vcspull add: Fix more issues with --no-merge (#482)

why:
- `vcspull add --no-merge` rewrote configs by flattening duplicate sections
- users lost repositories when opting out of automatic merging

what:
- extend loader to expose ordered duplicate items for downstream writers
- add duplicate-safe YAML writer that replays top-level sections faithfully
- update CLI add flow to write through the duplicate-aware helper under
  `--no-merge`
- broaden regression coverage for duplicate workspace roots in loader and CLI

verification:
- uv run ruff check . --fix --show-fixes
- uv run ruff format .
- uv run mypy
- uv run py.test

Author: tony

CHANGES

@@ -33,6 +33,15 @@ $ uvx --from 'vcspull' --prerelease allow vcspull
 
 _Upcoming changes will be written here._
 
+### Bug Fixes
+
+#### `vcspull add --no-merge` preserves duplicate workspace roots (#482)
+
+- Duplicate workspace sections are no longer flattened when adding a repository
+  with `--no-merge`; all previously configured repositories stay intact.
+- The configuration loader now exposes ordered duplicate entries so CLI writes
+  can target the correct section without data loss.
+
 ## vcspull v1.44.0 (2025-11-02)
 
 ### Improvements

src/vcspull/_internal/config_reader.py

@@ -228,6 +228,7 @@ def __init__(self, stream: str) -> None:
         super().__init__(stream)
         self.top_level_key_values: dict[t.Any, list[t.Any]] = {}
         self._mapping_depth = 0
+        self.top_level_items: list[tuple[t.Any, t.Any]] = []
 
 
 def _duplicate_tracking_construct_mapping(
@@ -248,7 +249,9 @@ def _duplicate_tracking_construct_mapping(
         value = construct(value_node)
 
         if loader._mapping_depth == 1:
-            loader.top_level_key_values.setdefault(key, []).append(copy.deepcopy(value))
+            duplicated_value = copy.deepcopy(value)
+            loader.top_level_key_values.setdefault(key, []).append(duplicated_value)
+            loader.top_level_items.append((copy.deepcopy(key), duplicated_value))
 
         mapping[key] = value
 
@@ -270,20 +273,27 @@ def __init__(
         content: RawConfigData,
         *,
         duplicate_sections: dict[str, list[t.Any]] | None = None,
+        top_level_items: list[tuple[str, t.Any]] | None = None,
     ) -> None:
         super().__init__(content)
         self._duplicate_sections = duplicate_sections or {}
+        self._top_level_items = top_level_items or []
 
     @property
     def duplicate_sections(self) -> dict[str, list[t.Any]]:
         """Mapping of top-level keys to the list of duplicated values."""
         return self._duplicate_sections
 
+    @property
+    def top_level_items(self) -> list[tuple[str, t.Any]]:
+        """Ordered list of top-level items, including duplicates."""
+        return copy.deepcopy(self._top_level_items)
+
     @classmethod
     def _load_yaml_with_duplicates(
         cls,
         content: str,
-    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]]]:
+    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]], list[tuple[str, t.Any]]]:
         loader = _DuplicateTrackingSafeLoader(content)
 
         try:
@@ -306,33 +316,42 @@ def _load_yaml_with_duplicates(
             if len(values) > 1
         }
 
-        return loaded, duplicate_sections
+        top_level_items = [
+            (t.cast("str", key), copy.deepcopy(value))
+            for key, value in loader.top_level_items
+        ]
+
+        return loaded, duplicate_sections, top_level_items
 
     @classmethod
     def _load_from_path(
         cls,
         path: pathlib.Path,
-    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]]]:
+    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]], list[tuple[str, t.Any]]]:
         if path.suffix.lower() in {".yaml", ".yml"}:
             content = path.read_text(encoding="utf-8")
             return cls._load_yaml_with_duplicates(content)
 
-        return ConfigReader._from_file(path), {}
+        return ConfigReader._from_file(path), {}, []
 
     @classmethod
     def from_file(cls, path: pathlib.Path) -> DuplicateAwareConfigReader:
-        content, duplicate_sections = cls._load_from_path(path)
-        return cls(content, duplicate_sections=duplicate_sections)
+        content, duplicate_sections, top_level_items = cls._load_from_path(path)
+        return cls(
+            content,
+            duplicate_sections=duplicate_sections,
+            top_level_items=top_level_items,
+        )
 
     @classmethod
     def _from_file(cls, path: pathlib.Path) -> dict[str, t.Any]:
-        content, _ = cls._load_from_path(path)
+        content, _, _ = cls._load_from_path(path)
         return content
 
     @classmethod
     def load_with_duplicates(
         cls,
         path: pathlib.Path,
-    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]]]:
+    ) -> tuple[dict[str, t.Any], dict[str, list[t.Any]], list[tuple[str, t.Any]]]:
         reader = cls.from_file(path)
-        return reader.content, reader.duplicate_sections
+        return reader.content, reader.duplicate_sections, reader.top_level_items

src/vcspull/cli/add.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import copy
 import logging
 import pathlib
 import subprocess
@@ -18,6 +19,7 @@
     merge_duplicate_workspace_roots,
     normalize_workspace_roots,
     save_config_yaml,
+    save_config_yaml_with_items,
     workspace_root_label,
 )
 from vcspull.util import contract_user_home
@@ -335,13 +337,15 @@ def add_repo(
     # Load existing config
     raw_config: dict[str, t.Any]
     duplicate_root_occurrences: dict[str, list[t.Any]]
+    top_level_items: list[tuple[str, t.Any]]
     display_config_path = contract_user_home(config_file_path)
 
     if config_file_path.exists() and config_file_path.is_file():
         try:
             (
                 raw_config,
                 duplicate_root_occurrences,
+                top_level_items,
             ) = DuplicateAwareConfigReader.load_with_duplicates(config_file_path)
         except TypeError:
             log.exception(
@@ -357,11 +361,32 @@ def add_repo(
     else:
         raw_config = {}
         duplicate_root_occurrences = {}
+        top_level_items = []
         log.info(
             "Config file %s not found. A new one will be created.",
             display_config_path,
         )
 
+    config_items: list[tuple[str, t.Any]] = (
+        [(label, copy.deepcopy(section)) for label, section in top_level_items]
+        if top_level_items
+        else [(label, copy.deepcopy(section)) for label, section in raw_config.items()]
+    )
+
+    def _aggregate_items(items: list[tuple[str, t.Any]]) -> dict[str, t.Any]:
+        aggregated: dict[str, t.Any] = {}
+        for label, section in items:
+            if isinstance(section, dict):
+                workspace_section = aggregated.setdefault(label, {})
+                for repo_name, repo_config in section.items():
+                    workspace_section[repo_name] = copy.deepcopy(repo_config)
+            else:
+                aggregated[label] = copy.deepcopy(section)
+        return aggregated
+
+    if not merge_duplicates:
+        raw_config = _aggregate_items(config_items)
+
     duplicate_merge_conflicts: list[str] = []
     duplicate_merge_changes = 0
     duplicate_merge_details: list[tuple[str, int]] = []
@@ -416,14 +441,18 @@ def add_repo(
     cwd = pathlib.Path.cwd()
     home = pathlib.Path.home()
 
+    aggregated_config = (
+        raw_config if merge_duplicates else _aggregate_items(config_items)
+    )
+
     if merge_duplicates:
         (
             raw_config,
             workspace_map,
             merge_conflicts,
             merge_changes,
         ) = normalize_workspace_roots(
-            raw_config,
+            aggregated_config,
             cwd=cwd,
             home=home,
         )
@@ -435,7 +464,7 @@ def add_repo(
             merge_conflicts,
             _merge_changes,
         ) = normalize_workspace_roots(
-            raw_config,
+            aggregated_config,
             cwd=cwd,
             home=home,
         )
@@ -458,15 +487,24 @@ def add_repo(
         )
         workspace_map[workspace_path] = workspace_label
         raw_config.setdefault(workspace_label, {})
+        if not merge_duplicates:
+            config_items.append((workspace_label, {}))
 
     if workspace_label not in raw_config:
         raw_config[workspace_label] = {}
+        if not merge_duplicates:
+            config_items.append((workspace_label, {}))
     elif not isinstance(raw_config[workspace_label], dict):
         log.error(
             "Workspace root '%s' in configuration is not a dictionary. Aborting.",
             workspace_label,
         )
         return
+    workspace_sections: list[tuple[int, dict[str, t.Any]]] = [
+        (idx, section)
+        for idx, (label, section) in enumerate(config_items)
+        if label == workspace_label and isinstance(section, dict)
+    ]
 
     # Check if repo already exists
     if name in raw_config[workspace_label]:
@@ -517,7 +555,18 @@ def add_repo(
         return
 
     # Add the repository in verbose format
-    raw_config[workspace_label][name] = {"repo": url}
+    new_repo_entry = {"repo": url}
+    if merge_duplicates:
+        raw_config[workspace_label][name] = new_repo_entry
+    else:
+        target_section: dict[str, t.Any]
+        if workspace_sections:
+            _, target_section = workspace_sections[-1]
+        else:
+            target_section = {}
+            config_items.append((workspace_label, target_section))
+        target_section[name] = copy.deepcopy(new_repo_entry)
+        raw_config[workspace_label][name] = copy.deepcopy(new_repo_entry)
 
     # Save or preview config
     if dry_run:
@@ -540,7 +589,10 @@ def add_repo(
         )
     else:
         try:
-            save_config_yaml(config_file_path, raw_config)
+            if merge_duplicates:
+                save_config_yaml(config_file_path, raw_config)
+            else:
+                save_config_yaml_with_items(config_file_path, config_items)
             log.info(
                 "%s✓%s Successfully added %s'%s'%s (%s%s%s) to %s%s%s under '%s%s%s'.",
                 Fore.GREEN,

src/vcspull/cli/discover.py

@@ -203,6 +203,7 @@ def discover_repos(
             (
                 raw_config,
                 duplicate_root_occurrences,
+                _top_level_items,
             ) = DuplicateAwareConfigReader.load_with_duplicates(config_file_path)
         except TypeError:
             log.exception(

src/vcspull/cli/fmt.py

@@ -172,7 +172,7 @@ def format_single_config(
 
     # Load existing config
     try:
-        raw_config, duplicate_root_occurrences = (
+        raw_config, duplicate_root_occurrences, _top_level_items = (
             DuplicateAwareConfigReader.load_with_duplicates(config_file_path)
         )
     except TypeError:

src/vcspull/config.py

@@ -271,7 +271,7 @@ def load_configs(
             file = pathlib.Path(file)
         assert isinstance(file, pathlib.Path)
 
-        config_content, duplicate_roots = (
+        config_content, duplicate_roots, _top_level_items = (
             DuplicateAwareConfigReader.load_with_duplicates(file)
         )
 
@@ -481,6 +481,29 @@ def save_config_yaml(config_file_path: pathlib.Path, data: dict[t.Any, t.Any]) -
     config_file_path.write_text(yaml_content, encoding="utf-8")
 
 
+def save_config_yaml_with_items(
+    config_file_path: pathlib.Path,
+    items: list[tuple[str, t.Any]],
+) -> None:
+    """Persist configuration data while preserving duplicate top-level sections."""
+    documents: list[str] = []
+
+    for label, section in items:
+        dumped = ConfigReader._dump(
+            fmt="yaml",
+            content={label: section},
+            indent=2,
+        ).rstrip()
+        if dumped:
+            documents.append(dumped)
+
+    yaml_content = "\n".join(documents)
+    if yaml_content:
+        yaml_content += "\n"
+
+    config_file_path.write_text(yaml_content, encoding="utf-8")
+
+
 def merge_duplicate_workspace_root_entries(
     label: str,
     occurrences: list[t.Any],