fix(import[prune]) Scope prune skip-check to (workspace, name) pairs

why: fetched_repo_names was a flat set of names, so a stale entry in
workspace B was wrongly protected from pruning if a same-named repo
existed in the remote's workspace A.
what:
- Track imported repos as (workspace_label, name) tuples
- Prune skip-check now uses (ws_label, repo_name) membership test
- Add test for cross-workspace same-source same-name pruning

Author: tony

src/vcspull/cli/import_cmd/_common.py

@@ -855,6 +855,7 @@ def _run_import(
     added_count = updated_url_count = 0
     skip_existing_count = skip_pinned_count = skip_unchanged_count = 0
     provenance_tagged_count = 0
+    imported_workspace_repos: set[tuple[str, str]] = set()
 
     for repo in repos:
         # Determine workspace for this repo
@@ -933,6 +934,7 @@ def _run_import(
             existing_entry=existing_raw,
             sync=sync,
         )
+        imported_workspace_repos.add((repo_workspace_label, repo.name))
 
         if action == ImportAction.ADD:
             if not dry_run:
@@ -991,12 +993,11 @@ def _run_import(
     # Prune stale entries tagged by previous imports from this source
     pruned_count = 0
     if (sync or prune) and import_source:
-        fetched_repo_names = {repo.name for repo in repos}
-        for _ws_label, ws_entries in list(raw_config.items()):
+        for ws_label, ws_entries in list(raw_config.items()):
             if not isinstance(ws_entries, dict):
                 continue
             for repo_name in list(ws_entries):
-                if repo_name in fetched_repo_names:
+                if (ws_label, repo_name) in imported_workspace_repos:
                     continue
                 prune_action = _classify_prune_action(
                     existing_entry=ws_entries[repo_name],

tests/cli/test_import_repos.py

@@ -4288,6 +4288,72 @@ def test_import_sync_same_name_from_remote_not_pruned(
     assert entry["metadata"]["imported_from"] == "github:testuser"
 
 
+def test_import_prune_cross_workspace_same_source_same_name(
+    tmp_path: pathlib.Path,
+    monkeypatch: MonkeyPatch,
+) -> None:
+    """Stale entry in workspace B is pruned even if workspace A has same name."""
+    monkeypatch.setenv("HOME", str(tmp_path))
+    workspace_a = tmp_path / "code"
+    workspace_a.mkdir()
+    workspace_b = tmp_path / "work"
+    workspace_b.mkdir()
+    config_file = tmp_path / ".vcspull.yaml"
+
+    # Both workspaces have "myrepo" from the same import source
+    save_config_yaml(
+        config_file,
+        {
+            "~/code/": {
+                "myrepo": {
+                    "repo": "git+git@github.com:testuser/myrepo.git",
+                    "metadata": {"imported_from": "github:testuser"},
+                },
+            },
+            "~/work/": {
+                "myrepo": {
+                    "repo": "git+git@github.com:testuser/myrepo.git",
+                    "metadata": {"imported_from": "github:testuser"},
+                },
+            },
+        },
+    )
+
+    # Remote returns myrepo only to workspace A — workspace B's entry is stale
+    importer = MockImporter(repos=[_make_repo("myrepo")])
+    _run_import(
+        importer,
+        service_name="github",
+        target="testuser",
+        workspace=str(workspace_a),
+        mode="user",
+        language=None,
+        topics=None,
+        min_stars=0,
+        include_archived=False,
+        include_forks=False,
+        limit=100,
+        config_path_str=str(config_file),
+        dry_run=False,
+        yes=True,
+        output_json=False,
+        output_ndjson=False,
+        color="never",
+        sync=True,
+        import_source="github:testuser",
+    )
+
+    from vcspull._internal.config_reader import ConfigReader
+
+    final_config = ConfigReader._from_file(config_file)
+    assert final_config is not None
+
+    # Workspace A keeps myrepo (it was imported there)
+    assert "myrepo" in final_config["~/code/"]
+    # Workspace B's stale myrepo should be pruned
+    assert "myrepo" not in final_config.get("~/work/", {})
+
+
 def test_import_parser_has_prune_flag() -> None:
     """The shared parent parser must expose --prune."""
     from vcspull.cli.import_cmd._common import _create_shared_parent