diff --git a/CHANGES b/CHANGES
index 9dd1b1fd..2c0a4ac5 100644
--- a/CHANGES
+++ b/CHANGES
@@ -33,6 +33,24 @@ $ uvx --from 'vcspull' --prerelease allow vcspull
 
 _Upcoming changes will be written here._
 
+### Improvements
+
+#### `vcspull fmt` gains duplicate root merging (#479)
+
+- Detects repeated workspace root labels and merges their repositories during
+  formatting so users keep a single normalized section.
+- Adds `--no-merge` for workflows that need to preserve duplicate entries while
+  still seeing diagnostic warnings.
+
+### Development
+
+#### Snapshot coverage for formatter tests (#479)
+
+- Formatter scenarios now use [Syrupy]-backed JSON and YAML snapshots to guard
+  against regressions in duplicate workspace-root merging.
+
+[syrupy]: https://github.com/syrupy-project/syrupy
+
 ## vcspull v1.42.0 (2025-11-01)
 
 ### Breaking changes
diff --git a/pyproject.toml b/pyproject.toml
index 489e300a..3bd9b43d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -85,6 +85,7 @@ dev = [
   # Testing
   "gp-libs",
   "pytest",
+  "syrupy",
   "pytest-asyncio",
   "pytest-rerunfailures",
   "pytest-mock",
@@ -119,6 +120,7 @@ docs = [
 testing = [
   "gp-libs",
   "pytest",
+  "syrupy",
   "pytest-asyncio",
   "pytest-rerunfailures",
   "pytest-mock",
diff --git a/src/vcspull/cli/__init__.py b/src/vcspull/cli/__init__.py
index 4cb8c212..199f5875 100644
--- a/src/vcspull/cli/__init__.py
+++ b/src/vcspull/cli/__init__.py
@@ -386,4 +386,9 @@ def cli(_args: list[str] | None = None) -> None:
             dry_run=args.dry_run,
         )
     elif args.subparser_name == "fmt":
-        format_config_file(args.config, args.write, args.all)
+        format_config_file(
+            args.config,
+            args.write,
+            args.all,
+            merge_roots=args.merge_roots,
+        )
diff --git a/src/vcspull/cli/fmt.py b/src/vcspull/cli/fmt.py
index 41552e48..1ac60078 100644
--- a/src/vcspull/cli/fmt.py
+++ b/src/vcspull/cli/fmt.py
@@ -2,11 +2,13 @@
 
 from __future__ import annotations
 
+import copy
 import logging
 import pathlib
 import traceback
 import typing as t
 
+import yaml
 from colorama import Fore, Style
 
 from vcspull._internal.config_reader import ConfigReader
@@ -23,6 +25,149 @@
 log = logging.getLogger(__name__)
 
 
+class _DuplicateTrackingSafeLoader(yaml.SafeLoader):
+    """PyYAML loader that records duplicate top-level keys."""
+
+    def __init__(self, stream: str) -> None:
+        super().__init__(stream)
+        self.top_level_key_values: dict[t.Any, list[t.Any]] = {}
+        self._mapping_depth = 0
+
+
+def _duplicate_tracking_construct_mapping(
+    loader: _DuplicateTrackingSafeLoader,
+    node: yaml.nodes.MappingNode,
+    deep: bool = False,
+) -> dict[t.Any, t.Any]:
+    loader._mapping_depth += 1
+    loader.flatten_mapping(node)
+    mapping: dict[t.Any, t.Any] = {}
+
+    for key_node, value_node in node.value:
+        construct = t.cast(
+            t.Callable[[yaml.nodes.Node], t.Any],
+            loader.construct_object,
+        )
+        key = construct(key_node)
+        value = construct(value_node)
+
+        if loader._mapping_depth == 1:
+            loader.top_level_key_values.setdefault(key, []).append(copy.deepcopy(value))
+
+        mapping[key] = value
+
+    loader._mapping_depth -= 1
+    return mapping
+
+
+_DuplicateTrackingSafeLoader.add_constructor(
+    yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
+    _duplicate_tracking_construct_mapping,
+)
+
+
+def _load_yaml_config_with_duplicates(
+    config_file_path: pathlib.Path,
+) -> tuple[dict[str, t.Any], dict[str, list[t.Any]]]:
+    content = config_file_path.read_text(encoding="utf-8")
+    loader = _DuplicateTrackingSafeLoader(content)
+
+    try:
+        data = loader.get_single_data()
+    finally:
+        dispose = t.cast(t.Callable[[], None], loader.dispose)
+        dispose()
+
+    if data is None:
+        return {}, {}
+    if not isinstance(data, dict):
+        msg = f"Config file {config_file_path} is not a valid YAML dictionary."
+        raise TypeError(msg)
+
+    duplicates = {
+        t.cast(str, key): values
+        for key, values in loader.top_level_key_values.items()
+        if len(values) > 1
+    }
+
+    return t.cast("dict[str, t.Any]", data), duplicates
+
+
+def _load_config_with_duplicate_roots(
+    config_file_path: pathlib.Path,
+) -> tuple[dict[str, t.Any], dict[str, list[t.Any]]]:
+    if config_file_path.suffix.lower() in {".yaml", ".yml"}:
+        return _load_yaml_config_with_duplicates(config_file_path)
+
+    return ConfigReader._from_file(config_file_path), {}
+
+
+def _merge_duplicate_workspace_root_entries(
+    label: str,
+    occurrences: list[t.Any],
+) -> tuple[t.Any, list[str], int]:
+    conflicts: list[str] = []
+    change_count = max(len(occurrences) - 1, 0)
+
+    if not occurrences:
+        return {}, conflicts, change_count
+
+    if not all(isinstance(entry, dict) for entry in occurrences):
+        conflicts.append(
+            (
+                f"Workspace root '{label}' contains duplicate entries that are not "
+                "mappings. Keeping the last occurrence."
+            ),
+        )
+        return occurrences[-1], conflicts, change_count
+
+    merged: dict[str, t.Any] = {}
+
+    for entry in occurrences:
+        assert isinstance(entry, dict)
+        for repo_name, repo_config in entry.items():
+            if repo_name not in merged:
+                merged[repo_name] = copy.deepcopy(repo_config)
+            elif merged[repo_name] != repo_config:
+                conflicts.append(
+                    (
+                        f"Workspace root '{label}' contains conflicting definitions "
+                        f"for repository '{repo_name}'. Keeping the existing entry."
+                    ),
+                )
+
+    return merged, conflicts, change_count
+
+
+def _merge_duplicate_workspace_roots(
+    config_data: dict[str, t.Any],
+    duplicate_roots: dict[str, list[t.Any]],
+) -> tuple[dict[str, t.Any], list[str], int, list[tuple[str, int]]]:
+    if not duplicate_roots:
+        return config_data, [], 0, []
+
+    merged_config = copy.deepcopy(config_data)
+    conflicts: list[str] = []
+    change_count = 0
+    details: list[tuple[str, int]] = []
+
+    for label, occurrences in duplicate_roots.items():
+        (
+            merged_value,
+            entry_conflicts,
+            entry_changes,
+        ) = _merge_duplicate_workspace_root_entries(
+            label,
+            occurrences,
+        )
+        merged_config[label] = merged_value
+        conflicts.extend(entry_conflicts)
+        change_count += entry_changes
+        details.append((label, len(occurrences)))
+
+    return merged_config, conflicts, change_count, details
+
+
 def create_fmt_subparser(parser: argparse.ArgumentParser) -> None:
     """Create ``vcspull fmt`` argument subparser."""
     parser.add_argument(
@@ -43,6 +188,13 @@ def create_fmt_subparser(parser: argparse.ArgumentParser) -> None:
         action="store_true",
         help="Format all discovered config files (home, config dir, and current dir)",
     )
+    parser.add_argument(
+        "--no-merge",
+        dest="merge_roots",
+        action="store_false",
+        help="Do not merge duplicate workspace roots when formatting",
+    )
+    parser.set_defaults(merge_roots=True)
 
 
 def normalize_repo_config(repo_data: t.Any) -> dict[str, t.Any]:
@@ -130,6 +282,8 @@ def format_config(config_data: dict[str, t.Any]) -> tuple[dict[str, t.Any], int]
 def format_single_config(
     config_file_path: pathlib.Path,
     write: bool,
+    *,
+    merge_roots: bool,
 ) -> bool:
     """Format a single vcspull configuration file.
 
@@ -139,6 +293,8 @@ def format_single_config(
         Path to config file
     write : bool
         Whether to write changes back to file
+    merge_roots : bool
+        Merge duplicate workspace roots when True (default behavior)
 
     Returns
     -------
@@ -159,13 +315,18 @@ def format_single_config(
 
     # Load existing config
     try:
-        raw_config = ConfigReader._from_file(config_file_path)
+        raw_config, duplicate_root_occurrences = _load_config_with_duplicate_roots(
+            config_file_path,
+        )
         if not isinstance(raw_config, dict):
             log.error(
                 "Config file %s is not a valid YAML dictionary.",
                 config_file_path,
             )
             return False
+    except TypeError:
+        log.exception("Invalid configuration in %s", config_file_path)
+        return False
     except Exception:
         log.exception("Error loading config from %s", config_file_path)
         if log.isEnabledFor(logging.DEBUG):
@@ -176,18 +337,62 @@ def format_single_config(
     cwd = pathlib.Path.cwd()
     home = pathlib.Path.home()
 
-    normalization_result = normalize_workspace_roots(
-        raw_config,
-        cwd=cwd,
-        home=home,
-    )
-    raw_config, _workspace_map, merge_conflicts, merge_changes = normalization_result
+    duplicate_merge_conflicts: list[str] = []
+    duplicate_merge_changes = 0
+    duplicate_merge_details: list[tuple[str, int]] = []
+
+    working_config = copy.deepcopy(raw_config)
+
+    if merge_roots:
+        (
+            working_config,
+            duplicate_merge_conflicts,
+            duplicate_merge_changes,
+            duplicate_merge_details,
+        ) = _merge_duplicate_workspace_roots(working_config, duplicate_root_occurrences)
+    elif duplicate_root_occurrences:
+        duplicate_merge_details = [
+            (label, len(values)) for label, values in duplicate_root_occurrences.items()
+        ]
+        for label, occurrence_count in duplicate_merge_details:
+            log.warning(
+                "%s•%s Duplicate workspace root %s%s%s appears %s%d%s time%s; "
+                "skipping merge because --no-merge was provided.",
+                Fore.BLUE,
+                Style.RESET_ALL,
+                Fore.MAGENTA,
+                label,
+                Style.RESET_ALL,
+                Fore.YELLOW,
+                occurrence_count,
+                Style.RESET_ALL,
+                "" if occurrence_count == 1 else "s",
+            )
+
+    if merge_roots:
+        normalization_result = normalize_workspace_roots(
+            working_config,
+            cwd=cwd,
+            home=home,
+        )
+        (
+            normalized_config,
+            _workspace_map,
+            merge_conflicts,
+            normalization_changes,
+        ) = normalization_result
+    else:
+        normalized_config = working_config
+        merge_conflicts = []
+        normalization_changes = 0
 
     for message in merge_conflicts:
         log.warning(message)
+    for message in duplicate_merge_conflicts:
+        log.warning(message)
 
-    formatted_config, change_count = format_config(raw_config)
-    change_count += merge_changes
+    formatted_config, change_count = format_config(normalized_config)
+    change_count += normalization_changes + duplicate_merge_changes
 
     if change_count == 0:
         log.info(
@@ -215,17 +420,32 @@ def format_single_config(
     )
 
     # Analyze and report specific changes
-    if merge_changes > 0:
+    if merge_roots and normalization_changes > 0:
         log.info(
             "  %s•%s Normalized workspace root labels",
             Fore.BLUE,
             Style.RESET_ALL,
         )
 
+    if merge_roots and duplicate_merge_details:
+        for label, occurrence_count in duplicate_merge_details:
+            log.info(
+                "  %s•%s Merged %s%d%s duplicate entr%s for workspace root %s%s%s",
+                Fore.BLUE,
+                Style.RESET_ALL,
+                Fore.YELLOW,
+                occurrence_count,
+                Style.RESET_ALL,
+                "y" if occurrence_count == 1 else "ies",
+                Fore.MAGENTA,
+                label,
+                Style.RESET_ALL,
+            )
+
     compact_to_verbose = 0
     url_to_repo = 0
 
-    for repos in raw_config.values():
+    for repos in normalized_config.values():
         if isinstance(repos, dict):
             for repo_data in repos.values():
                 if isinstance(repo_data, str):
@@ -255,7 +475,7 @@ def format_single_config(
             "repository" if url_to_repo == 1 else "repositories",
         )
 
-    if list(raw_config.keys()) != sorted(raw_config.keys()):
+    if list(normalized_config.keys()) != sorted(normalized_config.keys()):
         log.info(
             "  %s•%s Directories will be sorted alphabetically",
             Fore.BLUE,
@@ -263,7 +483,7 @@ def format_single_config(
         )
 
     # Check if any repos need sorting
-    for directory, repos in raw_config.items():
+    for directory, repos in normalized_config.items():
         if isinstance(repos, dict) and list(repos.keys()) != sorted(repos.keys()):
             log.info(
                 "  %s•%s Repositories in %s%s%s will be sorted alphabetically",
@@ -308,6 +528,8 @@ def format_config_file(
     config_file_path_str: str | None,
     write: bool,
     format_all: bool = False,
+    *,
+    merge_roots: bool = True,
 ) -> None:
     """Format vcspull configuration file(s).
 
@@ -319,6 +541,8 @@ def format_config_file(
         Whether to write changes back to file
     format_all : bool
         If True, format all discovered config files
+    merge_roots : bool
+        Merge duplicate workspace roots when True (default)
     """
     if format_all:
         # Format all discovered config files
@@ -366,7 +590,11 @@ def format_config_file(
 
         success_count = 0
         for config_file in config_files:
-            if format_single_config(config_file, write):
+            if format_single_config(
+                config_file,
+                write,
+                merge_roots=merge_roots,
+            ):
                 success_count += 1
 
         # Summary
@@ -413,4 +641,8 @@ def format_config_file(
             else:
                 config_file_path = home_configs[0]
 
-        format_single_config(config_file_path, write)
+        format_single_config(
+            config_file_path,
+            write,
+            merge_roots=merge_roots,
+        )
diff --git a/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[merge-default][fmt-cli-merge].yaml b/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[merge-default][fmt-cli-merge].yaml
new file mode 100644
index 00000000..8e27120b
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[merge-default][fmt-cli-merge].yaml
@@ -0,0 +1,5 @@
+~/study/c/:
+  repo1:
+    repo: url1
+  repo2:
+    repo: url2
diff --git a/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[no-merge][fmt-cli-no-merge].yaml b/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[no-merge][fmt-cli-no-merge].yaml
new file mode 100644
index 00000000..176c8a90
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_fmt_cli_integration[no-merge][fmt-cli-no-merge].yaml
@@ -0,0 +1,3 @@
+~/study/c/:
+  repo2:
+    repo: url2
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_complex_changes.json b/tests/cli/__snapshots__/test_fmt/test_format_config_complex_changes.json
new file mode 100644
index 00000000..39df33d8
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_complex_changes.json
@@ -0,0 +1,21 @@
+{
+  "~/aaa/": {
+    "repo1": {
+      "repo": "another-compact"
+    }
+  },
+  "~/zzz/": {
+    "alpha": {
+      "repo": "verbose-url"
+    },
+    "beta": {
+      "remotes": {
+        "upstream": "upstream-url"
+      },
+      "repo": "already-good"
+    },
+    "zebra": {
+      "repo": "compact-url"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_converts_compact_entries.json b/tests/cli/__snapshots__/test_fmt/test_format_config_converts_compact_entries.json
new file mode 100644
index 00000000..bdc0c21c
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_converts_compact_entries.json
@@ -0,0 +1,13 @@
+{
+  "~/projects/": {
+    "repo1": {
+      "repo": "git+https://github.com/user/repo1.git"
+    },
+    "repo2": {
+      "repo": "git+https://github.com/user/repo2.git"
+    },
+    "repo3": {
+      "repo": "git+https://github.com/user/repo3.git"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_file_with_write[format-config-file-with-write].yaml b/tests/cli/__snapshots__/test_fmt/test_format_config_file_with_write[format-config-file-with-write].yaml
new file mode 100644
index 00000000..c8c9937a
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_file_with_write[format-config-file-with-write].yaml
@@ -0,0 +1,5 @@
+~/zzz/:
+  repo1:
+    repo: url1
+  repo2:
+    repo: url2
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_merges_duplicate_roots_when_writing[format-config-file-merge].yaml b/tests/cli/__snapshots__/test_fmt/test_format_config_merges_duplicate_roots_when_writing[format-config-file-merge].yaml
new file mode 100644
index 00000000..8e27120b
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_merges_duplicate_roots_when_writing[format-config-file-merge].yaml
@@ -0,0 +1,5 @@
+~/study/c/:
+  repo1:
+    repo: url1
+  repo2:
+    repo: url2
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_no_changes_when_already_normalized.json b/tests/cli/__snapshots__/test_fmt/test_format_config_no_changes_when_already_normalized.json
new file mode 100644
index 00000000..8105e421
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_no_changes_when_already_normalized.json
@@ -0,0 +1,15 @@
+{
+  "~/aaa/": {
+    "alpha": {
+      "repo": "url1"
+    },
+    "beta": {
+      "repo": "url2"
+    }
+  },
+  "~/bbb/": {
+    "charlie": {
+      "repo": "url3"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_no_merge_flag_skips_duplicate_merge[format-config-file-no-merge].yaml b/tests/cli/__snapshots__/test_fmt/test_format_config_no_merge_flag_skips_duplicate_merge[format-config-file-no-merge].yaml
new file mode 100644
index 00000000..176c8a90
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_no_merge_flag_skips_duplicate_merge[format-config-file-no-merge].yaml
@@ -0,0 +1,3 @@
+~/study/c/:
+  repo2:
+    repo: url2
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_directories.json b/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_directories.json
new file mode 100644
index 00000000..46c88ba4
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_directories.json
@@ -0,0 +1,17 @@
+{
+  "~/aaa/": {
+    "repo2": {
+      "repo": "url2"
+    }
+  },
+  "~/mmm/": {
+    "repo3": {
+      "repo": "url3"
+    }
+  },
+  "~/zzz/": {
+    "repo1": {
+      "repo": "url1"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_repositories.json b/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_repositories.json
new file mode 100644
index 00000000..51eb7545
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_format_config_sorts_repositories.json
@@ -0,0 +1,13 @@
+{
+  "~/projects/": {
+    "alpha": {
+      "repo": "url2"
+    },
+    "beta": {
+      "repo": "url3"
+    },
+    "zebra": {
+      "repo": "url1"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[home-vs-absolute].json b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[home-vs-absolute].json
new file mode 100644
index 00000000..ed99b593
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[home-vs-absolute].json
@@ -0,0 +1,10 @@
+{
+  "~/study/c/": {
+    "cpython": {
+      "repo": "git+https://github.com/python/cpython.git"
+    },
+    "tmux": {
+      "repo": "git+https://github.com/tmux/tmux.git"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[relative-vs-tilde].json b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[relative-vs-tilde].json
new file mode 100644
index 00000000..ed99b593
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[relative-vs-tilde].json
@@ -0,0 +1,10 @@
+{
+  "~/study/c/": {
+    "cpython": {
+      "repo": "git+https://github.com/python/cpython.git"
+    },
+    "tmux": {
+      "repo": "git+https://github.com/tmux/tmux.git"
+    }
+  }
+}
diff --git a/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[tilde-mixed-trailing-slash].json b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[tilde-mixed-trailing-slash].json
new file mode 100644
index 00000000..ed99b593
--- /dev/null
+++ b/tests/cli/__snapshots__/test_fmt/test_workspace_root_normalization[tilde-mixed-trailing-slash].json
@@ -0,0 +1,10 @@
+{
+  "~/study/c/": {
+    "cpython": {
+      "repo": "git+https://github.com/python/cpython.git"
+    },
+    "tmux": {
+      "repo": "git+https://github.com/tmux/tmux.git"
+    }
+  }
+}
diff --git a/tests/cli/test_fmt.py b/tests/cli/test_fmt.py
index 7078adb7..6d4e23a4 100644
--- a/tests/cli/test_fmt.py
+++ b/tests/cli/test_fmt.py
@@ -2,13 +2,16 @@
 
 from __future__ import annotations
 
+import contextlib
 import logging
 import pathlib
 import typing as t
 
 import pytest
 import yaml
+from syrupy.assertion import SnapshotAssertion
 
+from vcspull.cli import cli
 from vcspull.cli.fmt import format_config, format_config_file, normalize_repo_config
 from vcspull.config import (
     canonicalize_workspace_path,
@@ -78,6 +81,7 @@ class WorkspaceRootFixture(t.NamedTuple):
 def test_workspace_root_normalization(
     test_id: str,
     config_factory: t.Callable[[pathlib.Path], dict[str, t.Any]],
+    snapshot_json: SnapshotAssertion,
 ) -> None:
     """Ensure format_config merges duplicate workspace roots."""
     home_dir = pathlib.Path.home()
@@ -100,6 +104,7 @@ def test_workspace_root_normalization(
     assert sorted(normalized_config.keys()) == expected_labels
     formatted, _changes = format_config(normalized_config)
     assert sorted(formatted.keys()) == expected_labels
+    assert formatted == snapshot_json
     assert merge_changes >= len(config) - len(canonical_paths)
 
 
@@ -149,7 +154,7 @@ def test_normalize_repo_config_both_url_and_repo() -> None:
     assert normalized == config
 
 
-def test_format_config_sorts_directories() -> None:
+def test_format_config_sorts_directories(snapshot_json: SnapshotAssertion) -> None:
     """Workspace roots should be sorted alphabetically."""
     config = {
         "~/zzz/": {"repo1": "url1"},
@@ -157,11 +162,11 @@ def test_format_config_sorts_directories() -> None:
         "~/mmm/": {"repo3": "url3"},
     }
     formatted, changes = format_config(config)
-    assert list(formatted.keys()) == ["~/aaa/", "~/mmm/", "~/zzz/"]
+    assert formatted == snapshot_json
     assert changes > 0
 
 
-def test_format_config_sorts_repositories() -> None:
+def test_format_config_sorts_repositories(snapshot_json: SnapshotAssertion) -> None:
     """Repositories within a workspace root should be sorted."""
     config = {
         "~/projects/": {
@@ -171,11 +176,13 @@ def test_format_config_sorts_repositories() -> None:
         },
     }
     formatted, changes = format_config(config)
-    assert list(formatted["~/projects/"].keys()) == ["alpha", "beta", "zebra"]
+    assert formatted == snapshot_json
     assert changes > 0
 
 
-def test_format_config_converts_compact_entries() -> None:
+def test_format_config_converts_compact_entries(
+    snapshot_json: SnapshotAssertion,
+) -> None:
     """Compact repository entries should convert to verbose form."""
     config = {
         "~/projects/": {
@@ -185,19 +192,13 @@ def test_format_config_converts_compact_entries() -> None:
         },
     }
     formatted, changes = format_config(config)
-    assert formatted["~/projects/"]["repo1"] == {
-        "repo": "git+https://github.com/user/repo1.git",
-    }
-    assert formatted["~/projects/"]["repo2"] == {
-        "repo": "git+https://github.com/user/repo2.git",
-    }
-    assert formatted["~/projects/"]["repo3"] == {
-        "repo": "git+https://github.com/user/repo3.git",
-    }
+    assert formatted == snapshot_json
     assert changes == 2
 
 
-def test_format_config_no_changes_when_already_normalized() -> None:
+def test_format_config_no_changes_when_already_normalized(
+    snapshot_json: SnapshotAssertion,
+) -> None:
     """Formatter should report zero changes for already-normalized configs."""
     config = {
         "~/aaa/": {
@@ -209,11 +210,11 @@ def test_format_config_no_changes_when_already_normalized() -> None:
         },
     }
     formatted, changes = format_config(config)
-    assert formatted == config
+    assert formatted == snapshot_json
     assert changes == 0
 
 
-def test_format_config_complex_changes() -> None:
+def test_format_config_complex_changes(snapshot_json: SnapshotAssertion) -> None:
     """Formatter should handle sorting and conversions together."""
     config = {
         "~/zzz/": {
@@ -229,13 +230,7 @@ def test_format_config_complex_changes() -> None:
         },
     }
     formatted, changes = format_config(config)
-    assert list(formatted.keys()) == ["~/aaa/", "~/zzz/"]
-    assert list(formatted["~/zzz/"].keys()) == ["alpha", "beta", "zebra"]
-    assert formatted["~/aaa/"]["repo1"] == {"repo": "another-compact"}
-    assert formatted["~/zzz/"]["zebra"] == {"repo": "compact-url"}
-    assert formatted["~/zzz/"]["alpha"] == {"repo": "verbose-url"}
-    assert formatted["~/zzz/"]["beta"]["repo"] == "already-good"
-    assert formatted["~/zzz/"]["beta"]["remotes"] == {"upstream": "upstream-url"}
+    assert formatted == snapshot_json
     assert changes > 0
 
 
@@ -266,7 +261,10 @@ def test_format_config_file_without_write(
     assert "Run with --write to apply" in caplog.text
 
 
-def test_format_config_file_with_write(tmp_path: pathlib.Path) -> None:
+def test_format_config_file_with_write(
+    tmp_path: pathlib.Path,
+    snapshot_yaml: SnapshotAssertion,
+) -> None:
     """format_config_file should rewrite file when write=True."""
     config_file = tmp_path / ".vcspull.yaml"
     original_config = {
@@ -279,8 +277,8 @@ def test_format_config_file_with_write(tmp_path: pathlib.Path) -> None:
 
     format_config_file(str(config_file), write=True, format_all=False)
 
-    saved_config = yaml.safe_load(config_file.read_text(encoding="utf-8"))
-    assert saved_config["~/zzz/"]["repo1"] == {"repo": "url1"}
+    yaml_text = config_file.read_text(encoding="utf-8")
+    assert yaml_text == snapshot_yaml(name="format-config-file-with-write")
 
 
 def test_format_config_file_invalid_yaml(
@@ -404,3 +402,143 @@ def fake_find_home_config_files(
     assert "already formatted correctly" in text
     assert "Repositories in ~/work/ will be sorted alphabetically" in text
     assert "All 3 configuration files processed successfully" in text
+
+
+def test_format_config_detects_and_merges_duplicate_roots(
+    tmp_path: pathlib.Path,
+    caplog: LogCaptureFixture,
+) -> None:
+    """Duplicate workspace roots should be detected and merged by default."""
+    config_file = tmp_path / ".vcspull.yaml"
+    config_file.write_text(
+        """~/study/c/:
+  repo1: url1
+~/study/c/:
+  repo2: url2
+""",
+        encoding="utf-8",
+    )
+
+    with caplog.at_level(logging.INFO):
+        format_config_file(str(config_file), write=False, format_all=False)
+
+    text = caplog.text
+    assert "Merged" in text
+    assert "workspace root" in text
+
+
+def test_format_config_no_merge_flag_skips_duplicate_merge(
+    tmp_path: pathlib.Path,
+    caplog: LogCaptureFixture,
+    snapshot_yaml: SnapshotAssertion,
+) -> None:
+    """--no-merge should prevent duplicate workspace roots from being combined."""
+    config_file = tmp_path / ".vcspull.yaml"
+    config_file.write_text(
+        """~/study/c/:
+  repo1: url1
+~/study/c/:
+  repo2: url2
+""",
+        encoding="utf-8",
+    )
+
+    with caplog.at_level(logging.WARNING):
+        format_config_file(
+            str(config_file),
+            write=True,
+            format_all=False,
+            merge_roots=False,
+        )
+
+    text = caplog.text
+    assert "skipping merge" in text
+    yaml_text = config_file.read_text(encoding="utf-8")
+    assert yaml_text == snapshot_yaml(name="format-config-file-no-merge")
+
+
+def test_format_config_merges_duplicate_roots_when_writing(
+    tmp_path: pathlib.Path,
+    snapshot_yaml: SnapshotAssertion,
+) -> None:
+    """When merging, formatted file should contain combined repositories."""
+    config_file = tmp_path / ".vcspull.yaml"
+    config_file.write_text(
+        """~/study/c/:
+  repo1: url1
+~/study/c/:
+  repo2: url2
+""",
+        encoding="utf-8",
+    )
+
+    format_config_file(str(config_file), write=True, format_all=False)
+
+    yaml_text = config_file.read_text(encoding="utf-8")
+    assert yaml_text == snapshot_yaml(name="format-config-file-merge")
+
+
+class FmtIntegrationFixture(t.NamedTuple):
+    """Fixture for parametrized fmt CLI integration tests."""
+
+    test_id: str
+    cli_args: list[str]
+    expected_log_fragment: str
+    snapshot_name: str
+
+
+FMT_CLI_FIXTURES: list[FmtIntegrationFixture] = [
+    FmtIntegrationFixture(
+        test_id="merge-default",
+        cli_args=["fmt", "-f", "{config}", "--write"],
+        expected_log_fragment="Merged",
+        snapshot_name="fmt-cli-merge",
+    ),
+    FmtIntegrationFixture(
+        test_id="no-merge",
+        cli_args=["fmt", "-f", "{config}", "--write", "--no-merge"],
+        expected_log_fragment="skipping merge",
+        snapshot_name="fmt-cli-no-merge",
+    ),
+]
+
+
+@pytest.mark.parametrize(
+    list(FmtIntegrationFixture._fields),
+    FMT_CLI_FIXTURES,
+    ids=[fixture.test_id for fixture in FMT_CLI_FIXTURES],
+)
+def test_fmt_cli_integration(
+    tmp_path: pathlib.Path,
+    caplog: LogCaptureFixture,
+    monkeypatch: pytest.MonkeyPatch,
+    snapshot_yaml: SnapshotAssertion,
+    test_id: str,
+    cli_args: list[str],
+    expected_log_fragment: str,
+    snapshot_name: str,
+) -> None:
+    """Run vcspull fmt via CLI to ensure duplicate handling respects flags."""
+    config_file = tmp_path / ".vcspull.yaml"
+    config_file.write_text(
+        """~/study/c/:
+  repo1: url1
+~/study/c/:
+  repo2: url2
+""",
+        encoding="utf-8",
+    )
+
+    monkeypatch.chdir(tmp_path)
+
+    formatted_args = [
+        arg.format(config=str(config_file)) if "{config}" in arg else arg
+        for arg in cli_args
+    ]
+
+    with caplog.at_level(logging.INFO), contextlib.suppress(SystemExit):
+        cli(formatted_args)
+
+    yaml_text = config_file.read_text(encoding="utf-8")
+    assert yaml_text == snapshot_yaml(name=snapshot_name)
+    assert expected_log_fragment in caplog.text
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 00000000..3aa4072a
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,27 @@
+"""Shared pytest fixtures for snapshot testing."""
+
+from __future__ import annotations
+
+import pytest
+from syrupy.assertion import SnapshotAssertion
+from syrupy.extensions.json import JSONSnapshotExtension
+from syrupy.extensions.single_file import SingleFileSnapshotExtension, WriteMode
+
+
+class YamlSnapshotExtension(SingleFileSnapshotExtension):
+    """Snapshot extension that persists plain-text YAML files."""
+
+    file_extension = "yaml"
+    _write_mode = WriteMode.TEXT
+
+
+@pytest.fixture
+def snapshot_json(snapshot: SnapshotAssertion) -> SnapshotAssertion:
+    """JSON-formatted snapshot assertions."""
+    return snapshot.with_defaults(extension_class=JSONSnapshotExtension)
+
+
+@pytest.fixture
+def snapshot_yaml(snapshot: SnapshotAssertion) -> SnapshotAssertion:
+    """YAML-formatted snapshot assertions."""
+    return snapshot.with_defaults(extension_class=YamlSnapshotExtension)
diff --git a/uv.lock b/uv.lock
index c2605dc8..e1422d51 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1161,6 +1161,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/d9/52/1064f510b141bd54025f9b55105e26d1fa970b9be67ad766380a3c9b74b0/starlette-0.50.0-py3-none-any.whl", hash = "sha256:9e5391843ec9b6e472eed1365a78c8098cfceb7a74bfd4d6b1c0c0095efb3bca", size = 74033, upload-time = "2025-11-01T15:25:25.461Z" },
 ]
 
+[[package]]
+name = "syrupy"
+version = "5.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pytest" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/c1/90/1a442d21527009d4b40f37fe50b606ebb68a6407142c2b5cc508c34b696b/syrupy-5.0.0.tar.gz", hash = "sha256:3282fe963fa5d4d3e47231b16d1d4d0f4523705e8199eeb99a22a1bc9f5942f2", size = 48881, upload-time = "2025-09-28T21:15:12.783Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/9d/9a/6c68aad2ccfce6e2eeebbf5bb709d0240592eb51ff142ec4c8fbf3c2460a/syrupy-5.0.0-py3-none-any.whl", hash = "sha256:c848e1a980ca52a28715cd2d2b4d434db424699c05653bd1158fb31cf56e9546", size = 49087, upload-time = "2025-09-28T21:15:11.639Z" },
+]
+
 [[package]]
 name = "tomli"
 version = "2.3.0"
@@ -1323,6 +1335,7 @@ dev = [
     { name = "sphinx-inline-tabs" },
     { name = "sphinxext-opengraph" },
     { name = "sphinxext-rediraffe" },
+    { name = "syrupy" },
     { name = "types-colorama" },
     { name = "types-pyyaml" },
     { name = "types-requests" },
@@ -1355,6 +1368,7 @@ testing = [
     { name = "pytest-mock" },
     { name = "pytest-rerunfailures" },
     { name = "pytest-watcher" },
+    { name = "syrupy" },
 ]
 typings = [
     { name = "types-colorama" },
@@ -1398,6 +1412,7 @@ dev = [
     { name = "sphinx-inline-tabs" },
     { name = "sphinxext-opengraph" },
     { name = "sphinxext-rediraffe" },
+    { name = "syrupy" },
     { name = "types-colorama" },
     { name = "types-pyyaml" },
     { name = "types-requests" },
@@ -1427,6 +1442,7 @@ testing = [
     { name = "pytest-mock" },
     { name = "pytest-rerunfailures" },
     { name = "pytest-watcher" },
+    { name = "syrupy" },
 ]
 typings = [
     { name = "types-colorama" },