shutil.rmtree(dest_dir)' wiped
the preserved config and the backup-restore path never ran — silently
destroying user configuration the feature promised to keep. Capture the
top-level *-config.yml/*-config.local.yml from an existing dest_dir before
the rmtree and write them back after the fresh copytree, mirroring the
*-config filter the --force restore path already uses.

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

Author: jawwad-ali

src/specify_cli/extensions/__init__.py

@@ -1397,13 +1397,39 @@ def install_from_directory(
                 backup_config_dir.unlink()
             did_remove = self.remove(manifest.id)
 
+        # A prior `remove(keep_config=True)` leaves the top-level
+        # *-config.yml / *-config.local.yml in place while dropping the
+        # registry entry. A later reinstall is not a --force removal
+        # (did_remove is False), so the rmtree below would wipe those
+        # preserved configs and the backup-restore path never runs. Capture
+        # them here and write them back after the fresh copytree, mirroring
+        # the *-config filter the --force restore path uses.
+        preserved_configs: dict[str, bytes] = {}
+        if dest_dir.exists():
+            for cfg_file in dest_dir.iterdir():
+                if (
+                    cfg_file.is_file()
+                    and not cfg_file.is_symlink()
+                    and (
+                        cfg_file.name.endswith("-config.yml")
+                        or cfg_file.name.endswith("-config.local.yml")
+                    )
+                ):
+                    preserved_configs[cfg_file.name] = cfg_file.read_bytes()
+
         # Install extension (dest_dir computed above during self-install guard)
         if dest_dir.exists():
             shutil.rmtree(dest_dir)
 
         ignore_fn = self._load_extensionignore(source_dir)
         shutil.copytree(source_dir, dest_dir, ignore=ignore_fn)
 
+        # Restore configs preserved from a keep-config leftover (see above).
+        # The --force backup-restore below (did_remove) still takes precedence
+        # for that path, which uses .backup/ rather than an in-place leftover.
+        for name, data in preserved_configs.items():
+            (dest_dir / name).write_bytes(data)
+
         # Register commands with AI agents
         registered_commands = {}
         if register_commands:

tests/test_extensions.py

@@ -1557,6 +1557,29 @@ def test_config_backup_on_remove(self, extension_dir, project_dir):
         assert backup_file.exists()
         assert backup_file.read_text() == "test: config"
 
+    def test_reinstall_preserves_keep_config_leftover(self, extension_dir, project_dir):
+        """A reinstall after `remove(keep_config=True)` must not wipe the
+        preserved config. remove(keep_config=True) leaves the *-config.yml in
+        place and drops the registry entry; the subsequent reinstall is not a
+        --force removal, so the unconditional rmtree used to destroy it."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        config_file = ext_dir / "test-ext-config.yml"
+        config_file.write_text("api_key: MY-CUSTOMIZED-VALUE")
+
+        # keep-config removal: registry entry dropped, config left in place.
+        assert manager.remove("test-ext", keep_config=True) is True
+        assert config_file.exists()
+
+        # Reinstall (no --force; registry now reports not-installed).
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # The user's config must survive the reinstall (was silently wiped).
+        assert config_file.exists()
+        assert "MY-CUSTOMIZED-VALUE" in config_file.read_text()
+
 
 # ===== CommandRegistrar Tests =====