feat(webdav): add bearer_token_command for dynamic token acquisition (#10917 )

Co-authored-by: GreenHatHG <[email protected]> Co-authored-by: skshetry <[email protected]>
[pre-commit.ci] pre-commit autoupdate (#10921 )
2026-11-02 15:28:30 +01:00 · 2025-12-05 11:07:22 +05:45 · 2025-12-03 13:17:20 +05:45 · 2025-12-02 16:05:13 +05:45 · 2025-12-01 16:54:40 +05:45 · 2025-12-01 15:52:37 +05:45
188 changed files with 4273 additions and 1249 deletions
@@ -737,8 +737,8 @@
    "tests/func/test_config.py::test_config_gdrive_fields": 0.12703910000016094,
    "tests/func/test_config.py::test_config_get[args0-0-False]": 0.20948869999995168,
    "tests/func/test_config.py::test_config_get[args1-0-myremote]": 0.1829517000001033,
-    "tests/func/test_config.py::test_config_get[args2-0-iterative]": 0.19686669999998685,
-    "tests/func/test_config.py::test_config_get[args3-0-iterative]": 0.1675059000000374,
+    "tests/func/test_config.py::test_config_get[args2-0-treeverse]": 0.19686669999998685,
+    "tests/func/test_config.py::test_config_get[args3-0-treeverse]": 0.1675059000000374,
    "tests/func/test_config.py::test_config_get[args4-251-option 'profile' doesn't exist]": 0.18096200000002227,
    "tests/func/test_config.py::test_config_get[args5-0-gs://bucket/path]": 0.12368970000022728,
    "tests/func/test_config.py::test_config_get[args6-0-gs://bucket/path]": 0.13007389999995667,
@@ -2642,7 +2642,7 @@
    "tests/unit/test_updater.py::test_is_enabled[config0-True]": 0.13130560000013247,
    "tests/unit/test_updater.py::test_is_enabled[config1-True]": 0.14342600000009043,
    "tests/unit/test_updater.py::test_is_enabled[config2-False]": 0.13593219999984285,
-    "tests/unit/test_updater.py::test_notify_message[None-Find the latest release at https://github.com/iterative/dvc/releases/latest.]": 0.014024399999925663,
+    "tests/unit/test_updater.py::test_notify_message[None-Find the latest release at https://github.com/treeverse/dvc/releases/latest.]": 0.014024399999925663,
    "tests/unit/test_updater.py::test_notify_message[binary-To upgrade, uninstall dvc and reinstall from https://dvc.org.]": 0.013217200000326557,
    "tests/unit/test_updater.py::test_notify_message[brew-To upgrade, run 'brew upgrade dvc'.]": 0.013467300000229443,
    "tests/unit/test_updater.py::test_notify_message[choco-To upgrade, run 'choco upgrade dvc'.]": 0.014645900000004985,
@@ -2652,7 +2652,7 @@
    "tests/unit/test_updater.py::test_notify_message[osxpkg-To upgrade, uninstall dvc and reinstall from https://dvc.org.]": 0.013980499999888707,
    "tests/unit/test_updater.py::test_notify_message[pip-To upgrade, run 'pip install --upgrade dvc'.]": 0.015155299999833005,
    "tests/unit/test_updater.py::test_notify_message[rpm-To upgrade, run 'yum update dvc'.]": 0.014036500000202068,
-    "tests/unit/test_updater.py::test_notify_message[unknown-Find the latest release at https://github.com/iterative/dvc/releases/latest.]": 0.01609110000003966,
+    "tests/unit/test_updater.py::test_notify_message[unknown-Find the latest release at https://github.com/treeverse/dvc/releases/latest.]": 0.01609110000003966,
    "tests/unit/ui/test_console.py::test_capsys_works": 0.003642499999841675,
    "tests/unit/ui/test_console.py::test_write": 0.004320600000255581,
    "tests/unit/ui/test_console.py::test_write_json[False-{\"hello\": \"world\", \"date\": \"1970-01-01 00:00:00\"}\\n]": 0.004433300000073359,
@@ -57,7 +57,7 @@ $ dvc doctor
 **Additional Information (if any):**

 <!--
-Please check https://github.com/iterative/dvc/wiki/Debugging-DVC on ways to gather more information regarding the issue.
+Please check https://github.com/treeverse/dvc/wiki/Debugging-DVC on ways to gather more information regarding the issue.

 If applicable, please also provide a `--verbose` output of the command, eg: `dvc add --verbose`.
 If the issue is regarding the performance, please attach the profiling information and the benchmark comparisons.
@@ -1,5 +1,5 @@
 * [ ] ❗ I have followed the [Contributing to DVC](https://dvc.org/doc/user-guide/contributing/core) checklist.

-* [ ] 📖 If this PR requires [documentation](https://dvc.org/doc) updates, I have created a separate PR (or issue, at least) in [dvc.org](https://github.com/iterative/dvc.org) and linked it here.
+* [ ] 📖 If this PR requires [documentation](https://dvc.org/doc) updates, I have created a separate PR (or issue, at least) in [dvc.org](https://github.com/treeverse/dvc.org) and linked it here.

 Thank you for the contribution - we'll try to review it as soon as possible. 🙏
@@ -14,16 +14,16 @@ jobs:
    name: run benchmarks
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
        with:
-            python-version: "3.13"
+            python-version: "3.14"

-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          ref: ${{ github.event.pull_request.base.sha }}
          fetch-depth: 0

-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
        with:
          enable-cache: true
          cache-dependency-glob: pyproject.toml
@@ -32,7 +32,7 @@ jobs:
      - name: run benchmarks on base branch
        run: pytest --benchmark-autosave dvc/testing/benchmarks/ -k 'test_init or test_help'

-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          fetch-depth: 0
          clean: false
@@ -19,15 +19,15 @@ jobs:
    name: Build & Verify package
    runs-on: ubuntu-latest
    steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
      with:
        fetch-depth: 0

-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
      with:
-        python-version: 3.13
+        python-version: "3.14"

-    - uses: astral-sh/setup-uv@v6
+    - uses: astral-sh/setup-uv@v7

    - name: Omit local version for Test PyPI upload
      if: github.event_name == 'push' && github.ref == 'refs/heads/main'
@@ -41,7 +41,7 @@ jobs:
    - name: Check dist
      run: uv tool run twine check --strict dist/*

-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
      with:
        name: Packages
        path: dist/
@@ -51,17 +51,17 @@ jobs:
    name: Publish dev package to test.pypi.org
    runs-on: ubuntu-latest
    needs: build
-    if: ${{ github.event.action == 'published' || (github.repository == 'iterative/dvc' && github.event_name == 'push' && github.ref == 'refs/heads/main') }}
+    if: ${{ github.event.action == 'published' || (github.repository == 'treeverse/dvc' && github.event_name == 'push' && github.ref == 'refs/heads/main') }}

    environment:
      name: test-pypi
-      url: https://test.pypi.org/p/dvc
+      url: https://test.pypi.org/p/dvc/${{ github.event.release.tag_name }}

    permissions:
      id-token: write

    steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
      with:
        name: Packages
        path: dist
@@ -80,13 +80,13 @@ jobs:

    environment:
      name: pypi
-      url: https://pypi.org/p/dvc
+      url: https://pypi.org/p/dvc/${{ github.event.release.tag_name }}

    permissions:
      id-token: write

    steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
      with:
        name: Packages
        path: dist
@@ -28,13 +28,13 @@ jobs:

    steps:
    - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6

    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
      with:
        languages: ${{ matrix.language }}
        queries: security-extended

    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
@@ -19,26 +19,26 @@ jobs:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
-        pyv: ["3.13"]
+        pyv: ["3.14"]
        plugin: ["dvc-s3"]

    steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
      with:
        path: dvc

-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
      with:
-        repository: iterative/${{ matrix.plugin }}
+        repository: treeverse/${{ matrix.plugin }}
        ref: main
        path: ${{ matrix.plugin }}

    - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.pyv }}

-    - uses: astral-sh/setup-uv@v6
+    - uses: astral-sh/setup-uv@v7
      with:
        enable-cache: true
        cache-dependency-glob: "**/pyproject.toml"
@@ -26,14 +26,14 @@ jobs:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
    steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
      with:
        fetch-depth: 0
    - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
      with:
-        python-version: '3.13'
-    - uses: astral-sh/setup-uv@v6
+        python-version: '3.14'
+    - uses: astral-sh/setup-uv@v7
      with:
        enable-cache: true
        cache-dependency-glob: pyproject.toml
@@ -55,7 +55,7 @@ jobs:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest]
-        pyv: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        pyv: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
        include:
        - os: windows-latest
          pyv: "3.9"
@@ -117,15 +117,27 @@ jobs:
        - os: windows-latest
          pyv: "3.13"
          pytestargs: "--splitting-algorithm=least_duration --splits 4 --group 4"
+        - os: windows-latest
+          pyv: "3.14"
+          pytestargs: "--splitting-algorithm=least_duration --splits 4 --group 1"
+        - os: windows-latest
+          pyv: "3.14"
+          pytestargs: "--splitting-algorithm=least_duration --splits 4 --group 2"
+        - os: windows-latest
+          pyv: "3.14"
+          pytestargs: "--splitting-algorithm=least_duration --splits 4 --group 3"
+        - os: windows-latest
+          pyv: "3.14"
+          pytestargs: "--splitting-algorithm=least_duration --splits 4 --group 4"
    steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
      with:
        fetch-depth: 0
    - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.pyv }}
-    - uses: astral-sh/setup-uv@v6
+    - uses: astral-sh/setup-uv@v7
      with:
        enable-cache: true
        cache-dependency-glob: pyproject.toml
@@ -137,15 +149,13 @@ jobs:
    - name: run tests
      timeout-minutes: 40
      env:
+        COVERAGE_CORE: sysmon
        PYTHONUTF8: 1
      run: >
        pytest ${{ matrix.pytestargs }} -n=logical --dist=worksteal --timeout=300 --durations=0
        --cov --cov-report=xml --cov-report=term  --durations-path=./.github/.test_durations
    - name: upload coverage report
      uses: codecov/codecov-action@v5
-      with:
-        file: ./coverage.xml
-        fail_ci_if_error: false
  check:
    if: always()
    needs: [tests]
@@ -6,7 +6,7 @@ ci:

 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
    hooks:
      - id: check-added-large-files
      - id: check-case-conflict
@@ -22,9 +22,9 @@ repos:
      - id: sort-simple-yaml
      - id: trailing-whitespace
  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.11.8'
+    rev: 'v0.14.7'
    hooks:
-      - id: ruff
+      - id: ruff-check
        args: [--fix, --exit-non-zero-on-fix]
      - id: ruff-format
  - repo: https://github.com/codespell-project/codespell
@@ -4,5 +4,5 @@
    "data-science", "data-version-control", "machine-learning", "git",
    "developer-tools", "reproducibility", "collaboration", "ai", "python"],
  "contributors": [
-    {"name": "DVC team", "type": "Other", "affiliation": "Iterative"}]
+    {"name": "DVC team", "type": "Other", "affiliation": "Treeverse"}]
 }
@@ -6,8 +6,8 @@ message: >-
 type: software
 authors:
  - name: The DVC team and contributors
-    website: 'https://github.com/iterative'
-repository-code: 'https://github.com/iterative/dvc'
+    website: 'https://github.com/treeverse'
+repository-code: 'https://github.com/treeverse/dvc'
 url: 'https://dvc.org'
 abstract: >-
  DVC is a tool for data science that takes advantage of existing software engineering toolset.
@@ -186,7 +186,7 @@
      same "printed page" as the copyright notice for easier
      identification within third-party archives.

-   Copyright 2017-2021 Iterative, Inc.
+   Copyright 2025 Treeverse.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
@@ -167,7 +167,7 @@ To install the development version, run:

 .. code-block:: bash

-   pip install git+git://github.com/iterative/dvc
+   pip install "dvc @ git+https://github.com/treeverse/dvc"

 Package (Platform-specific)
 ---------------------------
@@ -175,7 +175,7 @@ Package (Platform-specific)
 |Packages|

 Self-contained packages for Linux, Windows, and Mac are available.
-The latest version of the packages can be found on the GitHub `releases page <https://github.com/iterative/dvc/releases>`_.
+The latest version of the packages can be found on the GitHub `releases page <https://github.com/treeverse/dvc/releases>`_.

 Ubuntu / Debian (deb)
 ^^^^^^^^^^^^^^^^^^^^^
@@ -198,8 +198,6 @@ Fedora / CentOS (rpm)
 Contributing
 ============

-|Maintainability|
-
 Contributions are welcome!
 Please see our `Contributing Guide <https://dvc.org/doc/user-guide/contributing/core>`_ for more details.
 Thanks to all our contributors!
@@ -213,7 +211,7 @@ Community and Support
 * `Forum <https://discuss.dvc.org/>`_
 * `Discord Chat <https://dvc.org/chat>`_
 * `Email <mailto:[email protected]>`_
-* `Mailing List <https://sweedom.us10.list-manage.com/subscribe/post?u=a08bf93caae4063c4e6a351f6&id=24c0ecc49a>`_
+* `Mailing List <https://dvc.org/community#subscribe>`_

 Copyright
 =========
@@ -237,23 +235,19 @@ Barrak, A., Eghan, E.E. and Adams, B. `On the Co-evolution of ML Pipelines and S
   :target: https://dvc.org
   :alt: DVC logo

-.. |VS Code Extension Overview| image:: https://raw.githubusercontent.com/iterative/vscode-dvc/main/extension/docs/overview.gif
+.. |VS Code Extension Overview| image:: https://raw.githubusercontent.com/treeverse/vscode-dvc/main/extension/docs/overview.gif
   :alt: DVC Extension for VS Code

-.. |CI| image:: https://github.com/iterative/dvc/workflows/Tests/badge.svg?branch=main
-   :target: https://github.com/iterative/dvc/actions
+.. |CI| image:: https://github.com/treeverse/dvc/actions/workflows/tests.yaml/badge.svg
+   :target: https://github.com/treeverse/dvc/actions/workflows/tests.yaml
   :alt: GHA Tests

-.. |Maintainability| image:: https://codeclimate.com/github/iterative/dvc/badges/gpa.svg
-   :target: https://codeclimate.com/github/iterative/dvc
-   :alt: Code Climate
-
 .. |Python Version| image:: https://img.shields.io/pypi/pyversions/dvc
   :target: https://pypi.org/project/dvc
   :alt: Python Version

-.. |Coverage| image:: https://codecov.io/gh/iterative/dvc/branch/main/graph/badge.svg
-   :target: https://codecov.io/gh/iterative/dvc
+.. |Coverage| image:: https://codecov.io/gh/treeverse/dvc/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/treeverse/dvc
   :alt: Codecov

 .. |Snap| image:: https://img.shields.io/badge/snap-install-82BEA0.svg?logo=snapcraft
@@ -268,7 +262,7 @@ Barrak, A., Eghan, E.E. and Adams, B. `On the Co-evolution of ML Pipelines and S
   :target: https://formulae.brew.sh/formula/dvc
   :alt: Homebrew

-.. |Conda| image:: https://img.shields.io/conda/v/conda-forge/dvc.svg?label=conda&logo=conda-forge
+.. |Conda| image:: https://anaconda.org/conda-forge/dvc/badges/version.svg
   :target: https://anaconda.org/conda-forge/dvc
   :alt: Conda-forge

@@ -292,8 +286,8 @@ Barrak, A., Eghan, E.E. and Adams, B. `On the Co-evolution of ML Pipelines and S
   :target: https://dvc.org/img/flow.gif
   :alt: how_dvc_works

-.. |Contribs| image:: https://contrib.rocks/image?repo=iterative/dvc
-   :target: https://github.com/iterative/dvc/graphs/contributors
+.. |Contribs| image:: https://contrib.rocks/image?repo=treeverse/dvc
+   :target: https://github.com/treeverse/dvc/graphs/contributors
   :alt: Contributors

 .. |VS Code| image:: https://img.shields.io/visual-studio-marketplace/v/Iterative.dvc?color=blue&label=VSCode&logo=visualstudiocode&logoColor=blue
@@ -14,7 +14,7 @@ def viztracer_profile(
    log_async: bool = False,
 ):
    try:
-        import viztracer
+        import viztracer  # ty: ignore[unresolved-import]
    except ImportError:
        print("Failed to run profiler, viztracer is not installed")  # noqa: T201
        yield
@@ -37,7 +37,7 @@ def yappi_profile(
    separate_threads: Optional[bool] = False,
 ):
    try:
-        import yappi
+        import yappi  # ty: ignore[unresolved-import]
    except ImportError:
        print("Failed to run profiler, yappi is not installed")  # noqa: T201
        yield
@@ -79,7 +79,7 @@ def yappi_profile(
 def instrument(html_output=False):
    """Run a statistical profiler"""
    try:
-        from pyinstrument import Profiler
+        from pyinstrument import Profiler  # ty: ignore[unresolved-import]
    except ImportError:
        print("Failed to run profiler, pyinstrument is not installed")  # noqa: T201
        yield
@@ -123,7 +123,7 @@ def debug():
        yield
    except Exception:
        try:
-            import ipdb as pdb  # noqa: T100
+            import ipdb as pdb  # noqa: T100  # ty: ignore[unresolved-import]
        except ImportError:
            import pdb  # type: ignore[no-redef]  # noqa: T100
        pdb.post_mortem()
@@ -206,7 +206,7 @@ def add_debugging_flags(parser):
    from argparse import SUPPRESS

    # For detailed info see:
-    # https://github.com/iterative/dvc/wiki/Debugging,-Profiling-and-Benchmarking-DVC
+    # https://github.com/treeverse/dvc/wiki/Debugging,-Profiling-and-Benchmarking-DVC
    args, _ = parser.parse_known_args()
    verbose = args.verbose

@@ -1,10 +1,14 @@
 import json
 import os
+from typing import TYPE_CHECKING, Optional

 from dvc.log import logger

 from .env import DVC_ANALYTICS_ENDPOINT, DVC_NO_ANALYTICS

+if TYPE_CHECKING:
+    from dvc.scm import Base
+
 logger = logger.getChild(__name__)


@@ -67,6 +71,7 @@ def send(path):
    thus, the need of removing such file afterwards.
    """
    import requests
+    from requests.exceptions import RequestException

    url = os.environ.get(DVC_ANALYTICS_ENDPOINT, "https://analytics.dvc.org")
    headers = {"content-type": "application/json"}
@@ -81,7 +86,7 @@ def send(path):

    try:
        requests.post(url, json=report, headers=headers, timeout=5)
-    except requests.exceptions.RequestException as e:
+    except RequestException as e:
        logger.trace("", exc_info=True)
        logger.debug("failed to send analytics report %s", str(e))

@@ -89,20 +94,62 @@ def send(path):
    os.remove(path)


-def _scm_in_use():
-    from dvc.exceptions import NotDvcRepoError
-    from dvc.repo import Repo
-    from dvc.scm import NoSCM
+def _git_remote_url(scm: Optional["Base"]) -> Optional[str]:
+    from dvc.scm import Git

-    from .scm import SCM, SCMError
+    if not isinstance(scm, Git):
+        return None
+
+    from dulwich.porcelain import get_remote_repo
+
+    dulwich_repo = scm.dulwich.repo
+    try:
+        _remote, url = get_remote_repo(dulwich_repo)
+    except IndexError:
+        # IndexError happens when the head is detached
+        _remote, url = get_remote_repo(dulwich_repo, b"origin")
+    # Dulwich returns (None, "origin") if no remote set
+    if (_remote, url) == (None, "origin"):
+        return None
+    return url
+
+
+def _scm_in_use(scm: Optional["Base"]) -> Optional[str]:
+    return type(scm).__name__ if scm else None
+
+
+def _parse_git_remote_path(remote_url: str) -> str:
+    from urllib.parse import urlparse
+
+    from scmrepo.urls import is_scp_style_url
+
+    parsed = urlparse(remote_url)
+    # Windows Path also gets parsed with a drive letter as scheme
+    # https://github.com/python/cpython/issues/86381
+    if parsed.scheme and parsed.scheme in ("http", "https", "git", "ssh"):
+        return parsed.path.strip("/")
+
+    if is_scp_style_url(remote_url):
+        # handle scp-style URL
+        parts = remote_url.split(":", 1)
+        if len(parts) == 2:
+            _, path = parts
+            return path.rstrip("/")
+    return remote_url
+
+
+def _git_remote_path_hash(scm: Optional["Base"]) -> Optional[str]:
+    """Return a hash of the git remote path."""
+    import hashlib

    try:
-        scm = SCM(root_dir=Repo.find_root())
-        return type(scm).__name__
-    except SCMError:
-        return NoSCM.__name__
-    except NotDvcRepoError:
-        pass
+        if remote_url := _git_remote_url(scm):
+            path = _parse_git_remote_path(remote_url)
+            h = hashlib.md5(path.encode("utf-8"), usedforsecurity=False)  # for FIPS
+            return h.hexdigest()
+    except Exception:  # noqa: BLE001
+        logger.debug("Failed to get git remote path", exc_info=True)
+    return None


 def _runtime_info():
@@ -112,6 +159,8 @@ def _runtime_info():
    from iterative_telemetry import _generate_ci_id, find_or_create_user_id

    from dvc import __version__
+    from dvc.info import _get_remotes
+    from dvc.repo import Repo
    from dvc.utils import is_binary

    ci_id = _generate_ci_id()
@@ -120,13 +169,24 @@ def _runtime_info():
    else:
        group_id, user_id = None, find_or_create_user_id()

+    scm = None
+    remotes = None
+    try:
+        repo = Repo()
+        scm = repo.scm
+        remotes = _get_remotes(repo.config)
+    except Exception as exc:  # noqa: BLE001
+        logger.debug("failed to open repo: %s", exc)
+
    return {
        "dvc_version": __version__,
        "is_binary": is_binary(),
-        "scm_class": _scm_in_use(),
+        "scm_class": _scm_in_use(scm),
        "system_info": _system_info(),
        "user_id": user_id,
        "group_id": group_id,
+        "remotes": remotes,
+        "git_remote_hash": _git_remote_path_hash(scm),
    }


@@ -64,3 +64,4 @@ def get(name: str) -> Union[DatachainDataset, DVCDataset, URLDataset]:
            for file in dataset.lock.files
        ]
        return URLDataset(type="url", files=files, path=versioned_path)
+    raise AssertionError("unreachable")
@@ -86,7 +86,7 @@ class CacheManager:
        return FileStorage(
            key=(),
            fs=self.local.fs,
-            path=self.local.fs.join(self.default_local_cache_dir, self.FS_DIR),
+            path=self.local.fs.join(self.local_cache_dir, self.FS_DIR),
        )

    def _init_odb(self, schemes):
@@ -96,7 +96,7 @@ def _log_exceptions(exc: Exception) -> Optional[int]:
                f"See {link} for more info."
            )
        else:
-            link = format_link("https://github.com/iterative/dvc/issues")
+            link = format_link("https://github.com/treeverse/dvc/issues")
            hint = f"\nPlease report this bug to {link}. Thank you!"

        logger.exception(
@@ -157,6 +157,8 @@ def main(argv=None):  # noqa: C901, PLR0912, PLR0915
    Returns:
        int: command's return code.
    """
+    from contextlib import ExitStack
+
    from dvc._debug import debugtools
    from dvc.config import ConfigError
    from dvc.exceptions import DvcException, NotDvcRepoError
@@ -173,12 +175,11 @@ def main(argv=None):  # noqa: C901, PLR0912, PLR0915
        logging.disable(logging.INFO)

    args = None
-
-    outer_log_level = logger.level
-    level = None
+    stack = ExitStack()
    try:
        args = parse_args(argv)

+        level = None
        if args.quiet:
            level = logging.CRITICAL
        elif args.verbose == 1:
@@ -187,7 +188,7 @@ def main(argv=None):  # noqa: C901, PLR0912, PLR0915
            level = logging.TRACE  # type: ignore[attr-defined]

        if level is not None:
-            set_loggers_level(level)
+            stack.enter_context(set_loggers_level(level))

        if level and level <= logging.DEBUG:
            from platform import platform, python_implementation, python_version
@@ -247,7 +248,7 @@ def main(argv=None):  # noqa: C901, PLR0912, PLR0915

        return ret
    finally:
-        logger.setLevel(outer_log_level)
+        stack.close()

        from dvc.repo.open_repo import clean_repos

@@ -18,7 +18,10 @@ class CmdBase(ABC):

        os.chdir(args.cd)

-        self.repo: Repo = Repo(uninitialized=self.UNINITIALIZED)
+        self.repo: Repo = Repo(
+            uninitialized=self.UNINITIALIZED,
+            _wait_for_lock=args.wait_for_lock,
+        )
        self.config: Config = self.repo.config
        self.args = args

@@ -22,6 +22,15 @@ _dvc_compgen_exps() {
    local _dvc_exps=($(dvc exp list -q --all-commits --names-only))
    compgen -W "${_dvc_exps[*]}" -- $1
 }
+
+_dvc_compgen_remotes() {
+    local _dvc_remotes=($(dvc remote list | cut -d' ' -f1))
+    compgen -W "${_dvc_remotes[*]}" -- $1
+}
+
+_dvc_compgen_config_vars() {
+    compgen -W "${_dvc_config_vars[*]}" -- $1
+}
 """

 ZSH_PREAMBLE = """
@@ -55,6 +64,14 @@ _dvc_compadd_stages_and_files() {
 _dvc_compadd_exps() {
    _describe 'experiments' "($(dvc exp list -q --all-commits --names-only))"
 }
+
+_dvc_compadd_remotes() {
+    _describe 'remotes' "($(dvc remote list | cut -d' ' -f1))"
+}
+
+_dvc_compadd_config_vars() {
+    _describe 'config_vars' _dvc_config_vars
+}
 """

 PREAMBLE = {
@@ -71,3 +88,22 @@ DVCFILES_AND_STAGE = {
    "zsh": "_dvc_compadd_stages_and_files",
 }
 EXPERIMENT = {"bash": "_dvc_compgen_exps", "zsh": "_dvc_compadd_exps"}
+REMOTE = {"bash": "_dvc_compgen_remotes", "zsh": "_dvc_compadd_remotes"}
+CONFIG_VARS = {"bash": "_dvc_compgen_config_vars", "zsh": "_dvc_compadd_config_vars"}
+
+
+def get_preamble() -> dict[str, str]:
+    from dvc.config_schema import config_vars_for_completion
+
+    ret: dict[str, str] = {}
+    config_vars = list(config_vars_for_completion())
+
+    nl = "\n\t".expandtabs(4)
+    config_vars_arr = f"""
+_dvc_config_vars=(
+    {nl.join(config_vars)}
+)
+"""
+    for shell, preamble in PREAMBLE.items():
+        ret[shell] = config_vars_arr + preamble
+    return ret
@@ -200,6 +200,14 @@ def get_main_parser():
        type=str,
    )

+    parser.add_argument(
+        "--wait-for-lock",
+        action="store_true",
+        default=False,
+        help="Wait for the lock if it is already held by another process, instead of"
+        " failing immediately.",
+    )
+
    # Sub commands
    subparsers = parser.add_subparsers(
        title="Available Commands",
@@ -101,7 +101,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        help="Remote storage to download to",
        metavar="<name>",
-    )
+    ).complete = completion.REMOTE
    parser.add_argument(
        "--remote-jobs",
        type=int,
@@ -149,7 +149,7 @@ def add_parser(subparsers, parent_parser):
            "Remote name to set as a default in the target repository "
            "(only applicable when downloading from DVC remote)."
        ),
-    )
+    ).complete = completion.REMOTE
    get_parser.add_argument(
        "--remote-config",
        type=str,
@@ -1,20 +1,28 @@
+from typing import TYPE_CHECKING
+
 from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBase
 from dvc.cli.utils import append_doc_link
 from dvc.ui import ui

+if TYPE_CHECKING:
+    from dvc.ignore import CheckIgnoreResult
+

 class CmdCheckIgnore(CmdBase):
    def __init__(self, args):
        super().__init__(args)
        self.ignore_filter = self.repo.dvcignore

-    def _show_results(self, result):
-        if not result.match and not self.args.non_matching:
-            return
+    def _show_results(self, result: "CheckIgnoreResult"):
+        if not result.match and not self.args.details:
+            return None

        if self.args.details:
-            patterns = result.patterns
+            pattern_infos = result.pattern_infos
+            patterns = [str(pi) for pi in pattern_infos]
+            if not patterns and self.args.non_matching:
+                patterns = ["::"]
            if not self.args.all:
                patterns = patterns[-1:]

@@ -22,13 +30,11 @@ class CmdCheckIgnore(CmdBase):
                ui.write(pattern, result.file, sep="\t")
        else:
            ui.write(result.file)
+        return bool(result.pattern_infos)

    def _check_one_file(self, target):
        result = self.ignore_filter.check_ignore(target)
-        self._show_results(result)
-        if result.match:
-            return 0
-        return 1
+        return bool(self._show_results(result))

    def _interactive_mode(self):
        ret = 1
@@ -39,14 +45,14 @@ class CmdCheckIgnore(CmdBase):
                break
            if not target:
                break
-            if not self._check_one_file(target):
+            if self._check_one_file(target):
                ret = 0
        return ret

    def _normal_mode(self):
        ret = 1
        for target in self.args.targets:
-            if not self._check_one_file(target):
+            if self._check_one_file(target):
                ret = 0
        return ret

@@ -76,6 +82,8 @@ class CmdCheckIgnore(CmdBase):


 def add_parser(subparsers, parent_parser):
+    import argparse
+
    ADD_HELP = "Check whether files or directories are excluded due to `.dvcignore`."

    parser = subparsers.add_parser(
@@ -93,14 +101,7 @@ def add_parser(subparsers, parent_parser):
        help="Show the exclude patterns along with each target path.",
    )
    parser.add_argument(
-        "-a",
-        "--all",
-        action="store_true",
-        default=False,
-        help=(
-            "Include the target paths which don't match any pattern "
-            "in the `--details` list."
-        ),
+        "-a", "--all", action="store_true", default=False, help=argparse.SUPPRESS
    )
    parser.add_argument(
        "-n",
@@ -1,5 +1,3 @@
-import operator
-
 from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBase
 from dvc.cli.utils import append_doc_link
@@ -30,7 +28,7 @@ class CmdCheckout(CmdBase):

        stats, exc = None, None
        try:
-            stats = self.repo.checkout(
+            result = self.repo.checkout(
                targets=self.args.targets,
                with_deps=self.args.with_deps,
                force=self.args.force,
@@ -40,14 +38,17 @@ class CmdCheckout(CmdBase):
            )
        except CheckoutError as _exc:
            exc = _exc
-            stats = exc.stats
+            result = exc.result

        if self.args.summary:
            default_message = "No changes."
-            msg = get_summary(sorted(stats.items(), key=operator.itemgetter(0)))
+            stats = result["stats"]
+            assert isinstance(stats, dict)
+            msg = get_summary(stats.items())
            ui.write(msg or default_message)
        else:
-            log_changes(stats)
+            result.pop("stats", {})
+            log_changes(result)

        if exc:
            raise exc
@@ -1,6 +1,6 @@
 from dvc.cli import formatter
 from dvc.cli.command import CmdBaseNoRepo
-from dvc.cli.completion import PREAMBLE
+from dvc.cli.completion import get_preamble
 from dvc.cli.utils import append_doc_link
 from dvc.log import logger
 from dvc.ui import ui
@@ -17,7 +17,7 @@ class CmdCompletion(CmdBaseNoRepo):

        shell = self.args.shell
        parser = self.args.parser
-        script = shtab.complete(parser, shell=shell, preamble=PREAMBLE)
+        script = shtab.complete(parser, shell=shell, preamble=get_preamble())
        ui.write(script, force=True)
        return 0

@@ -3,7 +3,7 @@ import os

 from funcy import set_in

-from dvc.cli import formatter
+from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBaseNoRepo
 from dvc.cli.utils import append_doc_link
 from dvc.log import logger
@@ -224,7 +224,7 @@ def add_parser(subparsers, parent_parser):
        nargs="?",
        type=_name_type,
        help="Option name (section.option or remote.name.option).",
-    )
+    ).complete = completion.CONFIG_VARS
    config_parser.add_argument("value", nargs="?", help="Option value.")
    config_parser.add_argument(
        "-l",
@@ -2,7 +2,7 @@ from typing import TYPE_CHECKING, ClassVar

 from funcy import chunks, compact, log_durations

-from dvc.cli import formatter
+from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBase
 from dvc.cli.utils import append_doc_link
 from dvc.log import logger
@@ -10,6 +10,7 @@ from dvc.ui import ui
 from dvc.utils import colorize

 if TYPE_CHECKING:
+    from dvc.repo.data import GitInfo
    from dvc.repo.data import Status as DataStatus


@@ -55,20 +56,15 @@ class CmdDataStatus(CmdBase):
    def _process_status(status: "DataStatus"):
        """Flatten stage status, and filter empty stage status contents."""
        for stage, stage_status in status.items():
-            items = stage_status
-            if isinstance(stage_status, dict):
-                items = {
-                    file: state
-                    for state, files in stage_status.items()
-                    for file in files
-                }
-            if not items:
+            if not stage_status or (
+                isinstance(stage_status, dict) and not any(stage_status.values())
+            ):
                continue
-            yield stage, items
+            yield stage, stage_status

    @classmethod
    def _show_status(cls, status: "DataStatus") -> int:  # noqa: C901
-        git_info = status.pop("git")  # type: ignore[misc]
+        git_info: GitInfo = status.pop("git")  # type: ignore[misc]
        result = dict(cls._process_status(status))
        if not result:
            no_changes = "No changes"
@@ -90,7 +86,16 @@ class CmdDataStatus(CmdBase):
                    ui.write(f"  ({hint})")

            if isinstance(stage_status, dict):
-                items = [f"{state}: {file}" for file, state in stage_status.items()]
+                items = [
+                    f"{state}: "
+                    + (
+                        " -> ".join(change.values())
+                        if isinstance(change, dict)
+                        else change
+                    )
+                    for state, changes in stage_status.items()
+                    for change in changes
+                ]
            else:
                items = stage_status

@@ -108,8 +113,10 @@ class CmdDataStatus(CmdBase):
    def run(self) -> int:
        with log_durations(logger.trace, "in data_status"):
            status = self.repo.data_status(
+                targets=self.args.targets,
                granular=self.args.granular,
                untracked_files=self.args.untracked_files,
+                remote=self.args.remote,
                not_in_remote=self.args.not_in_remote,
                remote_refresh=self.args.remote_refresh,
            )
@@ -126,9 +133,12 @@ class CmdDataStatus(CmdBase):


 def add_parser(subparsers, parent_parser):
+    data_help = "Commands related to data management."
    data_parser = subparsers.add_parser(
        "data",
        parents=[parent_parser],
+        description=append_doc_link(data_help, "data/status"),
+        help=data_help,
        formatter_class=formatter.RawDescriptionHelpFormatter,
    )
    data_subparsers = data_parser.add_subparsers(
@@ -147,6 +157,14 @@ def add_parser(subparsers, parent_parser):
        formatter_class=formatter.RawDescriptionHelpFormatter,
        help=DATA_STATUS_HELP,
    )
+    data_status_parser.add_argument(
+        "targets",
+        nargs="*",
+        help=(
+            "Limit command scope to these tracked files/directories, "
+            ".dvc files and stage names."
+        ),
+    ).complete = completion.FILE  # type: ignore[attr-defined]
    data_status_parser.add_argument(
        "--json",
        action="store_true",
@@ -173,6 +191,12 @@ def add_parser(subparsers, parent_parser):
        nargs="?",
        help="Show untracked files.",
    )
+    data_status_parser.add_argument(
+        "-r",
+        "--remote",
+        help="Remote storage to check (only applicable with --not-in-remote).",
+        metavar="<name>",
+    ).complete = completion.REMOTE
    data_status_parser.add_argument(
        "--not-in-remote",
        action="store_true",
@@ -22,17 +22,18 @@ class CmdDataBase(CmdBase):


 class CmdDataPull(CmdDataBase):
-    def log_summary(self, stats):
+    def log_summary(self, result):
        from dvc.commands.checkout import log_changes

-        log_changes(stats)
+        stats = result.pop("stats", {})
+        log_changes(result)
        super().log_summary(stats)

    def run(self):
        from dvc.exceptions import CheckoutError, DvcException

        try:
-            stats = self.repo.pull(
+            result = self.repo.pull(
                targets=self.args.targets,
                jobs=self.args.jobs,
                remote=self.args.remote,
@@ -46,10 +47,10 @@ class CmdDataPull(CmdDataBase):
                glob=self.args.glob,
                allow_missing=self.args.allow_missing,
            )
-            self.log_summary(stats)
+            self.log_summary(result)
        except (CheckoutError, DvcException) as exc:
-            if stats := getattr(exc, "stats", {}):
-                self.log_summary(stats)
+            if result := getattr(exc, "result", {}):
+                self.log_summary(result)
            logger.exception("failed to pull data from the cloud")
            return 1

@@ -149,7 +150,7 @@ def add_parser(subparsers, _parent_parser):
    )
    pull_parser.add_argument(
        "-r", "--remote", help="Remote storage to pull from", metavar="<name>"
-    )
+    ).complete = completion.REMOTE
    pull_parser.add_argument(
        "-a",
        "--all-branches",
@@ -224,7 +225,7 @@ def add_parser(subparsers, _parent_parser):
    )
    push_parser.add_argument(
        "-r", "--remote", help="Remote storage to push to", metavar="<name>"
-    )
+    ).complete = completion.REMOTE
    push_parser.add_argument(
        "-a",
        "--all-branches",
@@ -286,7 +287,7 @@ def add_parser(subparsers, _parent_parser):
    )
    fetch_parser.add_argument(
        "-r", "--remote", help="Remote storage to fetch from", metavar="<name>"
-    )
+    ).complete = completion.REMOTE
    fetch_parser.add_argument(
        "-a",
        "--all-branches",
@@ -379,7 +380,7 @@ def add_parser(subparsers, _parent_parser):
        "--remote",
        help="Remote storage to compare local cache to",
        metavar="<name>",
-    )
+    ).complete = completion.REMOTE
    status_parser.add_argument(
        "-a",
        "--all-branches",
@@ -83,7 +83,7 @@ class CmdDatasetUpdate(CmdBase):
            return CmdDatasetAdd.display(name, new, action)
        if dataset == new:
            ui.write("[yellow]Nothing to update[/]", styled=True)
-            return
+            return None

        assert new.lock

@@ -112,6 +112,7 @@ class CmdDatasetUpdate(CmdBase):
            assert new.type == "url"
            stats = diff_files(dataset.lock.files, new.lock.files)
            log_changes(stats)
+        return None

    def run(self):
        from difflib import get_close_matches
@@ -60,7 +60,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        type=str,
        help="Remote name to set as a default in the target repository.",
-    )
+    ).complete = completion.REMOTE
    du_parser.add_argument(
        "--remote-config",
        type=str,
@@ -1,6 +1,6 @@
 import argparse

-from dvc.cli import formatter
+from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBase
 from dvc.cli.utils import append_doc_link
 from dvc.log import logger
@@ -71,7 +71,7 @@ def add_parser(experiments_subparsers, parent_parser):
        dest="dvc_remote",
        metavar="<name>",
        help="Name of the DVC remote to use when pulling cached outputs.",
-    )
+    ).complete = completion.REMOTE
    experiments_pull_parser.add_argument(
        "-j",
        "--jobs",
@@ -111,7 +111,7 @@ def add_parser(experiments_subparsers, parent_parser):
        dest="dvc_remote",
        metavar="<name>",
        help="Name of the DVC remote to use when pushing cached outputs.",
-    )
+    ).complete = completion.REMOTE
    experiments_push_parser.add_argument(
        "-j",
        "--jobs",
@@ -20,6 +20,7 @@ class CmdExperimentsRun(CmdRepro):
            tmp_dir=self.args.tmp_dir,
            copy_paths=self.args.copy_paths,
            message=self.args.message,
+            no_hydra=self.args.no_hydra,
            **self._common_kwargs,
        )

@@ -107,4 +108,14 @@ def _add_run_common(parser):
        default=None,
        help="Custom commit message to use when committing the experiment.",
    )
+    parser.add_argument(
+        "--no-hydra",
+        action="store_true",
+        default=False,
+        help=(
+            "Disables automatically updating `params.yaml` with Hydra configuration. "
+            " You can still use `--set-param` to update individual params if needed."
+            " Default is False."
+        ),
+    )
    parser.add_argument("-M", dest="message", help=argparse.SUPPRESS)  # obsolete
@@ -1,6 +1,6 @@
 import argparse
 import re
-from collections.abc import Iterable
+from collections.abc import Collection, Iterable
 from datetime import date, datetime
 from typing import TYPE_CHECKING

@@ -59,17 +59,16 @@ def baseline_styler(typ):
 def show_experiments(
    td: "TabularData",
    headers: dict[str, Iterable[str]],
-    keep=None,
-    drop=None,
+    keep: Collection[str] = (),
+    drop: Collection[str] = (),
    pager=True,
    csv=False,
    markdown=False,
    **kwargs,
 ):
    if keep:
-        for col in td.keys():  # noqa: SIM118
-            if re.match(keep, col):
-                td.protect(col)
+        keep_re = re.compile("|".join(keep))
+        td.protect(*(col for col in td.keys() if keep_re.match(col)))  # noqa: SIM118

    for col in ("State", "Executor"):
        if td.is_empty(col):
@@ -110,8 +109,9 @@ def show_experiments(
        td.drop_duplicates("cols", ignore_empty=False)

    cols_to_drop = set()
-    if drop is not None:
-        cols_to_drop = {col for col in td.keys() if re.match(drop, col)}  # noqa: SIM118
+    if drop:
+        drop_re = re.compile("|".join(drop))
+        cols_to_drop = {col for col in td.keys() if drop_re.match(col)}  # noqa: SIM118
    td.drop(*cols_to_drop)

    td.render(
@@ -150,6 +150,7 @@ class CmdExperimentsShow(CmdBase):
                all_commits=self.args.all_commits,
                hide_queued=self.args.hide_queued,
                hide_failed=self.args.hide_failed,
+                hide_workspace=self.args.hide_workspace,
                revs=self.args.rev,
                num=self.args.num,
                sha_only=self.args.sha,
@@ -236,11 +237,15 @@ def add_parser(experiments_subparsers, parent_parser):
    )
    experiments_show_parser.add_argument(
        "--drop",
+        action="append",
+        default=[],
        help="Remove the columns matching the specified regex pattern.",
        metavar="<regex_pattern>",
    )
    experiments_show_parser.add_argument(
        "--keep",
+        action="append",
+        default=[],
        help="Preserve the columns matching the specified regex pattern.",
        metavar="<regex_pattern>",
    )
@@ -279,6 +284,12 @@ def add_parser(experiments_subparsers, parent_parser):
        default=False,
        help="Hide queued experiments in the table.",
    )
+    experiments_show_parser.add_argument(
+        "--hide-workspace",
+        action="store_true",
+        default=False,
+        help="Hide workspace row in the table.",
+    )
    experiments_show_parser.add_argument(
        "--json",
        action="store_true",
@@ -1,6 +1,6 @@
 import os

-from dvc.cli import formatter
+from dvc.cli import completion, formatter
 from dvc.cli.command import CmdBase
 from dvc.cli.utils import append_doc_link
 from dvc.log import logger
@@ -188,7 +188,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        help="Remote storage to collect garbage in",
        metavar="<name>",
-    )
+    ).complete = completion.REMOTE
    gc_parser.add_argument(
        "--skip-failed",
        action="store_true",
@@ -121,7 +121,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        type=str,
        help="Remote name to set as a default in the target repository.",
-    )
+    ).complete = completion.REMOTE
    get_parser.add_argument(
        "--remote-config",
        type=str,
@@ -115,7 +115,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        type=str,
        help="Remote name to set as a default in the target repository.",
-    )
+    ).complete = completion.REMOTE
    import_parser.add_argument(
        "--remote-config",
        type=str,
@@ -73,7 +73,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        help="Remote storage to download to",
        metavar="<name>",
-    )
+    ).complete = completion.REMOTE
    no_download_exec_group = import_parser.add_mutually_exclusive_group()
    no_download_exec_group.add_argument(
        "--no-exec",
@@ -29,7 +29,7 @@ def _welcome_message():
        "{yellow}------------{nc}\n"
        f"- Check out the documentation: {fmt_link('https://dvc.org/doc')}\n"
        f"- Get help and share ideas: {fmt_link('https://dvc.org/chat')}\n"
-        f"- Star us on GitHub: {fmt_link('https://github.com/iterative/dvc')}"
+        f"- Star us on GitHub: {fmt_link('https://github.com/treeverse/dvc')}"
    ).format(yellow=colorama.Fore.YELLOW, nc=colorama.Fore.RESET)

    ui.write(msg)
@@ -42,7 +42,7 @@ class CmdInit(CmdBaseNoRepo):

        try:
            with Repo.init(
-                ".",
+                self.args.directory,
                no_scm=self.args.no_scm,
                force=self.args.force,
                subdir=self.args.subdir,
@@ -57,10 +57,11 @@ class CmdInit(CmdBaseNoRepo):

 def add_parser(subparsers, parent_parser):
    """Setup parser for `dvc init`."""
-    INIT_HELP = "Initialize DVC in the current directory."
+    INIT_HELP = "Initialize DVC repository."
    INIT_DESCRIPTION = (
-        "Initialize DVC in the current directory. Expects directory\n"
-        "to be a Git repository unless --no-scm option is specified."
+        "Initialize DVC repository in the given directory (defaults to the current "
+        "working directory).\n"
+        "Expects directory to be a Git repository unless --no-scm option is specified."
    )

    init_parser = subparsers.add_parser(
@@ -70,6 +71,14 @@ def add_parser(subparsers, parent_parser):
        help=INIT_HELP,
        formatter_class=formatter.RawDescriptionHelpFormatter,
    )
+    init_parser.add_argument(
+        "directory",
+        nargs="?",
+        default=".",
+        help=(
+            "Directory to initialize DVC in. Defaults to the current working directory."
+        ),
+    )
    init_parser.add_argument(
        "--no-scm",
        action="store_true",
@@ -250,7 +250,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        type=str,
        help="Remote name to set as a default in the target repository.",
-    )
+    ).complete = completion.REMOTE
    list_parser.add_argument(
        "--remote-config",
        type=str,
@@ -1,4 +1,4 @@
-from dvc.cli import formatter
+from dvc.cli import completion, formatter
 from dvc.cli.utils import append_doc_link
 from dvc.commands.config import CmdConfig
 from dvc.ui import ui
@@ -210,7 +210,9 @@ def add_parser(subparsers, parent_parser):
        help=REMOTE_DEFAULT_HELP,
        formatter_class=formatter.RawDescriptionHelpFormatter,
    )
-    remote_default_parser.add_argument("name", nargs="?", help="Name of the remote")
+    remote_default_parser.add_argument(
+        "name", nargs="?", help="Name of the remote"
+    ).complete = completion.REMOTE
    remote_default_parser.add_argument(
        "-u",
        "--unset",
@@ -228,7 +230,9 @@ def add_parser(subparsers, parent_parser):
        help=REMOTE_MODIFY_HELP,
        formatter_class=formatter.RawDescriptionHelpFormatter,
    )
-    remote_modify_parser.add_argument("name", help="Name of the remote")
+    remote_modify_parser.add_argument(
+        "name", help="Name of the remote"
+    ).complete = completion.REMOTE
    remote_modify_parser.add_argument("option", help="Name of the option to modify.")
    remote_modify_parser.add_argument(
        "value", nargs="?", help="(optional) Value of the option."
@@ -260,7 +264,9 @@ def add_parser(subparsers, parent_parser):
        help=REMOTE_REMOVE_HELP,
        formatter_class=formatter.RawDescriptionHelpFormatter,
    )
-    remote_remove_parser.add_argument("name", help="Name of the remote to remove.")
+    remote_remove_parser.add_argument(
+        "name", help="Name of the remote to remove."
+    ).complete = completion.REMOTE
    remote_remove_parser.set_defaults(func=CmdRemoteRemove)
    REMOTE_RENAME_HELP = "Rename a DVC remote"
    remote_rename_parser = remote_subparsers.add_parser(
@@ -71,7 +71,7 @@ class CmdDataStatus(CmdDataBase):
                return 0

            if self.args.quiet:
-                return bool(st)
+                return int(bool(st))

            if st:
                self._show(st, indent)
@@ -74,7 +74,7 @@ def add_parser(subparsers, parent_parser):
        "--remote",
        help="Remote storage to perform updates to",
        metavar="<name>",
-    )
+    ).complete = completion.REMOTE
    update_parser.add_argument(
        "-j",
        "--jobs",
@@ -139,6 +139,7 @@ class Config(dict):
            return global_config_dir()
        if level == "system":
            return system_config_dir()
+        return None

    @cached_property
    def files(self) -> dict[str, str]:
@@ -340,6 +341,7 @@ class Config(dict):
                    "gdrive_user_credentials_file": func,
                    "gdrive_service_account_json_file_path": func,
                    "credentialpath": func,
+                    "configpath": func,
                    "keyfile": func,
                    "cert_path": func,
                    "key_path": func,
@@ -1,4 +1,5 @@
 import os
+from typing import TYPE_CHECKING
 from urllib.parse import urlparse

 from funcy import once, walk_values
@@ -10,6 +11,7 @@ from voluptuous import (
    Exclusive,
    Invalid,
    Lower,
+    Marker,
    Optional,
    Range,
    Schema,
@@ -17,6 +19,9 @@ from voluptuous import (

 from dvc.log import logger

+if TYPE_CHECKING:
+    from collections.abc import Iterator
+
 logger = logger.getChild(__name__)

 Bool = All(
@@ -112,17 +117,19 @@ class FeatureSchema(Schema):
        return ret


+DEPRECATED = "==DEPRECATED=="
+
 REMOTE_COMMON = {
    "url": str,
    "checksum_jobs": All(Coerce(int), Range(1)),
    "jobs": All(Coerce(int), Range(1)),
    Optional("worktree"): Bool,
-    Optional("no_traverse"): Bool,  # obsoleted
+    Optional("no_traverse", description=DEPRECATED): Bool,  # obsoleted
    Optional("version_aware"): Bool,
 }
 LOCAL_COMMON = {
    "type": supported_cache_type,
-    Optional("protected", default=False): Bool,  # obsoleted
+    Optional("protected", default=False, description=DEPRECATED): Bool,  # obsoleted
    "shared": All(Lower, Choices("group")),
    Optional("slow_link_warning", default=True): Bool,
    Optional("verify", default=False): Bool,
@@ -144,6 +151,7 @@ WEBDAV_COMMON = {
    "password": str,
    "ask_password": Bool,
    "token": str,
+    "bearer_token_command": str,
    "custom_auth_header": str,
    "cert_path": str,
    "key_path": str,
@@ -152,6 +160,127 @@ WEBDAV_COMMON = {
    Optional("verify", default=False): Bool,
 }

+REMOTE_SCHEMAS = {
+    "": LOCAL_COMMON | REMOTE_COMMON,
+    "s3": {
+        "region": str,
+        "profile": str,
+        "credentialpath": str,
+        "configpath": str,
+        "endpointurl": str,
+        "access_key_id": str,
+        "secret_access_key": str,
+        "session_token": str,
+        Optional(
+            "listobjects", default=False, description=DEPRECATED
+        ): Bool,  # obsoleted
+        Optional("use_ssl", default=True): Bool,
+        Optional("allow_anonymous_login", default=False): Bool,
+        "ssl_verify": Any(Bool, str),
+        "sse": str,
+        "sse_kms_key_id": str,
+        "sse_customer_algorithm": str,
+        "sse_customer_key": str,
+        "acl": str,
+        "grant_read": str,
+        "grant_read_acp": str,
+        "grant_write_acp": str,
+        "grant_full_control": str,
+        "cache_regions": bool,
+        "read_timeout": Coerce(int),
+        "connect_timeout": Coerce(int),
+        Optional("verify", default=False): Bool,
+        **REMOTE_COMMON,
+    },
+    "gs": {
+        "projectname": str,
+        "credentialpath": str,
+        "endpointurl": str,
+        Optional("verify", default=False): Bool,
+        Optional("allow_anonymous_login", default=False): Bool,
+        **REMOTE_COMMON,
+    },
+    "ssh": {
+        "type": supported_cache_type,
+        "port": Coerce(int),
+        "user": str,
+        "password": str,
+        "ask_password": Bool,
+        "passphrase": str,
+        "ask_passphrase": Bool,
+        "keyfile": str,
+        "timeout": Coerce(int),
+        "gss_auth": Bool,
+        "allow_agent": Bool,
+        "max_sessions": Coerce(int),
+        Optional("verify", default=False): Bool,
+        **REMOTE_COMMON,
+    },
+    "hdfs": {
+        "user": str,
+        "kerb_ticket": str,
+        "replication": int,
+        **REMOTE_COMMON,
+    },
+    "webhdfs": {
+        "kerberos": Bool,
+        "kerberos_principal": str,
+        "proxy_to": str,
+        "ssl_verify": Any(Bool, str),
+        "token": str,
+        "use_https": Bool,
+        "user": str,
+        "password": str,
+        "data_proxy_target": str,
+        Optional("verify", default=False): Bool,
+        **REMOTE_COMMON,
+    },
+    "azure": {
+        "connection_string": str,
+        "sas_token": str,
+        "account_name": str,
+        "account_key": str,
+        "tenant_id": str,
+        "client_id": str,
+        "client_secret": str,
+        "allow_anonymous_login": Bool,
+        "exclude_environment_credential": Bool,
+        "exclude_visual_studio_code_credential": Bool,
+        "exclude_shared_token_cache_credential": Bool,
+        "exclude_managed_identity_credential": Bool,
+        Optional("verify", default=False): Bool,
+        "timeout": Coerce(int),
+        "read_timeout": Coerce(int),
+        "connection_timeout": Coerce(int),
+        **REMOTE_COMMON,
+    },
+    "oss": {
+        "oss_key_id": str,
+        "oss_key_secret": str,
+        "oss_endpoint": str,
+        Optional("verify", default=True): Bool,
+        **REMOTE_COMMON,
+    },
+    "gdrive": {
+        "profile": str,
+        "gdrive_use_service_account": Bool,
+        "gdrive_client_id": str,
+        "gdrive_client_secret": str,
+        "gdrive_user_credentials_file": str,
+        "gdrive_service_account_user_email": str,
+        "gdrive_service_account_json_file_path": str,
+        Optional("gdrive_trash_only", default=False): Bool,
+        Optional("gdrive_acknowledge_abuse", default=False): Bool,
+        Optional("verify", default=True): Bool,
+        **REMOTE_COMMON,
+    },
+    "http": HTTP_COMMON | REMOTE_COMMON,
+    "https": HTTP_COMMON | REMOTE_COMMON,
+    "webdav": WEBDAV_COMMON | REMOTE_COMMON,
+    "webdavs": WEBDAV_COMMON | REMOTE_COMMON,
+    "remote": {str: object},  # Any of the above options are valid
+}
+
 SCHEMA = {
    "core": {
        "remote": Lower,
@@ -161,151 +290,37 @@ SCHEMA = {
        Optional("hardlink_lock", default=False): Bool,
        Optional("no_scm", default=False): Bool,
        Optional("autostage", default=False): Bool,
-        Optional("experiments"): Bool,  # obsoleted
+        Optional("experiments", description=DEPRECATED): Bool,  # obsoleted
        Optional("check_update", default=True): Bool,
        "site_cache_dir": str,
        "machine": Lower,
    },
    "cache": {
-        "local": str,  # obsoleted
-        "s3": str,  # obsoleted
-        "gs": str,  # obsoleted
-        "hdfs": str,  # obsoleted
-        "webhdfs": str,  # obsoleted
-        "ssh": str,  # obsoleted
-        "azure": str,  # obsoleted
+        Marker("local", description=DEPRECATED): str,  # obsoleted
+        Marker("s3", description=DEPRECATED): str,  # obsoleted
+        Marker("gs", description=DEPRECATED): str,  # obsoleted
+        Marker("hdfs", description=DEPRECATED): str,  # obsoleted
+        Marker("webhdfs", description=DEPRECATED): str,  # obsoleted
+        Marker("ssh", description=DEPRECATED): str,  # obsoleted
+        Marker("azure", description=DEPRECATED): str,  # obsoleted
        # This is for default local cache
        "dir": str,
        **LOCAL_COMMON,
    },
    "remote": {
-        str: ByUrl(
-            {
-                "": LOCAL_COMMON | REMOTE_COMMON,
-                "s3": {
-                    "region": str,
-                    "profile": str,
-                    "credentialpath": str,
-                    "configpath": str,
-                    "endpointurl": str,
-                    "access_key_id": str,
-                    "secret_access_key": str,
-                    "session_token": str,
-                    Optional("listobjects", default=False): Bool,  # obsoleted
-                    Optional("use_ssl", default=True): Bool,
-                    Optional("allow_anonymous_login", default=False): Bool,
-                    "ssl_verify": Any(Bool, str),
-                    "sse": str,
-                    "sse_kms_key_id": str,
-                    "sse_customer_algorithm": str,
-                    "sse_customer_key": str,
-                    "acl": str,
-                    "grant_read": str,
-                    "grant_read_acp": str,
-                    "grant_write_acp": str,
-                    "grant_full_control": str,
-                    "cache_regions": bool,
-                    "read_timeout": Coerce(int),
-                    "connect_timeout": Coerce(int),
-                    Optional("verify", default=False): Bool,
-                    **REMOTE_COMMON,
-                },
-                "gs": {
-                    "projectname": str,
-                    "credentialpath": str,
-                    "endpointurl": str,
-                    Optional("verify", default=False): Bool,
-                    **REMOTE_COMMON,
-                },
-                "ssh": {
-                    "type": supported_cache_type,
-                    "port": Coerce(int),
-                    "user": str,
-                    "password": str,
-                    "ask_password": Bool,
-                    "passphrase": str,
-                    "ask_passphrase": Bool,
-                    "keyfile": str,
-                    "timeout": Coerce(int),
-                    "gss_auth": Bool,
-                    "allow_agent": Bool,
-                    "max_sessions": Coerce(int),
-                    Optional("verify", default=False): Bool,
-                    **REMOTE_COMMON,
-                },
-                "hdfs": {
-                    "user": str,
-                    "kerb_ticket": str,
-                    "replication": int,
-                    **REMOTE_COMMON,
-                },
-                "webhdfs": {
-                    "kerberos": Bool,
-                    "kerberos_principal": str,
-                    "proxy_to": str,
-                    "ssl_verify": Any(Bool, str),
-                    "token": str,
-                    "use_https": Bool,
-                    "user": str,
-                    "password": str,
-                    "data_proxy_target": str,
-                    Optional("verify", default=False): Bool,
-                    **REMOTE_COMMON,
-                },
-                "azure": {
-                    "connection_string": str,
-                    "sas_token": str,
-                    "account_name": str,
-                    "account_key": str,
-                    "tenant_id": str,
-                    "client_id": str,
-                    "client_secret": str,
-                    "allow_anonymous_login": Bool,
-                    "exclude_environment_credential": Bool,
-                    "exclude_visual_studio_code_credential": Bool,
-                    "exclude_shared_token_cache_credential": Bool,
-                    "exclude_managed_identity_credential": Bool,
-                    Optional("verify", default=False): Bool,
-                    "timeout": Coerce(int),
-                    "read_timeout": Coerce(int),
-                    "connection_timeout": Coerce(int),
-                    **REMOTE_COMMON,
-                },
-                "oss": {
-                    "oss_key_id": str,
-                    "oss_key_secret": str,
-                    "oss_endpoint": str,
-                    Optional("verify", default=True): Bool,
-                    **REMOTE_COMMON,
-                },
-                "gdrive": {
-                    "profile": str,
-                    "gdrive_use_service_account": Bool,
-                    "gdrive_client_id": str,
-                    "gdrive_client_secret": str,
-                    "gdrive_user_credentials_file": str,
-                    "gdrive_service_account_user_email": str,
-                    "gdrive_service_account_json_file_path": str,
-                    Optional("gdrive_trash_only", default=False): Bool,
-                    Optional("gdrive_acknowledge_abuse", default=False): Bool,
-                    Optional("verify", default=True): Bool,
-                    **REMOTE_COMMON,
-                },
-                "http": HTTP_COMMON | REMOTE_COMMON,
-                "https": HTTP_COMMON | REMOTE_COMMON,
-                "webdav": WEBDAV_COMMON | REMOTE_COMMON,
-                "webdavs": WEBDAV_COMMON | REMOTE_COMMON,
-                "remote": {str: object},  # Any of the above options are valid
-            }
-        )
+        str: ByUrl(REMOTE_SCHEMAS),
    },
    "state": {
-        "dir": str,  # obsoleted
-        "row_limit": All(Coerce(int), Range(1)),  # obsoleted
-        "row_cleanup_quota": All(Coerce(int), Range(0, 100)),  # obsoleted
+        Marker("dir", description=DEPRECATED): str,  # obsoleted
+        Marker("row_limit", description=DEPRECATED): All(
+            Coerce(int), Range(1)
+        ),  # obsoleted
+        Marker("row_cleanup_quota", description=DEPRECATED): All(
+            Coerce(int), Range(0, 100)
+        ),  # obsoleted
    },
    "index": {
-        "dir": str,  # obsoleted
+        Marker("dir", description=DEPRECATED): str,  # obsoleted
    },
    "machine": {
        str: {
@@ -335,13 +350,13 @@ SCHEMA = {
        "out_dir": str,
    },
    "exp": {
-        "code": str,
-        "data": str,
-        "models": str,
-        "metrics": str,
-        "params": str,
-        "plots": str,
-        "live": str,
+        Marker("code", description=DEPRECATED): str,
+        Marker("data", description=DEPRECATED): str,
+        Marker("models", description=DEPRECATED): str,
+        Marker("metrics", description=DEPRECATED): str,
+        Marker("params", description=DEPRECATED): str,
+        Marker("plots", description=DEPRECATED): str,
+        Marker("live", description=DEPRECATED): str,
        "auto_push": Bool,
        "git_remote": str,
    },
@@ -370,3 +385,21 @@ SCHEMA = {
        },
    },
 }
+
+
+def config_vars_for_completion(d: dict = SCHEMA, path: str = "") -> "Iterator[str]":
+    for k, v in d.items():
+        if k in ("machine", "feature"):
+            continue
+        if isinstance(k, Marker):
+            if k.description == DEPRECATED:
+                continue
+            k = k.schema
+        if not isinstance(k, str):
+            continue
+
+        keypath = path + k
+        if isinstance(v, dict):
+            yield from config_vars_for_completion(v, keypath + ".")
+        else:
+            yield keypath
@@ -32,10 +32,10 @@ def _win_detached_subprocess(args: Sequence[str], **kwargs) -> int:
    assert os.name == "nt"

    from subprocess import (  # type: ignore[attr-defined]
-        CREATE_NEW_PROCESS_GROUP,
-        CREATE_NO_WINDOW,
-        STARTF_USESHOWWINDOW,
-        STARTUPINFO,
+        CREATE_NEW_PROCESS_GROUP,  # ty: ignore[unresolved-import]
+        CREATE_NO_WINDOW,  # ty: ignore[unresolved-import]
+        STARTF_USESHOWWINDOW,  # ty: ignore[unresolved-import]
+        STARTUPINFO,  # ty: ignore[unresolved-import]
    )

    # https://stackoverflow.com/a/7006424
@@ -195,7 +195,7 @@ def _build_sugiyama_layout(vertices, edges):

    sug.yspace = VertexViewer.HEIGHT
    sug.xspace = minw
-    sug.route_edge = route_with_lines
+    sug.route_edge = route_with_lines  # ty: ignore[unresolved-attribute]

    sug.draw()

@@ -84,7 +84,7 @@ class Client:
        except Exception as exc:
            if callable(onerror):
                onerror()
-            logger.exception(
+            logger.exception(  # noqa: LOG007
                "Could not connect to the database. "
                "Check your database credentials and try again.",
                exc_info=False,
@@ -41,7 +41,7 @@ def _get(stage, p, info, **kwargs):
    return Dependency(stage, p, info, **kwargs)


-def loadd_from(stage, d_list):
+def loadd_from(stage, d_list) -> list[Dependency]:
    ret = []
    for d in d_list:
        p = d.pop(Output.PARAM_PATH, None)
@@ -110,6 +110,7 @@ class ParamsDependency(Dependency):
        except MissingParamsFile:
            return {}

+        assert self.repo
        try:
            return read_param_file(
                self.repo.fs,
@@ -150,11 +150,12 @@ class RepoDependency(Dependency):
        # local cache instead of the remote's cache. This avoids re-streaming of data,
        # but messes up the call to `_get_remote_config()` downstream, which will need
        # to ignore cache parameters.
+        assert self.repo
        config["cache"] = self.repo.config["cache"]
        config["cache"]["dir"] = self.repo.cache.local_cache_dir

        return DVCFileSystem(
-            url=self.def_repo[self.PARAM_URL],
+            repo=self.def_repo[self.PARAM_URL],
            rev=rev or self._get_rev(locked=locked),
            subrepos=True,
            config=config,
@@ -1,4 +1,5 @@
 import os
+from typing import Optional

 import platformdirs

@@ -20,10 +21,16 @@ def global_config_dir():
    )


-def site_cache_dir():
+def site_cache_dir(config_site_cache_dir: Optional[str] = None):
    from platformdirs import PlatformDirs
    from platformdirs.unix import Unix

+    if dvc_site_cache_dir := os.getenv(env.DVC_SITE_CACHE_DIR):
+        return dvc_site_cache_dir
+
+    if config_site_cache_dir is not None:
+        return config_site_cache_dir
+
    if issubclass(Unix, PlatformDirs):
        # Return the cache directory shared by users, e.g. `/var/tmp/$appname`
        # NOTE: platformdirs>=5 changed `site_cache_dir` to return /var/cache/$appname.
@@ -34,6 +41,4 @@ def site_cache_dir():
        #        In the future, consider migrating to a more secure directory.
        return f"/var/tmp/{APPNAME}"  # noqa: S108

-    return os.getenv(env.DVC_SITE_CACHE_DIR) or platformdirs.site_cache_dir(
-        APPNAME, APPAUTHOR, opinion=True
-    )
+    return platformdirs.site_cache_dir(APPNAME, APPAUTHOR, opinion=True)
@@ -162,6 +162,9 @@ class FileMixin:
    def dump(self, stage, **kwargs):
        raise NotImplementedError

+    def dump_stages(self, stages, **kwargs):
+        raise NotImplementedError
+
    def merge(self, ancestor, other, allowed=None):
        raise NotImplementedError

@@ -198,6 +201,13 @@ class SingleStageFile(FileMixin):
        dump_yaml(self.path, serialize.to_single_stage_file(stage, **kwargs))
        self.repo.scm_context.track_file(self.relpath)

+    def dump_stages(self, stages, **kwargs) -> None:
+        if not stages:
+            return None
+
+        assert len(stages) == 1, "SingleStageFile can only dump one stage."
+        return self.dump(stages[0], **kwargs)
+
    def remove_stage(self, stage):  # noqa: ARG002
        self.remove()

@@ -228,17 +238,27 @@ class ProjectFile(FileMixin):

    def dump(self, stage, update_pipeline=True, update_lock=True, **kwargs):
        """Dumps given stage appropriately in the dvcfile."""
+        return self.dump_stages(
+            [stage], update_pipeline=update_pipeline, update_lock=update_lock, **kwargs
+        )
+
+    def dump_stages(self, stages, update_pipeline=True, update_lock=True, **kwargs):
        from dvc.stage import PipelineStage

-        assert isinstance(stage, PipelineStage)
+        if not stages:
+            return
+
+        for stage in stages:
+            assert isinstance(stage, PipelineStage)
+
        if self.verify:
            check_dvcfile_path(self.repo, self.path)

-        if update_pipeline and not stage.is_data_source:
-            self._dump_pipeline_file(stage)
+        if update_pipeline:
+            self._dump_pipeline_file(stages)

        if update_lock:
-            self._dump_lockfile(stage, **kwargs)
+            self._dump_lockfile(stages, **kwargs)

    def dump_dataset(self, dataset):
        with modify_yaml(self.path, fs=self.repo.fs) as data:
@@ -260,32 +280,37 @@ class ProjectFile(FileMixin):
                raw.append(dataset)
        self.repo.scm_context.track_file(self.relpath)

-    def _dump_lockfile(self, stage, **kwargs):
-        self._lockfile.dump(stage, **kwargs)
+    def _dump_lockfile(self, stages, **kwargs):
+        self._lockfile.dump_stages(stages, **kwargs)

    @staticmethod
    def _check_if_parametrized(stage, action: str = "dump") -> None:
        if stage.raw_data.parametrized:
            raise ParametrizedDumpError(f"cannot {action} a parametrized {stage}")

-    def _dump_pipeline_file(self, stage):
-        self._check_if_parametrized(stage)
-        stage_data = serialize.to_pipeline_file(stage)
+    def _dump_pipeline_file(self, stages):
+        stages = stages if isinstance(stages, list) else [stages]
+        if not stages:
+            return
+
+        for stage in stages:
+            self._check_if_parametrized(stage)

        with modify_yaml(self.path, fs=self.repo.fs) as data:
            if not data:
                logger.info("Creating '%s'", self.relpath)

            data["stages"] = data.get("stages", {})
-            existing_entry = stage.name in data["stages"]
-            action = "Modifying" if existing_entry else "Adding"
-            logger.info("%s stage '%s' in '%s'", action, stage.name, self.relpath)
-
-            if existing_entry:
-                orig_stage_data = data["stages"][stage.name]
-                apply_diff(stage_data[stage.name], orig_stage_data)
-            else:
-                data["stages"].update(stage_data)
+            for stage in stages:
+                stage_data = serialize.to_pipeline_file(stage)
+                existing_entry = stage.name in data["stages"]
+                action = "Modifying" if existing_entry else "Adding"
+                logger.info("%s stage '%s' in '%s'", action, stage.name, self.relpath)
+                if existing_entry:
+                    orig_stage_data = data["stages"][stage.name]
+                    apply_diff(stage_data[stage.name], orig_stage_data)
+                else:
+                    data["stages"].update(stage_data)

        self.repo.scm_context.track_file(self.relpath)

@@ -399,9 +424,12 @@ class Lockfile(FileMixin):
            data.setdefault("stages", {})
        self.repo.scm_context.track_file(self.relpath)

-    def dump(self, stage, **kwargs):
-        stage_data = serialize.to_lockfile(stage, **kwargs)
+    def dump_stages(self, stages, **kwargs):
+        if not stages:
+            return

+        is_modified = False
+        log_updated = False
        with modify_yaml(self.path, fs=self.repo.fs) as data:
            if not data:
                data.update({"schema": "2.0"})
@@ -409,17 +437,24 @@ class Lockfile(FileMixin):
                logger.info("Generating lock file '%s'", self.relpath)

            data["stages"] = data.get("stages", {})
-            modified = data["stages"].get(stage.name, {}) != stage_data.get(
-                stage.name, {}
-            )
-            if modified:
-                logger.info("Updating lock file '%s'", self.relpath)
+            for stage in stages:
+                stage_data = serialize.to_lockfile(stage, **kwargs)
+                modified = data["stages"].get(stage.name, {}) != stage_data.get(
+                    stage.name, {}
+                )
+                if modified:
+                    is_modified = True
+                    if not log_updated:
+                        logger.info("Updating lock file '%s'", self.relpath)
+                        log_updated = True
+                data["stages"].update(stage_data)

-            data["stages"].update(stage_data)
-
-        if modified:
+        if is_modified:
            self.repo.scm_context.track_file(self.relpath)

+    def dump(self, stage, **kwargs):
+        self.dump_stages([stage], **kwargs)
+
    def remove_stage(self, stage):
        if not self.exists():
            return
@@ -9,7 +9,7 @@ if TYPE_CHECKING:
    from dvc.stage import Stage


-class DvcException(Exception):
+class DvcException(Exception):  # noqa: N818
    """Base class for all dvc exceptions."""

    def __init__(self, msg, *args):
@@ -242,11 +242,11 @@ class UploadError(FileTransferError):


 class CheckoutError(DvcException):
-    def __init__(self, target_infos: list[str], stats: dict[str, list[str]]):
+    def __init__(self, target_infos: list[str], result: dict):
        from dvc.utils import error_link

        self.target_infos = target_infos
-        self.stats = stats
+        self.result = result
        targets = [str(t) for t in target_infos]
        m = (
            "Checkout failed for following targets:\n{}\nIs your "
@@ -1,8 +1,8 @@
 from contextlib import ExitStack
 from typing import TYPE_CHECKING, BinaryIO, Optional, Union

-import fsspec
 from fsspec.callbacks import DEFAULT_CALLBACK, Callback  # noqa: F401
+from fsspec.callbacks import TqdmCallback as _TqdmCallback

 from dvc.progress import Tqdm
 from dvc.utils.objects import cached_property
@@ -14,7 +14,7 @@ if TYPE_CHECKING:
    from dvc.ui._rich_progress import RichTransferProgress


-class TqdmCallback(fsspec.callbacks.TqdmCallback):
+class TqdmCallback(_TqdmCallback):
    def __init__(
        self,
        size: Optional[int] = None,
@@ -83,11 +83,10 @@ class _DVCFileSystem(AbstractFileSystem):
    cachable = False
    root_marker = "/"

-    def __init__(  # noqa: PLR0913
+    def __init__(
        self,
-        url: Optional[str] = None,
+        repo: Union["Repo", os.PathLike[str], str, None] = None,
        rev: Optional[str] = None,
-        repo: Optional["Repo"] = None,
        subrepos: bool = False,
        repo_factory: Optional[RepoFactory] = None,
        fo: Optional[str] = None,
@@ -101,7 +100,8 @@ class _DVCFileSystem(AbstractFileSystem):
        """DVC + git-tracked files fs.

        Args:
-            path (str, optional): URL or path to a DVC/Git repository.
+            repo (str | os.PathLike[str] | Repo, optional): A url or a path to a DVC/Git
+                repository, or a `Repo` instance.
                Defaults to a DVC repository in the current working directory.
                Both HTTP and SSH protocols are supported for remote Git repos
                (e.g. [user@]server:project.git).
@@ -111,7 +111,6 @@ class _DVCFileSystem(AbstractFileSystem):
                In case of a local repository, if rev is unspecified, it will
                default to the working directory.
                If the repo is not a Git repo, this option is ignored.
-            repo (:obj:`Repo`, optional): `Repo` instance.
            subrepos (bool): traverse to subrepos.
                By default, it ignores subrepos.
            repo_factory (callable): A function to initialize subrepo with.
@@ -136,13 +135,23 @@ class _DVCFileSystem(AbstractFileSystem):
            ...    rev="main",
            ... )
        """
+        from dvc.repo import Repo
+
+        # kwargs.get("url") is for maintaining backward compatibility
+        repo = repo or fo or kwargs.get("url")
+        if isinstance(repo, Repo):
+            self._repo: Optional[Repo] = repo
+            url = None
+        else:
+            self._repo = None
+            url = os.fspath(repo) if repo else None
+
        super().__init__()
-        self._repo = repo
        self._repo_factory = repo_factory
        self._traverse_subrepos = subrepos
        self._repo_stack = ExitStack()
        self._repo_kwargs = {
-            "url": url if url is not None else fo,
+            "url": url,
            "rev": rev,
            "subrepos": subrepos,
            "config": config,
@@ -15,7 +15,7 @@ Examples

 from urllib.parse import urlsplit

-from upath import UPath
+from upath import UPath  # ty: ignore[unresolved-import]


 class DVCPath(UPath):
@@ -1,8 +1,9 @@
+import functools
 import os
 import re
-from collections import namedtuple
+from collections.abc import Iterable, Iterator
 from itertools import chain, groupby, takewhile
-from typing import TYPE_CHECKING, Optional
+from typing import TYPE_CHECKING, Any, Literal, NamedTuple, Optional, Union, overload

 from pathspec.patterns import GitWildMatchPattern
 from pathspec.util import normalize_file
@@ -13,7 +14,9 @@ from dvc.log import logger
 from dvc.pathspec_math import PatternInfo, merge_patterns

 if TYPE_CHECKING:
-    from dvc.fs import AnyFSPath, FileSystem
+    from typing_extensions import Self
+
+    from dvc.fs import FileSystem

 logger = logger.getChild(__name__)

@@ -21,36 +24,79 @@ logger = logger.getChild(__name__)
 class DvcIgnore:
    DVCIGNORE_FILE = ".dvcignore"

-    def __call__(self, root, dirs, files):
+    def __call__(
+        self, root: str, dirs: list[str], files: list[str]
+    ) -> tuple[list[str], list[str]]:
        raise NotImplementedError


 class DvcIgnorePatterns(DvcIgnore):
-    def __init__(self, pattern_list, dirname, sep):
+    def __init__(
+        self, pattern_list: Iterable[Union[PatternInfo, str]], dirname: str, sep: str
+    ) -> None:
        from pathspec.patterns.gitwildmatch import _DIR_MARK

-        if pattern_list and isinstance(pattern_list[0], str):
-            pattern_list = [PatternInfo(pattern, "") for pattern in pattern_list]
-
-        self.sep = sep
-        self.pattern_list = pattern_list
-        self.dirname = dirname
-
-        self.regex_pattern_list = []
-        for count, pattern in enumerate(pattern_list):
-            pattern, group = GitWildMatchPattern.pattern_to_regex(pattern.patterns)
-            if pattern:
-                pattern = pattern.replace(f"<{_DIR_MARK}>", f"<{_DIR_MARK}{count}>")
-                self.regex_pattern_list.append((pattern, group))
-
-        self.ignore_spec = [
-            (ignore, re.compile("|".join(item[0] for item in group)))
-            for ignore, group in groupby(self.regex_pattern_list, lambda x: x[1])
-            if ignore is not None
+        pattern_infos = [
+            pattern if isinstance(pattern, PatternInfo) else PatternInfo(pattern, "")
+            for pattern in pattern_list
        ]

+        self.sep = sep
+        self.pattern_list: list[PatternInfo] = []
+        self.dirname = dirname
+        self.find_matching_pattern = functools.cache(self._find_matching_pattern)
+
+        regex_pattern_list: list[tuple[str, bool, bool, PatternInfo]] = []
+        for count, pattern_info in enumerate(pattern_infos):
+            regex, ignore = GitWildMatchPattern.pattern_to_regex(pattern_info.patterns)
+            if regex is not None and ignore is not None:
+                self.pattern_list.append(pattern_info)
+                regex = regex.replace(f"<{_DIR_MARK}>", f"<{_DIR_MARK}{count}>")
+                regex_pattern_list.append(
+                    (regex, ignore, pattern_info.patterns.endswith("/"), pattern_info)
+                )
+
+        def keyfunc(item: tuple[str, bool, bool, PatternInfo]) -> tuple[bool, bool]:
+            _, ignore, dir_only_pattern, _ = item
+            return ignore, dir_only_pattern
+
+        self.ignore_spec: list[
+            tuple[
+                re.Pattern[str],
+                bool,
+                bool,
+                dict[Optional[str], tuple[str, PatternInfo]],
+            ]
+        ]
+        self.ignore_spec = []
+        for (ignore, dir_only_pattern), group in groupby(
+            regex_pattern_list, key=keyfunc
+        ):
+            if ignore:
+                # For performance, we combine all exclude patterns.
+                # But we still need to figure out which pattern matched which rule,
+                # (eg: to show in `dvc check-ignore`).
+                # So, we use named groups and keep a map of group name to pattern.
+                pattern_map: dict[Optional[str], tuple[str, PatternInfo]] = {
+                    f"rule_{i}": (regex, pi)
+                    for i, (regex, _, _, pi) in enumerate(group)
+                }
+                combined_regex = "|".join(
+                    f"(?P<{name}>{regex})" for name, (regex, _) in pattern_map.items()
+                )
+                self.ignore_spec.append(
+                    (re.compile(combined_regex), ignore, dir_only_pattern, pattern_map)
+                )
+            else:
+                # unignored patterns are not combined with `|`.
+                for regex, _, _, pi in group:
+                    pattern_map = {None: (regex, pi)}
+                    self.ignore_spec.append(
+                        (re.compile(regex), ignore, dir_only_pattern, pattern_map)
+                    )
+
    @classmethod
-    def from_file(cls, path, fs, name):
+    def from_file(cls, path: str, fs: "FileSystem", name: str) -> "Self":
        assert fs.isabs(path)
        dirname = fs.normpath(fs.dirname(path))
        with fs.open(path, encoding="utf-8") as fobj:
@@ -62,13 +108,15 @@ class DvcIgnorePatterns(DvcIgnore):

        return cls(path_spec_lines, dirname, fs.sep)

-    def __call__(self, root: list[str], dirs: list[str], files: list[str]):
+    def __call__(
+        self, root: str, dirs: list[str], files: list[str]
+    ) -> tuple[list[str], list[str]]:
        files = [f for f in files if not self.matches(root, f)]
        dirs = [d for d in dirs if not self.matches(root, d, True)]

        return dirs, files

-    def _get_normalize_path(self, dirname, basename):
+    def _get_normalize_path(self, dirname: str, basename: str) -> Optional[str]:
        # NOTE: `relpath` is too slow, so we have to assume that both
        # `dirname` and `self.dirname` are relative or absolute together.

@@ -81,62 +129,105 @@ class DvcIgnorePatterns(DvcIgnore):
            # NOTE: `os.path.join` is ~x5.5 slower
            path = f"{rel}{self.sep}{basename}"
        else:
-            return False
+            return None

        if os.name == "nt":
            return normalize_file(path)
        return path

-    def matches(self, dirname, basename, is_dir=False, details: bool = False):
+    @overload
+    def matches(
+        self,
+        dirname: str,
+        basename: str,
+        is_dir: bool = False,
+        details: Literal[False] = ...,
+    ) -> bool: ...
+
+    @overload
+    def matches(
+        self,
+        dirname: str,
+        basename: str,
+        is_dir: bool = False,
+        details: Literal[True] = ...,
+    ) -> tuple[bool, list[PatternInfo]]: ...
+
+    @overload
+    def matches(
+        self,
+        dirname: str,
+        basename: str,
+        is_dir: bool = False,
+        details: bool = False,
+    ) -> Union[bool, tuple[bool, list[PatternInfo]]]: ...
+
+    def matches(
+        self,
+        dirname: str,
+        basename: str,
+        is_dir: bool = False,
+        details: bool = False,
+    ) -> Union[bool, tuple[bool, list[PatternInfo]]]:
        path = self._get_normalize_path(dirname, basename)
-        if not path:
-            return False
-
-        if details:
-            return self._ignore_details(path, is_dir)
-        return self.ignore(path, is_dir)
-
-    def ignore(self, path, is_dir):
-        def matches(pattern, path, is_dir) -> bool:
-            matches_ = bool(pattern.match(path))
-
-            if is_dir:
-                matches_ |= bool(pattern.match(f"{path}/"))
-
-            return matches_
-
        result = False
+        _match: list[PatternInfo] = []
+        if path:
+            result, _match = self._ignore(path, is_dir)
+        return (result, _match) if details else result

-        for ignore, pattern in self.ignore_spec[::-1]:
-            if matches(pattern, path, is_dir):
-                result = ignore
-                break
-        return result
+    def _find_matching_pattern(
+        self, path: str, is_dir: bool
+    ) -> tuple[bool, list[PatternInfo]]:
+        paths = [path]
+        if is_dir and not path.endswith("/"):
+            paths.append(f"{path}/")

-    def _ignore_details(self, path, is_dir: bool):
-        result = []
-        for (regex, _), pattern_info in list(
-            zip(self.regex_pattern_list, self.pattern_list)
+        for pattern, ignore, dir_only_pattern, pattern_map in reversed(
+            self.ignore_spec
        ):
-            # skip system pattern
-            if not pattern_info.file_info:
+            if dir_only_pattern and not is_dir:
                continue
+            for p in paths:
+                match = pattern.match(p)
+                if not match:
+                    continue
+                if ignore:
+                    group_name, _match = next(
+                        (
+                            (name, _match)
+                            for name, _match in match.groupdict().items()
+                            if name.startswith("rule_") and _match is not None
+                        )
+                    )
+                else:
+                    # unignored patterns are not combined with `|`,
+                    # so there are no groups.
+                    group_name = None
+                _regex, pattern_info = pattern_map[group_name]
+                return ignore, [pattern_info]
+        return False, []

-            regex = re.compile(regex)
+    def _ignore(self, path: str, is_dir: bool) -> tuple[bool, list[PatternInfo]]:
+        parts = path.split("/")
+        result = False
+        matches: list[PatternInfo] = []
+        for i in range(1, len(parts) + 1):
+            rel_path = "/".join(parts[:i])
+            result, _matches = self.find_matching_pattern(
+                rel_path, is_dir or i < len(parts)
+            )
+            if i < len(parts) and not result:
+                continue
+            matches.extend(_matches)
+            if result:
+                break
+        return result, matches

-            matches = bool(regex.match(path))
-            if is_dir:
-                matches |= bool(regex.match(f"{path}/"))
-
-            if matches:
-                result.append(pattern_info.file_info)
-
-        return result
-
-    def __hash__(self):
+    def __hash__(self) -> int:
        return hash(self.dirname + ":" + str(self.pattern_list))

-    def __eq__(self, other):
+    def __eq__(self, other: object) -> bool:
        if not isinstance(other, DvcIgnorePatterns):
            return NotImplemented
        return (self.dirname == other.dirname) & (
@@ -144,21 +235,18 @@ class DvcIgnorePatterns(DvcIgnore):
            == [pattern.patterns for pattern in other.pattern_list]
        )

-    def __bool__(self):
+    def __bool__(self) -> bool:
        return bool(self.pattern_list)


-CheckIgnoreResult = namedtuple(  # noqa: PYI024
-    "CheckIgnoreResult", ["file", "match", "patterns"]
-)
-
-
-def _no_match(path):
-    return CheckIgnoreResult(path, False, ["::"])
+class CheckIgnoreResult(NamedTuple):
+    file: str
+    match: bool
+    pattern_infos: list[PatternInfo]


 class DvcIgnoreFilter:
-    def __init__(self, fs, root_dir):
+    def __init__(self, fs: "FileSystem", root_dir: str) -> None:
        from dvc.repo import Repo

        default_ignore_patterns = [
@@ -193,7 +281,7 @@ class DvcIgnoreFilter:
            ignore_subrepos=True,
        )

-    def _get_key(self, path):
+    def _get_key(self, path: str) -> tuple[str, ...]:
        parts = self.fs.relparts(path, self.root_dir)
        if parts == (os.curdir,):
            return ()
@@ -241,7 +329,7 @@ class DvcIgnoreFilter:
            for dname in dnames:
                self._update_sub_repo(self.fs.join(dirname, dname), ignore_trie)

-    def _update_sub_repo(self, path, ignore_trie: Trie):
+    def _update_sub_repo(self, path: str, ignore_trie: Trie) -> None:
        from dvc.repo import Repo

        if path == self.root_dir:
@@ -268,7 +356,9 @@ class DvcIgnoreFilter:
        else:
            ignore_trie[key] = new_pattern

-    def __call__(self, root, dirs, files, ignore_subrepos=True):
+    def __call__(
+        self, root: str, dirs: list[str], files: list[str], ignore_subrepos: bool = True
+    ) -> tuple[list[str], list[str]]:
        abs_root = self.fs.abspath(root)
        ignore_pattern = self._get_trie_pattern(
            abs_root, dnames=dirs, ignore_subrepos=ignore_subrepos
@@ -277,7 +367,24 @@ class DvcIgnoreFilter:
            dirs, files = ignore_pattern(abs_root, dirs, files)
        return dirs, files

-    def ls(self, fs, path, detail=True, **kwargs):
+    @overload
+    def ls(
+        self, fs: "FileSystem", path: str, detail: Literal[True], **kwargs: Any
+    ) -> list[dict[str, Any]]: ...
+
+    @overload
+    def ls(
+        self, fs: "FileSystem", path: str, detail: Literal[False], **kwargs
+    ) -> list[str]: ...
+
+    @overload
+    def ls(
+        self, fs: "FileSystem", path: str, detail: bool = True, **kwargs
+    ) -> Union[list[str], list[dict[str, Any]]]: ...
+
+    def ls(
+        self, fs: "FileSystem", path: str, detail: bool = True, **kwargs: Any
+    ) -> Union[list[str], list[dict[str, Any]]]:
        fs_dict = {}
        dirs = []
        nondirs = []
@@ -297,22 +404,29 @@ class DvcIgnoreFilter:

        return [fs_dict[name] for name in chain(dirs, nondirs)]

-    def walk(self, fs: "FileSystem", path: "AnyFSPath", **kwargs):
+    def walk(
+        self, fs: "FileSystem", path: str, **kwargs: Any
+    ) -> Iterator[
+        Union[
+            tuple[str, list[str], list[str]],
+            tuple[str, dict[str, dict], dict[str, dict]],
+        ]
+    ]:
        detail = kwargs.get("detail", False)
        ignore_subrepos = kwargs.pop("ignore_subrepos", True)
        if fs.protocol == Schemes.LOCAL:
            for root, dirs, files in fs.walk(path, **kwargs):
                if detail:
-                    all_dnames = set(dirs.keys())
-                    all_fnames = set(files.keys())
+                    assert isinstance(dirs, dict)
+                    assert isinstance(files, dict)
                    dnames, fnames = self(
                        root,
-                        all_dnames,
-                        all_fnames,
+                        list(dirs),
+                        list(files),
                        ignore_subrepos=ignore_subrepos,
                    )
-                    list(map(dirs.pop, all_dnames - set(dnames)))
-                    list(map(files.pop, all_fnames - set(fnames)))
+                    list(map(dirs.pop, dirs.keys() - set(dnames)))
+                    list(map(files.pop, files.keys() - set(fnames)))
                else:
                    dirs[:], files[:] = self(
                        root, dirs, files, ignore_subrepos=ignore_subrepos
@@ -321,7 +435,7 @@ class DvcIgnoreFilter:
        else:
            yield from fs.walk(path, **kwargs)

-    def find(self, fs: "FileSystem", path: "AnyFSPath", **kwargs):
+    def find(self, fs: "FileSystem", path: str, **kwargs: Any) -> Iterator[str]:
        if fs.protocol == Schemes.LOCAL:
            for root, _, files in self.walk(fs, path, **kwargs):
                for file in files:
@@ -331,7 +445,7 @@ class DvcIgnoreFilter:
            yield from fs.find(path)

    def _get_trie_pattern(
-        self, dirname, dnames: Optional["list"] = None, ignore_subrepos=True
+        self, dirname: str, dnames: Optional[list[str]] = None, ignore_subrepos=True
    ) -> Optional["DvcIgnorePatterns"]:
        if ignore_subrepos:
            ignores_trie = self.ignores_trie_fs
@@ -367,7 +481,7 @@ class DvcIgnoreFilter:

    def _is_ignored(
        self, path: str, is_dir: bool = False, ignore_subrepos: bool = True
-    ):
+    ) -> bool:
        if self._outside_repo(path):
            return False
        dirname, basename = self.fs.split(self.fs.normpath(path))
@@ -389,30 +503,29 @@ class DvcIgnoreFilter:
        path = self.fs.abspath(path)
        return self._is_ignored(path, False, ignore_subrepos=ignore_subrepos)

-    def _outside_repo(self, path):
+    def _outside_repo(self, path: str) -> bool:
        return not self.fs.isin_or_eq(path, self.root_dir)

-    def check_ignore(self, target):
+    def check_ignore(self, target: str) -> CheckIgnoreResult:
        # NOTE: can only be used in `dvc check-ignore`, see
-        # https://github.com/iterative/dvc/issues/5046
+        # https://github.com/treeverse/dvc/issues/5046
        full_target = self.fs.abspath(target)
+        matched_patterns: list[PatternInfo] = []
+        ignore = False
        if not self._outside_repo(full_target):
            dirname, basename = self.fs.split(self.fs.normpath(full_target))
            pattern = self._get_trie_pattern(dirname)
            if pattern:
-                matches = pattern.matches(
-                    dirname, basename, self.fs.isdir(full_target), True
+                ignore, matched_patterns = pattern.matches(
+                    dirname, basename, self.fs.isdir(full_target), details=True
                )
-
-                if matches:
-                    return CheckIgnoreResult(target, True, matches)
-        return _no_match(target)
+        return CheckIgnoreResult(target, ignore, matched_patterns)

    def is_ignored(
        self, fs: "FileSystem", path: str, ignore_subrepos: bool = True
    ) -> bool:
        # NOTE: can't use self.check_ignore(path).match for now, see
-        # https://github.com/iterative/dvc/issues/4555
+        # https://github.com/treeverse/dvc/issues/4555
        if fs.protocol != Schemes.LOCAL:
            return False
        if fs.isfile(path):
@@ -424,7 +537,7 @@ class DvcIgnoreFilter:
        )


-def init(path):
+def init(path: Union[str, os.PathLike[str]]) -> str:
    dvcignore = os.path.join(path, DvcIgnore.DVCIGNORE_FILE)
    if os.path.exists(dvcignore):
        return dvcignore
@@ -439,7 +552,7 @@ def init(path):
    return dvcignore


-def destroy(path):
+def destroy(path: Union[str, os.PathLike[str]]) -> None:
    from dvc.utils.fs import remove

    dvcignore = os.path.join(path, DvcIgnore.DVCIGNORE_FILE)
@@ -48,7 +48,10 @@ def get_dvc_info():
                info.append("Cache types: " + error_link("no-dvc-cache"))

            info.append(f"Caches: {_get_caches(repo.cache)}")
-            info.append(f"Remotes: {_get_remotes(repo.config)}")
+
+            configured_remotes = _get_remotes(repo.config)
+            remotes = ", ".join(configured_remotes) if configured_remotes else None
+            info.append(f"Remotes: {remotes}")

            root_directory = repo.root_dir
            fs_root = _get_fs_type(os.path.abspath(root_directory))
@@ -75,12 +78,10 @@ def _get_caches(cache):


 def _get_remotes(config):
-    schemes = (
+    return [
        get_fs_cls(get_fs_config(config, name=remote)).protocol
        for remote in config["remote"]
-    )
-
-    return ", ".join(schemes) or "None"
+    ]


 def _get_linktype_support_info(repo):
@@ -157,7 +158,7 @@ def _get_fs_type(path):
            except PermissionError:
                pass

-    # need to follow the symlink: https://github.com/iterative/dvc/issues/5065
+    # need to follow the symlink: https://github.com/treeverse/dvc/issues/5065
    path = pathlib.Path(path).resolve()

    for parent in itertools.chain([path], path.parents):
@@ -2,13 +2,13 @@

 import hashlib
 import os
+import time
 from abc import ABC, abstractmethod
 from datetime import timedelta
 from typing import Optional, Union

 import flufl.lock
 import zc.lockfile
-from funcy import retry

 from dvc.exceptions import DvcException
 from dvc.progress import Tqdm
@@ -88,9 +88,10 @@ class Lock(LockBase):
    Uses zc.lockfile as backend.
    """

-    def __init__(self, lockfile, friendly=False, **kwargs):
+    def __init__(self, lockfile, friendly=False, wait=False, **kwargs):
        super().__init__(lockfile)
        self._friendly = friendly
+        self._wait = wait
        self._lock = None
        self._lock_failed = False

@@ -101,23 +102,38 @@ class Lock(LockBase):
    def _do_lock(self):
        try:
            self._lock_failed = False
-            with Tqdm(
-                bar_format="{desc}",
-                disable=not self._friendly,
-                desc="If DVC froze, see `hardlink_lock` in {}".format(
-                    format_link("https://man.dvc.org/config#core")
-                ),
-            ):
-                self._lock = zc.lockfile.LockFile(self._lockfile)
+            self._lock = zc.lockfile.LockFile(self._lockfile)
        except zc.lockfile.LockError:
            self._lock_failed = True
            raise LockError(FAILED_TO_LOCK_MESSAGE)  # noqa: B904

    def lock(self):
-        retries = 6
-        delay = DEFAULT_TIMEOUT / retries
-        lock_retry = retry(retries, LockError, timeout=delay)(self._do_lock)
-        lock_retry()
+        """Acquire the lock, either waiting forever, or after default_retries."""
+        default_retries = 6
+        delay = DEFAULT_TIMEOUT / default_retries
+        attempts = 0
+
+        max_retries = float("inf") if self._wait else default_retries
+
+        with Tqdm(
+            bar_format="{desc}",
+            disable=not self._friendly,
+            desc="Waiting to acquire lock. "
+            "If DVC froze, see `hardlink_lock` in {}.".format(
+                format_link("https://man.dvc.org/config#core")
+            ),
+        ) as pbar:
+            while True:
+                try:
+                    self._do_lock()
+                    return
+                except LockError:
+                    attempts += 1
+                    if attempts > max_retries:
+                        raise
+                    time.sleep(delay)
+                finally:
+                    pbar.update()

    def unlock(self):
        if self._lock_failed:
@@ -150,7 +166,7 @@ class HardlinkLock(flufl.lock.Lock, LockBase):
        tmp_dir (str): a directory to store claim files.
    """

-    def __init__(self, lockfile, tmp_dir=None, **kwargs):
+    def __init__(self, lockfile, tmp_dir=None, wait=False, **kwargs):
        import socket

        self._tmp_dir = tmp_dir
@@ -166,18 +182,28 @@ class HardlinkLock(flufl.lock.Lock, LockBase):
        # number to generate the resulting lock file name, which is unique
        # enough for our application.
        #
-        # [1] https://github.com/iterative/dvc/issues/2582
+        # [1] https://github.com/treeverse/dvc/issues/2582
        self._hostname = socket.gethostname()

        self._lifetime = timedelta(days=365)  # Lock for good by default
        self._separator = flufl.lock.SEP
        self._set_claimfile()
        self._owned = True
+        self._wait = wait
        self._retry_errnos = []
+        self._friendly = kwargs.get("friendly", False)

    def lock(self, timeout: Optional[Union[timedelta, int]] = None):
        try:
-            super().lock(timeout or timedelta(seconds=DEFAULT_TIMEOUT))
+            if not self._wait:
+                timeout = timeout or timedelta(seconds=DEFAULT_TIMEOUT)
+
+            with Tqdm(
+                bar_format="{desc}",
+                disable=not (self._wait and self._friendly),
+                desc="Waiting to acquire lock",
+            ):
+                super().lock(timeout)
        except flufl.lock.TimeOutError:
            raise LockError(FAILED_TO_LOCK_MESSAGE)  # noqa: B904

@@ -186,11 +212,11 @@ class HardlinkLock(flufl.lock.Lock, LockBase):

        if self._tmp_dir is not None:
            # Under Windows file path length is limited so we hash it
-            hasher = hashlib.md5(self._claimfile.encode())  # noqa: S324
+            hasher = hashlib.md5(self._claimfile.encode(), usedforsecurity=False)
            filename = hasher.hexdigest()
            self._claimfile = os.path.join(self._tmp_dir, filename + ".lock")


-def make_lock(lockfile, tmp_dir=None, friendly=False, hardlink_lock=False):
+def make_lock(lockfile, tmp_dir=None, friendly=False, hardlink_lock=False, wait=False):
    cls = HardlinkLock if hardlink_lock else Lock
-    return cls(lockfile, tmp_dir=tmp_dir, friendly=friendly)
+    return cls(lockfile, tmp_dir=tmp_dir, friendly=friendly, wait=wait)
@@ -1,10 +1,10 @@
 """Manages logging configuration for DVC repo."""

 import logging
-import logging.config
-import logging.handlers
 import os
 import sys
+from collections.abc import Iterator
+from contextlib import contextmanager
 from typing import ClassVar

 import colorama
@@ -53,7 +53,7 @@ def add_logging_level(level_name, level_num, method_name=None):
        setattr(logging, method_name, log_to_root)


-class LoggingException(Exception):
+class LoggingException(Exception):  # noqa: N818
    def __init__(self, record):
        msg = f"failed to log {record!s}"
        super().__init__(msg)
@@ -174,9 +174,19 @@ def _iter_causes(exc):
        exc = exc.__cause__


-def set_loggers_level(level: int = logging.INFO) -> None:
+@contextmanager
+def set_loggers_level(level: int = logging.INFO) -> Iterator[None]:
+    ret: dict[logging.Logger, int] = {}
    for name in ["dvc", "dvc_objects", "dvc_data"]:
-        logging.getLogger(name).setLevel(level)
+        _logger = logging.getLogger(name)
+        ret[_logger] = _logger.getEffectiveLevel()
+        _logger.setLevel(level)
+
+    try:
+        yield
+    finally:
+        for _logger, old_lvl in ret.items():
+            _logger.setLevel(old_lvl)


 def setup(level: int = logging.INFO, log_colors: bool = True) -> None:
@@ -42,10 +42,11 @@ from .utils import relpath
 from .utils.fs import path_isin

 if TYPE_CHECKING:
+    from dvc.repo import Repo
    from dvc_data.hashfile.obj import HashFile
    from dvc_data.index import DataIndexKey

-    from .ignore import DvcIgnoreFilter
+    from .ignore import CheckIgnoreResult, DvcIgnoreFilter

 logger = logger.getChild(__name__)

@@ -83,7 +84,7 @@ def _get(stage, path, **kwargs):
    return Output(stage, path, **kwargs)


-def loadd_from(stage, d_list):
+def loadd_from(stage, d_list) -> list["Output"]:
    ret = []
    for d in d_list:
        p = d.pop(Output.PARAM_PATH)
@@ -267,9 +268,9 @@ class OutputIsStageFileError(DvcException):


 class OutputIsIgnoredError(DvcException):
-    def __init__(self, match):
-        lines = "\n".join(match.patterns)
-        super().__init__(f"Path '{match.file}' is ignored by\n{lines}")
+    def __init__(self, result: "CheckIgnoreResult"):
+        pi = result.pattern_infos[-1]
+        super().__init__(f"Path {result.file!r} is ignored by {pi!s}")


 class CheckoutCallback(TqdmCallback):
@@ -329,7 +330,7 @@ class Output:
        self.annot = Annotation(
            desc=desc, type=type, labels=labels or [], meta=meta or {}
        )
-        self.repo = stage.repo if not repo and stage else repo
+        self.repo: Optional[Repo] = stage.repo if not repo and stage else repo
        meta_d = merge_file_meta_from_cloud(info or {})
        meta = Meta.from_dict(meta_d)
        # NOTE: when version_aware is not passed into get_cloud_fs, it will be
@@ -511,6 +512,7 @@ class Output:
        from dvc.cachemgr import LEGACY_HASH_NAMES

        assert self.is_in_repo
+        assert self.repo
        odb_name = "legacy" if self.hash_name in LEGACY_HASH_NAMES else "repo"
        return getattr(self.repo.cache, odb_name)

@@ -518,6 +520,7 @@ class Output:
    def local_cache(self):
        from dvc.cachemgr import LEGACY_HASH_NAMES

+        assert self.repo
        if self.hash_name in LEGACY_HASH_NAMES:
            return self.repo.cache.legacy
        return self.repo.cache.local
@@ -585,6 +588,7 @@ class Output:
    def index_key(self) -> tuple[str, "DataIndexKey"]:
        if self.is_in_repo:
            workspace = "repo"
+            assert self.repo
            key = self.repo.fs.relparts(self.fs_path, self.repo.root_dir)
        else:
            workspace = self.fs.protocol
@@ -640,6 +644,7 @@ class Output:
    @property
    def dvcignore(self) -> Optional["DvcIgnoreFilter"]:
        if self.fs.protocol == "local":
+            assert self.repo
            return self.repo.dvcignore
        return None

@@ -661,6 +666,7 @@ class Output:
        if not self.use_scm_ignore:
            return

+        assert self.repo
        if self.repo.scm.is_tracked(self.fspath):
            raise OutputAlreadyTrackedError(self)

@@ -670,6 +676,7 @@ class Output:
        if not self.use_scm_ignore:
            return

+        assert self.repo
        self.repo.scm_context.ignore_remove(self.fspath)

    def save(self) -> None:
@@ -776,6 +783,7 @@ class Output:
                        callback=cb,
                    )
            if relink:
+                assert self.repo
                rel = self.fs.relpath(filter_info or self.fs_path)
                with CheckoutCallback(desc=f"Checking out {rel}", unit="files") as cb:
                    self._checkout(
@@ -957,6 +965,7 @@ class Output:
        added = not self.exists

        try:
+            assert self.repo
            modified = self._checkout(
                filter_info or self.fs_path,
                self.fs,
@@ -987,18 +996,24 @@ class Output:
        if ignore_remove:
            self.ignore_remove()

-    def move(self, out):
+    def move(self, out: "Output") -> None:
+        src_exists = self.exists
+        if src_exists:
+            self.fs.move(self.fs_path, out.fs_path)
+        else:
+            logger.warning("%r missing", self.fspath)
+
        if self.protocol == "local" and self.use_scm_ignore:
+            assert self.repo
            self.repo.scm_context.ignore_remove(self.fspath)

-        self.fs.move(self.fs_path, out.fs_path)
        self.def_path = out.def_path
        self.fs_path = out.fs_path
-        self.save()
-        self.commit()
-
-        if self.protocol == "local" and self.use_scm_ignore:
-            self.repo.scm_context.ignore(self.fspath)
+        try:
+            self.save()
+            self.commit()
+        except self.DoesNotExistError:
+            self.ignore()

    def transfer(
        self, source, odb=None, jobs=None, update=False, no_progress_bar=False
@@ -1079,6 +1094,7 @@ class Output:
            if self.remote:
                kwargs["remote"] = self.remote
            with suppress(Exception):
+                assert self.repo
                self.repo.cloud.pull([obj.hash_info], **kwargs)

        if self.obj:
@@ -1172,6 +1188,7 @@ class Output:
            return {}

        if self.remote:
+            assert self.repo
            remote_odb = self.repo.cloud.get_remote_odb(
                name=self.remote, hash_name=self.hash_name
            )
@@ -1203,8 +1220,9 @@ class Output:
        if stage:
            abs_path = os.path.join(stage.wdir, path)
            if self._is_path_dvcignore(abs_path):
-                check = stage.repo.dvcignore.check_ignore(abs_path)
-                raise self.IsIgnoredError(check)
+                check: CheckIgnoreResult = stage.repo.dvcignore.check_ignore(abs_path)
+                if check.match:
+                    raise self.IsIgnoredError(check)

    def _check_can_merge(self, out):
        if self.protocol != out.protocol:
@@ -1452,25 +1470,44 @@ class Output:
        self.remote = other.remote
        self.can_push = other.can_push

-    def merge_version_meta(self, other: "Output"):
+    def _get_versioned_meta(
+        self,
+    ) -> Optional[
+        tuple["HashInfo", Optional["Meta"], Optional[Union["HashFile", "Tree"]]]
+    ]:
+        if self.files is not None or (
+            self.meta is not None and self.meta.version_id is not None
+        ):
+            old_obj = self.obj if self.obj is not None else self.get_obj()
+            return self.hash_info, self.meta, old_obj
+        return None
+
+    def merge_version_meta(
+        self,
+        old_hi: "HashInfo",
+        old_meta: Optional["Meta"],
+        old_obj: Optional[Union["HashFile", "Tree"]],
+    ):
        """Merge version meta for files which are unchanged from other."""
        if not self.hash_info:
-            return
+            return None
        if self.hash_info.isdir:
-            return self._merge_dir_version_meta(other)
-        if self.hash_info != other.hash_info:
-            return
-        self.meta = other.meta
+            return self._merge_dir_version_meta(old_hi, old_obj)
+        if self.hash_info != old_hi:
+            return None
+        self.meta = old_meta
+        return None

-    def _merge_dir_version_meta(self, other: "Output"):
+    def _merge_dir_version_meta(
+        self, old_hi: "HashInfo", old_obj: Optional[Union["HashFile", "Tree"]]
+    ):
        from dvc_data.hashfile.tree import update_meta

-        if not self.obj or not other.hash_info.isdir:
+        if not self.obj or not old_hi.isdir:
            return
-        other_obj = other.obj if other.obj is not None else other.get_obj()
        assert isinstance(self.obj, Tree)
-        assert isinstance(other_obj, Tree)
-        updated = update_meta(self.obj, other_obj)
+        assert isinstance(old_obj, Tree)
+        updated = update_meta(self.obj, old_obj)
        assert updated.hash_info == self.obj.hash_info
        self.obj = updated
        self.files = updated.as_list(with_meta=True)
@@ -66,7 +66,7 @@ class ParamsLoadError(ContextError):
    pass


-class KeyNotInContext(ContextError, KeyError):
+class KeyNotInContext(ContextError, KeyError):  # noqa: N818
    def __init__(self, key: str) -> None:
        self.key: str = key
        super().__init__(f"Could not find '{key}'")
@@ -75,7 +75,7 @@ class KeyNotInContext(ContextError, KeyError):
        return self.msg


-class VarsAlreadyLoaded(ContextError):
+class VarsAlreadyLoaded(ContextError):  # noqa: N818
    pass


@@ -155,7 +155,7 @@ class Value(Node):
 PRIMITIVES = (int, float, str, bytes, bool)


-class Container(Node, ABC):
+class Container(Node, ABC):  # noqa: PLW1641
    meta: Meta
    data: Union[list, dict]
    _key_transform = staticmethod(identity)
@@ -272,7 +272,7 @@ class CtxDict(Container, MutableMapping):
        if not isinstance(key, str):
            # limitation for the interpolation
            # ignore other kinds of keys
-            return
+            return None
        return super().__setitem__(key, value)

    def merge_update(self, other, overwrite=False):
@@ -202,6 +202,7 @@ def validate_value(value, key):
        if isinstance(value, dict) and key == "cmd":
            return True
        raise ParseError(f"Cannot interpolate data of type '{type(value).__name__}'")
+    return None


 def str_interpolate(
@@ -2,13 +2,19 @@
 # Including changing base dir of path specification patterns and merging
 # of two path specification patterns with different base
 # All the operations follow the documents of `gitignore`
-from collections import namedtuple
+from typing import NamedTuple

 from pathspec.util import normalize_file

 from dvc.utils import relpath

-PatternInfo = namedtuple("PatternInfo", ["patterns", "file_info"])  # noqa: PYI024
+
+class PatternInfo(NamedTuple):
+    patterns: str
+    file_info: str
+
+    def __str__(self) -> str:
+        return self.file_info or f":{self.patterns}"


 def _not_ignore(rule):
@@ -167,7 +167,7 @@ class VegaConverter(Converter):
        if isinstance(y, list):
            return "y"
        if not isinstance(y, dict):
-            return
+            return None

        fields = {field for _, field in _file_field(y)}
        if len(fields) == 1:
@@ -2,7 +2,6 @@ import os
 from collections import defaultdict
 from typing import TYPE_CHECKING, NamedTuple, Optional

-import dpath
 import dpath.options
 from funcy import get_in, last

@@ -20,6 +20,7 @@ if TYPE_CHECKING:
    from dvc.fs.data import DataFileSystem
    from dvc.fs.dvc import DVCFileSystem
    from dvc.lock import LockBase
+    from dvc.output import Output
    from dvc.scm import Git, NoSCM
    from dvc.stage import Stage
    from dvc.types import DictStrAny
@@ -144,6 +145,7 @@ class Repo:
        scm: Optional[Union["Git", "NoSCM"]] = None,
        remote: Optional[str] = None,
        remote_config: Optional["DictStrAny"] = None,
+        _wait_for_lock: bool = False,
    ):
        from dvc.cachemgr import CacheManager
        from dvc.data_cloud import DataCloud
@@ -166,7 +168,8 @@ class Repo:
        self._config = config
        self._remote = remote
        self._remote_config = remote_config
-        self._data_index = None
+        self._data_index: Optional[DataIndex] = None
+        self._wait_for_lock = _wait_for_lock

        if rev and not fs:
            self._scm = scm = SCM(root_dir or os.curdir)
@@ -204,6 +207,7 @@ class Repo:
                    tmp_dir=self.tmp_dir,
                    hardlink_lock=self.config["core"].get("hardlink_lock", False),
                    friendly=True,
+                    wait=self._wait_for_lock,
                )
                os.makedirs(self.site_cache_dir, exist_ok=True)
                if not fs and (
@@ -541,7 +545,9 @@ class Repo:

        return used

-    def find_outs_by_path(self, path, outs=None, recursive=False, strict=True):
+    def find_outs_by_path(
+        self, path, outs=None, recursive=False, strict=True
+    ) -> list["Output"]:
        # using `outs_graph` to ensure graph checks are run
        outs = outs or self.index.outs_graph

@@ -609,7 +615,7 @@ class Repo:
        from dvc.fs import GitFileSystem
        from dvc.version import version_tuple

-        cache_dir = self.config["core"].get("site_cache_dir") or site_cache_dir()
+        cache_dir = site_cache_dir(self.config["core"].get("site_cache_dir"))

        subdir = None
        if isinstance(self.fs, GitFileSystem):
@@ -638,10 +644,11 @@ class Repo:
        # that just happened to be at the same path as old deleted ones.
        btime = self._btime or getattr(os.stat(root_dir), "st_birthtime", None)

-        md5 = hashlib.md5(  # noqa: S324
+        md5 = hashlib.md5(
            str(
                (root_dir, subdir, btime, getpass.getuser(), version_tuple[0], salt)
-            ).encode()
+            ).encode(),
+            usedforsecurity=False,
        )
        repo_token = md5.hexdigest()
        return os.path.join(repos_dir, repo_token)
@@ -40,7 +40,7 @@ def check_name_format(name: str) -> None:

 def name_is_compatible(name: str) -> bool:
    """
-    Only needed by DVCLive per iterative/dvclive#715
+    Only needed by DVCLive per treeverse/dvclive#715
    Will be removed in future release.
    """
    from gto.constants import assert_name_is_valid
@@ -1,4 +1,5 @@
 import os
+from collections import defaultdict
 from typing import TYPE_CHECKING

 from dvc.exceptions import (
@@ -14,7 +15,9 @@ from dvc.utils import relpath
 from . import locked

 if TYPE_CHECKING:
-    from dvc_data.index import BaseDataIndex, DataIndexEntry
+    from dvc.repo.index import IndexView
+    from dvc_data.index import BaseDataIndex, DataIndexEntry, DataIndexKey
+    from dvc_data.index.diff import Change
    from dvc_objects.fs.base import FileSystem

 logger = logger.getChild(__name__)
@@ -36,10 +39,12 @@ def _remove_unused_links(repo):
    return ret


-def _build_out_changes(index, changes):
+def _build_out_changes(
+    index: "IndexView", changes: dict["DataIndexKey", "Change"]
+) -> dict["DataIndexKey", tuple[str, dict[str, int]]]:
    from dvc_data.index.checkout import MODIFY

-    out_keys = []
+    out_keys: list[DataIndexKey] = []
    for out in index.outs:
        if not out.use_cache:
            continue
@@ -47,19 +52,28 @@ def _build_out_changes(index, changes):
        ws, key = out.index_key
        if ws != "repo":
            continue
-
        out_keys.append(key)

-    out_changes = {}
+    out_stats: dict[DataIndexKey, dict[str, int]]
+    out_stats = defaultdict(lambda: defaultdict(int))
+
+    out_changes: dict[DataIndexKey, tuple[str, dict[str, int]]] = {}
    for key, change in changes.items():
+        typ = change.typ
+        isdir = change.new and change.new.isdir
        for out_key in out_keys:
            if len(out_key) > len(key) or key[: len(out_key)] != out_key:
                continue

+            stats = out_stats[out_key]
+            if not isdir:
+                stats[typ] += 1
+
            if key == out_key:
-                out_changes[out_key] = change.typ
-            elif not out_changes.get(out_key):
-                out_changes[out_key] = MODIFY
+                out_changes[out_key] = typ, stats
+            elif out_key not in out_changes:
+                typ = MODIFY
+                out_changes[out_key] = typ, stats
            break

    return out_changes
@@ -107,14 +121,13 @@ def checkout(  # noqa: C901
    from dvc.stage.exceptions import StageFileBadNameError, StageFileDoesNotExistError
    from dvc_data.index.checkout import ADD, DELETE, MODIFY, apply, compare

-    stats: dict[str, list[str]] = {
-        "added": [],
-        "deleted": [],
-        "modified": [],
-    }
+    stats = {"modified": 0, "added": 0, "deleted": 0}
+    changes: dict[str, list[str]] = {"modified": [], "added": [], "deleted": []}
+
    if not targets:
        targets = [None]
-        stats["deleted"] = _remove_unused_links(self)
+        changes["deleted"] = _remove_unused_links(self)
+        stats["deleted"] = len(changes["deleted"])

    if isinstance(targets, str):
        targets = [targets]
@@ -127,8 +140,10 @@ def checkout(  # noqa: C901
            raise CheckoutErrorSuggestGit(target) from exc
        raise  # noqa: PLE0704

-    view = self.index.targets_view(
-        targets, recursive=recursive, with_deps=with_deps, onerror=onerror
+    from .index import index_from_targets
+
+    view = index_from_targets(
+        self, targets=targets, recursive=recursive, with_deps=with_deps, onerror=onerror
    )

    with ui.progress(unit="entry", desc="Building workspace index", leave=True) as pb:
@@ -149,7 +164,10 @@ def checkout(  # noqa: C901

    def checkout_onerror(src_path, dest_path, _exc):
        logger.debug(
-            "failed to create '%s' from '%s'", dest_path, src_path, exc_info=True
+            "failed to create '%s' from '%s'",
+            dest_path,
+            src_path,
+            exc_info=True,  # noqa: LOG014
        )

        for out_path in out_paths:
@@ -171,16 +189,26 @@ def checkout(  # noqa: C901
    out_changes = _build_out_changes(view, diff.changes)

    typ_map = {ADD: "added", DELETE: "deleted", MODIFY: "modified"}
-    for key, typ in out_changes.items():
+    for key, (typ, _stats) in out_changes.items():
        out_path = self.fs.join(self.root_dir, *key)

        if out_path in failed:
            self.fs.remove(out_path, recursive=True)
-        else:
-            self.state.save_link(out_path, self.fs)
-            stats[typ_map[typ]].append(_fspath_dir(out_path))
+            continue

+        self.state.save_link(out_path, self.fs)
+        for t, count in _stats.items():
+            stats_typ = typ_map[t]
+            stats[stats_typ] += count
+
+        changes[typ_map[typ]].append(_fspath_dir(out_path))
+
+    for changelist in changes.values():
+        # group directories first, then files. But keep them alphabetically sorted
+        changelist.sort(key=lambda p: (not p.endswith(os.sep), p))
+
+    result = changes | {"stats": stats}
    if failed and not allow_missing:
-        raise CheckoutError([relpath(out_path) for out_path in failed], stats)
-
-    return stats
+        result["failed"] = [relpath(out_path) for out_path in failed]
+        raise CheckoutError([relpath(out_path) for out_path in failed], result)
+    return result
@@ -43,13 +43,13 @@ def _collect_paths(


 def _filter_outs(
-    outs: Outputs, fs_paths: StrPaths, duplicates=False
+    repo: "Repo", outs: Outputs, fs_paths: StrPaths, duplicates=False
 ) -> tuple[Outputs, StrPaths]:
    res_outs: Outputs = []
    fs_res_paths = fs_paths

    for out in outs:
-        fs_path = out.repo.dvcfs.from_os_path(out.fs_path)
+        fs_path = repo.dvcfs.from_os_path(out.fs_path)
        if fs_path in fs_paths:
            res_outs.append(out)
            if not duplicates:
@@ -77,4 +77,4 @@ def collect(

    target_paths = _collect_paths(repo, targets, recursive=recursive)

-    return _filter_outs(outs, target_paths, duplicates=duplicates)
+    return _filter_outs(repo, outs, target_paths, duplicates=duplicates)
@@ -1,3 +1,4 @@
+from itertools import groupby
 from typing import TYPE_CHECKING

 from dvc import prompt
@@ -52,29 +53,38 @@ def commit(
    data_only=False,
    relink=True,
 ):
-    stages_info = [
-        info
-        for info in self.stage.collect_granular(
-            target, with_deps=with_deps, recursive=recursive
-        )
-        if not data_only or info.stage.is_data_source
-    ]
-    for stage_info in stages_info:
-        stage = stage_info.stage
-        if force:
-            stage.save(allow_missing=allow_missing)
-        else:
-            changes = stage.changed_entries()
-            if any(changes):
-                prompt_to_commit(stage, changes, force=force)
+    committed_stages = []
+    groups = groupby(
+        [
+            info
+            for info in self.stage.collect_granular(
+                target, with_deps=with_deps, recursive=recursive
+            )
+            if not data_only or info.stage.is_data_source
+        ],
+        key=lambda info: info.stage.dvcfile,
+    )
+
+    for dvcfile, stages_info_group in groups:
+        to_dump = []
+        for stage_info in stages_info_group:
+            stage = stage_info.stage
+            if force:
                stage.save(allow_missing=allow_missing)
-        stage.commit(
-            filter_info=stage_info.filter_info,
-            allow_missing=allow_missing,
-            relink=relink,
-        )
-        stage.dump(update_pipeline=False)
-    return [s.stage for s in stages_info]
+            else:
+                changes = stage.changed_entries()
+                if any(changes):
+                    prompt_to_commit(stage, changes, force=force)
+                    stage.save(allow_missing=allow_missing)
+            stage.commit(
+                filter_info=stage_info.filter_info,
+                allow_missing=allow_missing,
+                relink=relink,
+            )
+            to_dump.append(stage)
+        dvcfile.dump_stages(to_dump, update_pipeline=False)
+        committed_stages.extend(to_dump)
+    return committed_stages


@locked
@@ -1,38 +1,34 @@
 import os
 import posixpath
-from collections.abc import Iterable
-from typing import TYPE_CHECKING, Any, TypedDict, Union
+from collections import defaultdict, deque
+from collections.abc import Iterable, Iterator, Mapping
+from typing import TYPE_CHECKING, Optional, TypedDict, Union

-from dvc.fs.callbacks import DEFAULT_CALLBACK
+from dvc.fs.callbacks import DEFAULT_CALLBACK, Callback, TqdmCallback
+from dvc.log import logger
 from dvc.ui import ui
+from dvc_data.index import DataIndexDirError

 if TYPE_CHECKING:
-    from dvc.fs.callbacks import Callback
    from dvc.repo import Repo
    from dvc.scm import Git, NoSCM
-    from dvc_data.index import DataIndex
+    from dvc_data.index import (
+        BaseDataIndex,
+        DataIndex,
+        DataIndexEntry,
+        DataIndexKey,
+        DataIndexView,
+    )
    from dvc_data.index.diff import Change
+    from dvc_objects.fs.base import FileSystem
+
+logger = logger.getChild(__name__)


 def posixpath_to_os_path(path: str) -> str:
    return path.replace(posixpath.sep, os.path.sep)


-def _adapt_typ(typ: str) -> str:
-    from dvc_data.index.diff import ADD, DELETE, MODIFY
-
-    if typ == MODIFY:
-        return "modified"
-
-    if typ == ADD:
-        return "added"
-
-    if typ == DELETE:
-        return "deleted"
-
-    return typ
-
-
 def _adapt_path(change: "Change") -> str:
    isdir = False
    if change.new and change.new.meta:
@@ -45,27 +41,98 @@ def _adapt_path(change: "Change") -> str:
    return os.path.sep.join(key)


+def _adapt_path_from_entry(entry: "DataIndexEntry") -> str:
+    key = entry.key
+    assert key
+    if entry.meta and entry.meta.isdir:
+        key = (*key, "")
+    return os.sep.join(key)
+
+
+def _get_missing_paths(
+    to_check: Mapping["FileSystem", Mapping[str, Iterable["DataIndexEntry"]]],
+    batch_size: Optional[int] = None,
+    callback: "Callback" = DEFAULT_CALLBACK,
+) -> Iterator[str]:
+    for fs, paths_map in to_check.items():
+        if batch_size == 1 or (batch_size is None and fs.protocol == "local"):
+            results = list(callback.wrap(map(fs.exists, paths_map)))
+        else:
+            results = fs.exists(
+                list(paths_map), batch_size=batch_size, callback=callback
+            )
+
+        for cache_path, exists in zip(paths_map, results):
+            if exists:
+                continue
+
+            for entry in paths_map[cache_path]:
+                yield _adapt_path_from_entry(entry)
+
+
+class StorageCallback(Callback):
+    def __init__(self, parent_cb: Callback) -> None:
+        super().__init__(size=0, value=0)
+        self.parent_cb = parent_cb
+
+    def set_size(self, size: int) -> None:
+        # This is a no-op to prevent `fs.exists` from trying to set the size
+        pass
+
+    def relative_update(self, value: int = 1) -> None:
+        self.parent_cb.relative_update(value)
+
+    def absolute_update(self, value: int) -> None:
+        self.parent_cb.relative_update(value - self.value)
+
+
+class Rename(TypedDict):
+    old: str
+    new: str
+
+
+class DiffResult(TypedDict, total=False):
+    modified: list[str]
+    added: list[str]
+    deleted: list[str]
+    renamed: list[Rename]
+    unchanged: list[str]
+    unknown: list[str]
+    not_in_cache: list[str]
+
+
 def _diff(
-    old: "DataIndex",
-    new: "DataIndex",
+    old: "BaseDataIndex",
+    new: "BaseDataIndex",
    *,
+    filter_keys: Optional[Iterable["DataIndexKey"]] = None,
    granular: bool = False,
    not_in_cache: bool = False,
-    not_in_remote: bool = False,
-    remote_refresh: bool = False,
+    batch_size: Optional[int] = None,
    callback: "Callback" = DEFAULT_CALLBACK,
-) -> dict[str, list[str]]:
-    from dvc_data.index import StorageError
-    from dvc_data.index.diff import UNCHANGED, UNKNOWN, diff
+    with_renames: bool = False,
+) -> DiffResult:
+    from dvc_data.index.diff import (
+        ADD,
+        DELETE,
+        MODIFY,
+        RENAME,
+        UNCHANGED,
+        UNKNOWN,
+        diff,
+    )

-    ret: dict[str, list[str]] = {}
+    ret: DiffResult = defaultdict(list)  # type: ignore[assignment]
+    change_types = {
+        MODIFY: "modified",
+        ADD: "added",
+        DELETE: "deleted",
+        RENAME: "renamed",
+    }

-    def _add_change(typ, change):
-        typ = _adapt_typ(typ)
-        if typ not in ret:
-            ret[typ] = []
-
-        ret[typ].append(_adapt_path(change))
+    to_check: dict[FileSystem, dict[str, list[DataIndexEntry]]] = defaultdict(
+        lambda: defaultdict(list)
+    )

    for change in diff(
        old,
@@ -74,45 +141,72 @@ def _diff(
        shallow=not granular,
        hash_only=True,
        with_unknown=True,
+        with_renames=with_renames,
        callback=callback,
    ):
+        typ = change.typ
+
+        # The index is a trie, so even when we filter by a specific path
+        # like `dir/file`, all parent nodes leading to that path (e.g., `dir/`)
+        # still appear in the view. As a result, keys like `dir/` will be present
+        # even if only `dir/file` matches the filter.
+        # We need to skip such entries to avoid showing root of tracked directories.
+        if filter_keys:
+            # RENAME does not have a `change.key`
+            if typ == RENAME:
+                assert change.new
+                key = change.new.key
+                # match with "new" key only
+                assert key
+            else:
+                key = change.key
+
+            if not any(key[: len(fk)] == fk for fk in filter_keys):
+                continue
+
        if (
-            change.typ == UNCHANGED
+            typ == UNCHANGED
            and (not change.old or not change.old.hash_info)
            and (not change.new or not change.new.hash_info)
        ):
            # NOTE: emulating previous behaviour
            continue

-        if change.typ == UNKNOWN and not change.new:
+        if typ == UNKNOWN and not change.new:
            # NOTE: emulating previous behaviour
            continue

-        if (
-            not_in_cache
-            and change.old
-            and change.old.hash_info
-            and not old.storage_map.cache_exists(change.old)
-        ):
-            # NOTE: emulating previous behaviour
-            _add_change("not_in_cache", change)
+        if not_in_cache and change.old and change.old.hash_info:
+            old_entry = change.old
+            cache_fs, cache_path = old.storage_map.get_cache(old_entry)
+            # check later in batches
+            to_check[cache_fs][cache_path].append(old_entry)

-        try:
-            if (
-                not_in_remote
-                and change.old
-                and change.old.hash_info
-                and not old.storage_map.remote_exists(
-                    change.old, refresh=remote_refresh
-                )
-            ):
-                _add_change("not_in_remote", change)
-        except StorageError:
-            pass
+        change_typ = change_types.get(typ, typ)
+        if typ == RENAME:
+            assert change.old is not None
+            assert change.new is not None
+            ret["renamed"].append(
+                {
+                    "old": _adapt_path_from_entry(change.old),
+                    "new": _adapt_path_from_entry(change.new),
+                }
+            )
+        else:
+            ret[change_typ].append(_adapt_path(change))  # type: ignore[literal-required]

-        _add_change(change.typ, change)
-
-    return ret
+    total_items = sum(
+        len(entries) for paths in to_check.values() for entries in paths.values()
+    )
+    with TqdmCallback(size=total_items, desc="Checking cache", unit="entry") as cb:
+        missing_items = list(
+            _get_missing_paths(
+                to_check, batch_size=batch_size, callback=StorageCallback(cb)
+            ),
+        )
+        if missing_items:
+            ret["not_in_cache"] = missing_items
+    return dict(ret)  # type: ignore[return-value]


 class GitInfo(TypedDict, total=False):
@@ -151,7 +245,49 @@ def _git_info(scm: Union["Git", "NoSCM"], untracked_files: str = "all") -> GitIn
    )


-def _diff_index_to_wtree(repo: "Repo", **kwargs: Any) -> dict[str, list[str]]:
+def filter_index(
+    index: Union["DataIndex", "DataIndexView"],
+    filter_keys: Optional[Iterable["DataIndexKey"]] = None,
+) -> "BaseDataIndex":
+    from dvc_data.index.view import DataIndexView
+
+    if not filter_keys:
+        return index
+
+    if isinstance(index, DataIndexView):
+        orig_index = index._index
+        parent_filter_fn = index.filter_fn
+    else:
+        orig_index = index
+        parent_filter_fn = None
+
+    def filter_fn(key: "DataIndexKey") -> bool:
+        if parent_filter_fn is not None and not parent_filter_fn(key):
+            return False
+
+        for filter_key in filter_keys:
+            # eg: if key is "dir/file" and filter_key is "dir/", return True
+            if key[: len(filter_key)] == filter_key:
+                return True
+            # eg: if key is `dir/` and filter_key is `dir/file`, also return True.
+            # This ensures we include parent prefixes needed to reach matching leaves.
+            # Intermediate prefixes must be retained to access nested keys.
+            if filter_key[: len(key)] == key:
+                return True
+        return False
+
+    from dvc_data.index import view
+
+    return view(orig_index, filter_fn=filter_fn)
+
+
+def _diff_index_to_wtree(
+    repo: "Repo",
+    filter_keys: Optional[Iterable["DataIndexKey"]] = None,
+    granular: bool = False,
+    batch_size: Optional[int] = None,
+    with_renames: bool = False,
+) -> DiffResult:
    from .index import build_data_index

    with ui.progress(desc="Building workspace index", unit="entry") as pb:
@@ -162,37 +298,69 @@ def _diff_index_to_wtree(repo: "Repo", **kwargs: Any) -> dict[str, list[str]]:
            compute_hash=True,
            callback=pb.as_callback(),
        )
+        workspace_view = filter_index(workspace, filter_keys=filter_keys)

    with ui.progress(
        desc="Calculating diff between index/workspace",
        unit="entry",
    ) as pb:
+        index = repo.index.data["repo"]
+        view = filter_index(index, filter_keys=filter_keys)
        return _diff(
-            repo.index.data["repo"],
-            workspace,
+            view,
+            workspace_view,
+            filter_keys=filter_keys,
+            granular=granular,
            not_in_cache=True,
+            with_renames=with_renames,
+            batch_size=batch_size,
            callback=pb.as_callback(),
-            **kwargs,
        )


 def _diff_head_to_index(
-    repo: "Repo", head: str = "HEAD", **kwargs: Any
-) -> dict[str, list[str]]:
-    index = repo.index.data["repo"]
+    repo: "Repo",
+    head: str = "HEAD",
+    filter_keys: Optional[Iterable["DataIndexKey"]] = None,
+    granular: bool = False,
+    with_renames: bool = False,
+) -> DiffResult:
+    from dvc.exceptions import NotDvcRepoError
+    from dvc.scm import RevError
+    from dvc_data.index import DataIndex

-    with repo.switch(head):
-        head_index = repo.index.data["repo"]
+    index = repo.index.data["repo"]
+    index_view = filter_index(index, filter_keys=filter_keys)
+
+    try:
+        with repo.switch(head):
+            head_index = repo.index.data["repo"]
+            head_view = filter_index(head_index, filter_keys=filter_keys)
+    except RevError:
+        logger.debug("failed to switch to '%s'", head)
+        head_view = DataIndex()
+    except NotDvcRepoError as exc:
+        # NOTE: this only gets raised on subdir repos at the moment,
+        # which looks like a bug in `repo.switch`.
+        logger.warning(exc)
+        head_view = DataIndex()

    with ui.progress(desc="Calculating diff between head/index", unit="entry") as pb:
-        return _diff(head_index, index, callback=pb.as_callback(), **kwargs)
+        return _diff(
+            head_view,
+            index_view,
+            filter_keys=filter_keys,
+            granular=granular,
+            with_renames=with_renames,
+            callback=pb.as_callback(),
+        )


 class Status(TypedDict):
    not_in_cache: list[str]
    not_in_remote: list[str]
-    committed: dict[str, list[str]]
-    uncommitted: dict[str, list[str]]
+    committed: DiffResult
+    uncommitted: DiffResult
    untracked: list[str]
    unchanged: list[str]
    git: GitInfo
@@ -217,27 +385,178 @@ def _transform_git_paths_to_dvc(repo: "Repo", files: Iterable[str]) -> list[str]
    return [repo.fs.relpath(file, start) for file in files]


-def status(repo: "Repo", untracked_files: str = "no", **kwargs: Any) -> Status:
+def iter_index(
+    index: Union["BaseDataIndex", "DataIndexView"], shallow: bool = False
+) -> Iterator[tuple["DataIndexKey", Optional["DataIndexEntry"]]]:
+    if not shallow:
+        yield from index.iteritems(shallow=shallow)
+        return
+
+    # only iterate until we find entries with hash_info in shallow mode
+    todo: deque[tuple[DataIndexKey, dict]] = deque([((), index.info(()))])
+    while todo:
+        key, info = todo.popleft()
+        entry = info.get("entry")
+        if info.get("type") == "directory" and not (entry and entry.hash_info):
+            try:
+                todo.extend(index.ls(key, detail=True))
+            except (KeyError, DataIndexDirError):
+                pass
+        yield key, entry
+
+
+def _get_entries_not_in_remote(
+    repo: "Repo",
+    filter_keys: Optional[Iterable["DataIndexKey"]] = None,
+    granular: bool = False,
+    remote_refresh: bool = False,
+) -> list[str]:
+    """Get entries that are not in remote storage."""
+    from dvc.repo.worktree import worktree_view
+    from dvc_data.index import StorageKeyError
+
+    entries: dict[DataIndexKey, DataIndexEntry] = {}
+
+    def _onerror(entry, exc):
+        if not isinstance(exc, DataIndexDirError):
+            raise exc
+        # We don't have the contents of this dir file, so we will only check this key.
+        entries[entry.key] = entry
+
+    # View into the index, with only pushable entries
+    index = worktree_view(repo.index, push=True)
+    data_index = index.data["repo"]
+
+    orig_data_index_onerror = data_index.onerror
+    data_index.onerror = _onerror
+
+    view = filter_index(data_index, filter_keys=filter_keys)  # type: ignore[arg-type]
+
+    missing_entries = []
+
+    storage_map = view.storage_map
+
+    n = 0
+    with TqdmCallback(size=n, desc="Checking remote", unit="entry") as cb:
+        for key, entry in iter_index(view, shallow=not granular):
+            if not (entry and entry.hash_info):
+                continue
+
+            # The index is a trie, so even when we filter by a specific path
+            # like `dir/file`, all parent nodes leading to that path (e.g., `dir/`)
+            # still appear in the view. As a result, keys like `dir/` will be present
+            # even if only `dir/file` matches the filter.
+            # We need to skip such entries to avoid showing root of tracked directories.
+            if filter_keys and not any(
+                key[: len(filter_key)] == filter_key for filter_key in filter_keys
+            ):
+                continue
+
+            entries[key] = entry
+            n += 1
+            cb.set_size(n)
+
+        for key, entry in entries.items():
+            k = (*key, "") if entry.meta and entry.meta.isdir else key
+            try:
+                if not storage_map.remote_exists(entry, refresh=remote_refresh):
+                    missing_entries.append(os.path.sep.join(k))
+            except StorageKeyError:
+                pass
+            finally:
+                cb.relative_update()
+    data_index.onerror = orig_data_index_onerror
+    return missing_entries
+
+
+def _matches_target(p: str, targets: Iterable[str]) -> bool:
+    sep = os.sep
+    return any(p == t or p.startswith(t + sep) for t in targets)
+
+
+def _prune_keys(filter_keys: Iterable["DataIndexKey"]) -> list["DataIndexKey"]:
+    sorted_keys = sorted(set(filter_keys), key=len)
+    result: list[DataIndexKey] = []
+
+    for key in sorted_keys:
+        if not any(key[: len(prefix)] == prefix for prefix in result):
+            result.append(key)
+    return result
+
+
+def status(  # noqa: PLR0913
+    repo: "Repo",
+    targets: Optional[Iterable[Union[os.PathLike[str], str]]] = None,
+    *,
+    granular: bool = False,
+    untracked_files: str = "no",
+    remote: Optional[str] = None,
+    not_in_remote: bool = False,
+    remote_refresh: bool = False,
+    config: Optional[dict] = None,
+    batch_size: Optional[int] = None,
+    head: str = "HEAD",
+    with_renames: bool = True,
+) -> Status:
    from dvc.scm import NoSCMError, SCMError

-    head = kwargs.pop("head", "HEAD")
-    uncommitted_diff = _diff_index_to_wtree(repo, **kwargs)
+    config = config or {}
+    if remote and not_in_remote:
+        logger.debug("Using remote %r", remote)
+        core = config.setdefault("core", {})
+        core["remote"] = remote
+    repo.config.merge(config)
+
+    targets = targets or []
+    filter_keys: list[DataIndexKey] = [repo.fs.relparts(os.fspath(t)) for t in targets]
+    # try to remove duplicate and overlapping keys
+    filter_keys = _prune_keys(filter_keys)
+
+    uncommitted_diff = _diff_index_to_wtree(
+        repo,
+        filter_keys=filter_keys,
+        granular=granular,
+        batch_size=batch_size,
+        with_renames=with_renames,
+    )
    unchanged = set(uncommitted_diff.pop("unchanged", []))

+    entries_not_in_remote: list[str] = []
+    if not_in_remote:
+        entries_not_in_remote = _get_entries_not_in_remote(
+            repo,
+            filter_keys=filter_keys,
+            granular=granular,
+            remote_refresh=remote_refresh,
+        )
+
    try:
-        committed_diff = _diff_head_to_index(repo, head=head, **kwargs)
+        committed_diff = _diff_head_to_index(
+            repo,
+            filter_keys=filter_keys,
+            head=head,
+            granular=granular,
+            with_renames=with_renames,
+        )
    except (SCMError, NoSCMError):
        committed_diff = {}
    else:
        unchanged &= set(committed_diff.pop("unchanged", []))

    git_info = _git_info(repo.scm, untracked_files=untracked_files)
-    untracked = git_info.get("untracked", [])
-    untracked = _transform_git_paths_to_dvc(repo, untracked)
+    scm_filter_targets = {
+        os.path.relpath(os.path.abspath(t), repo.scm.root_dir) for t in targets
+    }
+    untracked_it: Iterable[str] = git_info.get("untracked", [])
+    if scm_filter_targets:
+        untracked_it = (
+            f for f in untracked_it if _matches_target(f, scm_filter_targets)
+        )
+    untracked = _transform_git_paths_to_dvc(repo, untracked_it)
    # order matters here
    return Status(
        not_in_cache=uncommitted_diff.pop("not_in_cache", []),
-        not_in_remote=uncommitted_diff.pop("not_in_remote", []),
+        not_in_remote=entries_not_in_remote,
        committed=committed_diff,
        uncommitted=uncommitted_diff,
        untracked=untracked,
@@ -45,6 +45,12 @@ def _diff(old, new, data_keys, with_missing=False):
        with_renames=True,
        meta_cmp_key=meta_cmp_key,
        roots=data_keys,
+        # Include unknown entries from missing dir entry, so that they don't
+        # get reported as added/modified/deleted.
+        # Also return unchanged entries so that we can check if they are missing
+        # from cache.
+        with_unknown=True,
+        with_unchanged=with_missing,
    ):
        if (change.old and change.old.isdir and not change.old.hash_info) or (
            change.new and change.new.isdir and not change.new.hash_info
@@ -274,6 +274,7 @@ def collect(
    num: int = 1,
    hide_queued: bool = False,
    hide_failed: bool = False,
+    hide_workspace: bool = False,
    sha_only: bool = False,
    **kwargs,
 ) -> list["ExpState"]:
@@ -303,8 +304,11 @@ def collect(
            repo.scm, baseline_revs, refs=cached_refs, logger=logger
        )

-    workspace_data = collect_rev(repo, "workspace", **kwargs)
-    result: list[ExpState] = [workspace_data]
+    result: list[ExpState] = []
+    if not hide_workspace:
+        workspace_data = collect_rev(repo, "workspace", **kwargs)
+        result.append(workspace_data)
+
    queued = collect_queued(repo, baseline_revs, **kwargs) if not hide_queued else {}
    active = collect_active(repo, baseline_revs, **kwargs)
    failed = collect_failed(repo, baseline_revs, **kwargs) if not hide_failed else {}
@@ -50,7 +50,7 @@ class MultipleBranchError(DvcException):
        self.ref_infos = ref_infos


-class AmbiguousExpRefInfo(InvalidArgumentError):
+class AmbiguousExpRefInfo(InvalidArgumentError):  # noqa: N818
    def __init__(self, exp_name: str, exp_ref_list: Iterable["ExpRefInfo"]):
        msg = [
            (
@@ -1,20 +1,22 @@
-import logging
 import os
 import pickle
 import shutil
 from abc import ABC, abstractmethod
 from collections.abc import Iterable, Iterator
-from contextlib import contextmanager
+from contextlib import AbstractContextManager, contextmanager
 from dataclasses import asdict, dataclass
 from enum import IntEnum
 from itertools import chain
 from typing import TYPE_CHECKING, Any, Callable, NamedTuple, Optional, Union

+import funcy
+from funcy import nullcontext
 from scmrepo.exceptions import SCMError

 from dvc.env import DVC_EXP_AUTO_PUSH, DVC_EXP_GIT_REMOTE
 from dvc.exceptions import DvcException
 from dvc.log import logger
+from dvc.logger import set_loggers_level
 from dvc.repo.experiments.exceptions import ExperimentExistsError
 from dvc.repo.experiments.refs import EXEC_BASELINE, EXEC_BRANCH, ExpRefInfo
 from dvc.repo.experiments.utils import to_studio_params
@@ -297,7 +299,9 @@ class BaseExecutor(ABC):
                stages = dvc.commit([], recursive=recursive, force=True, relink=False)
            exp_hash = cls.hash_exp(stages)
            if include_untracked:
-                dvc.scm.add(include_untracked, force=True)  # type: ignore[call-arg]
+                from dvc.scm import add_no_submodules
+
+                add_no_submodules(dvc.scm, include_untracked, force=True)  # type: ignore[call-arg]

            with cls.auto_push(dvc):
                cls.commit(
@@ -466,8 +470,8 @@ class BaseExecutor(ABC):

        if queue is not None:
            queue.put((rev, os.getpid()))
-        if log_errors and log_level is not None:
-            cls._set_log_level(log_level)
+
+        log_ctx = cls._set_log_level(log_level) if log_errors else nullcontext()

        exp_hash: Optional[str] = None
        exp_ref: Optional[ExpRefInfo] = None
@@ -476,14 +480,17 @@ class BaseExecutor(ABC):
        if info.name:
            ui.write(f"Reproducing experiment '{info.name}'")

-        with cls._repro_dvc(
-            info,
-            infofile,
-            log_errors=log_errors,
-            copy_paths=copy_paths,
-            message=message,
-            **kwargs,
-        ) as dvc:
+        with (
+            log_ctx,
+            cls._repro_dvc(
+                info,
+                infofile,
+                log_errors=log_errors,
+                copy_paths=copy_paths,
+                message=message,
+                **kwargs,
+            ) as dvc,
+        ):
            args, kwargs = cls._repro_args(dvc)
            if args:
                targets: Optional[Union[list, str]] = args[0]
@@ -509,7 +516,9 @@ class BaseExecutor(ABC):
            stages = dvc.reproduce(*args, **kwargs)
            if paths := cls._get_top_level_paths(dvc):
                logger.debug("Staging top-level files: %s", paths)
-                dvc.scm_context.add(paths)
+                from dvc.scm import add_no_submodules
+
+                add_no_submodules(dvc.scm, paths)

            exp_hash = cls.hash_exp(stages)
            if not repro_dry:
@@ -786,13 +795,10 @@ class BaseExecutor(ABC):
        return orig_rev

    @staticmethod
-    def _set_log_level(level):
-        # When executor.reproduce is run in a multiprocessing child process,
-        # dvc.cli.main will not be called for that child process so we need to
-        # setup logging ourselves
-        dvc_logger = logging.getLogger("dvc")
+    def _set_log_level(level: Optional[int]) -> AbstractContextManager[None]:
        if level is not None:
-            dvc_logger.setLevel(level)
+            return set_loggers_level(level)
+        return nullcontext()

    @staticmethod
    def _copy_path(src, dst):
@@ -810,11 +816,22 @@ class BaseExecutor(ABC):

    @contextmanager
    def set_temp_refs(self, scm: "Git", temp_dict: dict[str, str]):
+        # Retry ref set, get, and remove operations to handle transient issues during
+        # concurrent Git access.
+        # Dulwich deletes parent directories of refs if they happen to be empty after
+        # removing a ref, which can interfere with `set_ref` in other processes.
+        # `remove_ref` may also fail with a `FileLocked` error when refs are packed,
+        # since multiple processes might attempt to write to the same file.
+        retry = funcy.retry(10, errors=Exception, timeout=0.1)
+        set_ref = retry(scm.set_ref)
+        get_ref = retry(scm.get_ref)
+        remove_ref = retry(scm.remove_ref)
+
        try:
            for ref, rev in temp_dict.items():
-                scm.set_ref(ref, rev)
+                set_ref(ref, rev)
            yield
        finally:
            for ref in temp_dict:
-                if scm.get_ref(ref):
-                    scm.remove_ref(ref)
+                if get_ref(ref):
+                    remove_ref(ref)
@@ -38,7 +38,7 @@ logger = logger.getChild(__name__)


@dataclass(frozen=True)
-class QueueEntry:
+class QueueEntry:  # noqa: PLW1641
    dvc_root: str
    scm_root: str
    stash_ref: str
@@ -287,6 +287,7 @@ class BaseStashQueue(ABC):
        baseline_rev: Optional[str] = None,
        branch: Optional[str] = None,
        name: Optional[str] = None,
+        no_hydra: bool = False,
        **kwargs,
    ) -> QueueEntry:
        """Stash changes from the workspace as an experiment.
@@ -302,6 +303,7 @@ class BaseStashQueue(ABC):
            name: Optional experiment name. If specified this will be used as
                the human-readable name in the experiment branch ref. Has no
                effect of branch is specified.
+            no_hydra: Disable Hydra from automatically overwriting all params.

        .. _Hydra Override:
            https://hydra.cc/docs/next/advanced/override_grammar/basic/
@@ -318,7 +320,7 @@ class BaseStashQueue(ABC):

                    # update experiment params from command line
                    if params:
-                        self._update_params(params)
+                        self._update_params(params, no_hydra=no_hydra)

                    # DVC commit data deps to preserve state across workspace
                    # & tempdir runs
@@ -441,12 +443,13 @@ class BaseStashQueue(ABC):
            f"from '{config_path}': {param_list}"
        )

-    def _update_params(self, params: dict[str, list[str]]):
+    def _update_params(self, params: dict[str, list[str]], no_hydra: bool = False):
        """Update param files with the provided `Hydra Override`_ patterns.

        Args:
            params: Dict mapping paths to `Hydra Override`_ patterns,
                provided via `exp run --set-param`.
+            no_hydra: Disable Hydra from automatically overwriting all params.

        .. _Hydra Override:
            https://hydra.cc/docs/advanced/override_grammar/basic/
@@ -456,7 +459,7 @@ class BaseStashQueue(ABC):
        logger.debug("Using experiment params '%s'", params)

        hydra_config = self.repo.config.get("hydra", {})
-        hydra_enabled = hydra_config.get("enabled", False)
+        hydra_enabled = hydra_config.get("enabled", False) and not no_hydra
        hydra_output_file = ParamsDependency.DEFAULT_PARAMS_FILE
        for path, overrides in params.items():
            if hydra_enabled and path == hydra_output_file:
@@ -1,3 +1,4 @@
+import glob
 import hashlib
 import locale
 import logging
@@ -69,7 +70,7 @@ class LocalCeleryQueue(BaseStashQueue):
    def celery(self) -> "FSApp":
        from kombu.transport.filesystem import Channel

-        # related to https://github.com/iterative/dvc-task/issues/61
+        # related to https://github.com/treeverse/dvc-task/issues/61
        Channel.QoS.restore_at_shutdown = False

        from dvc_task.app import FSApp
@@ -434,9 +435,13 @@ class LocalCeleryQueue(BaseStashQueue):
        try:
            proc_info = self.proc[queue_entry.stash_rev]
        except KeyError:
-            raise DvcException(  # noqa: B904
-                f"No output logs found for experiment '{rev}'"
-            )
+            message = f"No output logs found for experiment '{rev}'"
+            if self.match_queue_entry_by_name({rev}, self.iter_failed()).get(rev):
+                message += "\nExperiment likely failed during setup."
+                if celery_logs := glob.glob(os.path.join(self.wdir, "*.out")):
+                    message += " Check the celery logs for more details:"
+                    message += f"\n\tcat {' '.join(celery_logs)}".expandtabs(4)
+            raise DvcException(message)  # noqa: B904
        with open(
            proc_info.stdout, encoding=encoding or locale.getpreferredencoding()
        ) as fobj:
@@ -22,6 +22,7 @@ def run(  # noqa: C901, PLR0912
    queue: bool = False,
    copy_paths: Optional[Iterable[str]] = None,
    message: Optional[str] = None,
+    no_hydra: bool = False,
    **kwargs,
 ) -> dict[str, str]:
    """Reproduce the specified targets as an experiment.
@@ -67,7 +68,7 @@ def run(  # noqa: C901, PLR0912
    else:
        path_overrides = {}

-    hydra_enabled = repo.config.get("hydra", {}).get("enabled", False)
+    hydra_enabled = repo.config.get("hydra", {}).get("enabled", False) and not no_hydra
    hydra_output_file = ParamsDependency.DEFAULT_PARAMS_FILE
    if hydra_enabled and hydra_output_file not in path_overrides:
        # Force `_update_params` even if `--set-param` was not used
@@ -80,6 +81,7 @@ def run(  # noqa: C901, PLR0912
            tmp_dir=tmp_dir,
            copy_paths=copy_paths,
            message=message,
+            no_hydra=no_hydra,
            **kwargs,
        )

@@ -100,6 +102,7 @@ def run(  # noqa: C901, PLR0912
            params=sweep_overrides,
            copy_paths=copy_paths,
            message=message,
+            no_hydra=no_hydra,
            **kwargs,
        )
        if sweep_overrides:
@@ -30,6 +30,7 @@ def show(
    num: int = 1,
    hide_queued: bool = False,
    hide_failed: bool = False,
+    hide_workspace: bool = False,
    sha_only: bool = False,
    **kwargs,
 ) -> list["ExpState"]:
@@ -42,6 +43,7 @@ def show(
        num=num,
        hide_queued=hide_queued,
        hide_failed=hide_failed,
+        hide_workspace=hide_workspace,
        sha_only=sha_only,
        **kwargs,
    )
@@ -10,6 +10,7 @@ from . import locked

 if TYPE_CHECKING:
    from dvc.output import Output
+    from dvc.repo import Repo
    from dvc.stage import Stage

 logger = logger.getChild(__name__)
@@ -19,12 +20,13 @@ def _make_index_onerror(onerror, rev):
    def _onerror(entry, exc):
        if onerror:
            return onerror(rev, entry, exc)
+        return None

    return _onerror


 def _collect_indexes(  # noqa: PLR0913
-    repo,
+    repo: "Repo",
    targets=None,
    remote=None,
    all_branches=False,
@@ -40,6 +42,8 @@ def _collect_indexes(  # noqa: PLR0913
    onerror=None,
    push=False,
 ):
+    from .index import index_from_targets
+
    indexes = {}
    collection_exc = None

@@ -67,7 +71,8 @@ def _collect_indexes(  # noqa: PLR0913
        try:
            repo.config.merge(config)

-            idx = repo.index.targets_view(
+            idx = index_from_targets(
+                repo,
                targets,
                with_deps=with_deps,
                recursive=recursive,
@@ -94,7 +99,7 @@ def _collect_indexes(  # noqa: PLR0913

@locked
 def fetch(  # noqa: PLR0913
-    self,
+    self: "Repo",
    targets=None,
    jobs=None,
    remote=None,
@@ -17,6 +17,7 @@ from dvc.utils.objects import cached_property
 if TYPE_CHECKING:
    from networkx import DiGraph
    from pygtrie import Trie
+    from typing_extensions import Self

    from dvc.dependency import Dependency
    from dvc.fs.callbacks import Callback
@@ -66,14 +67,14 @@ def collect_files(

    is_local_fs = isinstance(fs, LocalFileSystem)

-    def is_ignored(path):
+    def is_ignored(path: str) -> bool:
        # apply only for the local fs
        return is_local_fs and scm.is_ignored(path)

-    def is_dvcfile_and_not_ignored(root, file):
+    def is_dvcfile_and_not_ignored(root: str, file: str) -> bool:
        return is_valid_filename(file) and not is_ignored(f"{root}{sep}{file}")

-    def is_out_or_ignored(root, directory):
+    def is_out_or_ignored(root: str, directory: str) -> bool:
        dir_path = f"{root}{sep}{directory}"
        # trailing slash needed to check if a directory is gitignored
        return dir_path in outs or is_ignored(f"{dir_path}{sep}")
@@ -83,6 +84,8 @@ def collect_files(
        walk_iter = log_walk(walk_iter)

    for root, dirs, files in walk_iter:
+        assert isinstance(dirs, list)
+        assert isinstance(files, list)
        dvcfile_filter = partial(is_dvcfile_and_not_ignored, root)
        for file in filter(dvcfile_filter, files):
            file_path = fs.join(root, file)
@@ -318,32 +321,9 @@ class Index:
        repo: "Repo",
        onerror: Optional[Callable[[str, Exception], None]] = None,
    ) -> "Index":
-        stages = []
-        metrics = {}
-        plots = {}
-        params = {}
-        artifacts = {}
-        datasets = {}
-        datasets_lock = {}
-
        onerror = onerror or repo.stage_collection_error_handler
-        for _, idx in collect_files(repo, onerror=onerror):
-            stages.extend(idx.stages)
-            metrics.update(idx._metrics)
-            plots.update(idx._plots)
-            params.update(idx._params)
-            artifacts.update(idx._artifacts)
-            datasets.update(idx._datasets)
-            datasets_lock.update(idx._datasets_lock)
-        return cls(
-            repo,
-            stages=stages,
-            metrics=metrics,
-            plots=plots,
-            params=params,
-            artifacts=artifacts,
-            datasets=datasets,
-            datasets_lock=datasets_lock,
+        return cls.from_indexes(
+            repo, (idx for _, idx in collect_files(repo, onerror=onerror))
        )

    @classmethod
@@ -364,7 +344,7 @@ class Index:
            else {},
        )

-    def update(self, stages: Iterable["Stage"]) -> "Index":
+    def update(self, stages: Iterable["Stage"]) -> "Self":
        stages = set(stages)
        # we remove existing stages with same hashes at first
        # and then re-add the new ones later.
@@ -379,6 +359,36 @@ class Index:
            datasets=self._datasets,
        )

+    @classmethod
+    def from_indexes(cls, repo, idxs: Iterable["Self"]) -> "Self":
+        stages = []
+        metrics = {}
+        plots = {}
+        params = {}
+        artifacts = {}
+        datasets = {}
+        datasets_lock = {}
+
+        for idx in idxs:
+            stages.extend(idx.stages)
+            metrics.update(idx._metrics)
+            plots.update(idx._plots)
+            params.update(idx._params)
+            artifacts.update(idx._artifacts)
+            datasets.update(idx._datasets)
+            datasets_lock.update(idx._datasets_lock)
+
+        return cls(
+            repo,
+            stages=stages,
+            metrics=metrics,
+            plots=plots,
+            params=params,
+            artifacts=artifacts,
+            datasets=datasets,
+            datasets_lock=datasets_lock,
+        )
+
    @cached_property
    def outs_trie(self) -> "Trie":
        from dvc.repo.trie import build_outs_trie
@@ -735,6 +745,10 @@ class IndexView:
        for stage in self.stages:
            yield from stage.deps

+    @property
+    def index(self) -> "Index":
+        return self._index
+
    @property
    def _filtered_outs(self) -> Iterator[tuple["Output", Optional[str]]]:
        for stage, filter_info in self._stage_infos:
@@ -927,3 +941,51 @@ def _get_entry_hash_name(
            return src_entry.hash_info.name

    return DEFAULT_ALGORITHM
+
+
+def index_from_targets(
+    repo: "Repo",
+    targets: Optional["TargetType"] = None,
+    stage_filter: Optional[Callable[["Stage"], bool]] = None,
+    outs_filter: Optional[Callable[["Output"], bool]] = None,
+    max_size: Optional[int] = None,
+    types: Optional[list[str]] = None,
+    with_deps: bool = False,
+    recursive: bool = False,
+    **kwargs: Any,
+) -> "IndexView":
+    from dvc.stage.exceptions import StageFileDoesNotExistError, StageNotFound
+    from dvc.utils import parse_target
+
+    index: Optional[Index] = None
+    if targets and all(targets) and not with_deps and not recursive:
+        indexes: list[Index] = []
+        try:
+            for target in targets:
+                if not target:
+                    continue
+                file, name = parse_target(target)
+                if file and not name:
+                    index = Index.from_file(repo, file)
+                else:
+                    stages = repo.stage.collect(target)
+                    index = Index(repo, stages=list(stages))
+                indexes.append(index)
+        except (StageFileDoesNotExistError, StageNotFound):
+            pass
+        else:
+            index = Index.from_indexes(repo, indexes)
+            targets = None
+
+    if index is None:
+        index = repo.index
+    return index.targets_view(
+        targets,
+        stage_filter=stage_filter,
+        outs_filter=outs_filter,
+        max_size=max_size,
+        types=types,
+        recursive=recursive,
+        with_deps=with_deps,
+        **kwargs,
+    )
@@ -63,7 +63,7 @@ def init(root_dir=os.curdir, no_scm=False, force=False, subdir=False):  # noqa:

        remove(dvc_dir)

-    os.mkdir(dvc_dir)
+    os.makedirs(dvc_dir, exist_ok=True)

    config = Config.init(dvc_dir)

@@ -16,7 +16,7 @@ def pre_commit_install(scm: "Git") -> None:
    config_path = os.path.join(scm.root_dir, ".pre-commit-config.yaml")
    with modify_yaml(config_path) as config:
        entry = {
-            "repo": "https://github.com/iterative/dvc",
+            "repo": "https://github.com/treeverse/dvc",
            "rev": ".".join(map(str, version_tuple[:3])),
            "hooks": [
                {
@@ -75,7 +75,7 @@ def install(self: "Repo", use_pre_commit_tool: bool = False) -> None:

    scm = self.scm
    if not isinstance(scm, Git):
-        return
+        return None

    driver = "dvc git-hook merge-driver --ancestor %O --our %A --their %B "
    scm.install_merge_driver("dvc", "DVC merge driver", driver)
@@ -1,10 +1,13 @@
 import os
+from typing import TYPE_CHECKING

-from dvc.exceptions import MoveNotDataSourceError
 from dvc.repo.scm_context import scm_context

 from . import locked

+if TYPE_CHECKING:
+    from . import Repo
+

 def _expand_target_path(from_path, to_path):
    if os.path.isdir(to_path):
@@ -14,7 +17,7 @@ def _expand_target_path(from_path, to_path):

@locked
@scm_context
-def move(self, from_path, to_path):
+def move(self: "Repo", from_path, to_path):
    """
    Renames an output file and modifies the stage associated
    to reflect the change on the pipeline.
@@ -32,9 +35,12 @@ def move(self, from_path, to_path):
    It only works with outputs generated by `add` or `import`,
    also known as data sources.
    """
-    from dvc import output
+    from dvc import dependency, output
    from dvc.dvcfile import DVC_FILE_SUFFIX
+    from dvc.exceptions import MoveNotDataSourceError
    from dvc.stage import Stage
+    from dvc.stage.exceptions import StageFileAlreadyExistsError
+    from dvc_objects.fs.local import LocalFileSystem

    from_out = output.loads_from(Stage(self), [from_path])[0]
    assert from_out.protocol == "local"
@@ -45,6 +51,7 @@ def move(self, from_path, to_path):
    assert len(outs) == 1
    out = outs[0]
    stage = out.stage
+    deps = stage.deps

    if not stage.is_data_source:
        raise MoveNotDataSourceError(stage.addressing)
@@ -58,21 +65,38 @@ def move(self, from_path, to_path):
        )
        new_wdir = os.path.abspath(os.path.join(os.curdir, os.path.dirname(to_path)))
        to_path = os.path.relpath(to_path, new_wdir)
-        new_stage = self.stage.create(
-            single_stage=True,
-            fname=new_fname,
-            wdir=new_wdir,
-            outs=[to_path],
-            meta=stage.meta,
-        )
-
-        os.unlink(stage.path)
-        stage = new_stage
+        try:
+            new_stage = self.stage.create(
+                single_stage=True,
+                fname=new_fname,
+                wdir=new_wdir,
+                outs=[to_path],
+                meta=stage.meta,
+                frozen=stage.frozen,
+                always_changed=stage.always_changed,
+                desc=stage.desc,
+            )
+        except StageFileAlreadyExistsError:
+            # reraise to remove `--force` hint
+            raise StageFileAlreadyExistsError(f"{new_fname!r} already exists") from None
    else:
+        new_stage = stage
        to_path = os.path.relpath(to_path, stage.wdir)

-    to_out = output.loads_from(stage, [to_path], out.use_cache, out.metric)[0]
+    def with_dep_path_adjusted(dep: dependency.Dependency):
+        d = dep.dumpd()
+        if isinstance(dep.fs, LocalFileSystem) and not os.path.isabs(dep.def_path):
+            return d | {"path": os.path.relpath(dep.fspath, new_stage.wdir)}
+        return d

-    out.move(to_out)
-    stage.save()
-    stage.dump()
+    new_stage.outs = output.loadd_from(new_stage, [out.dumpd() | {"path": to_path}])
+    new_stage.deps = dependency.loadd_from(
+        new_stage, [with_dep_path_adjusted(dep) for dep in deps]
+    )
+    out.move(new_stage.outs[0])
+    new_stage.md5 = new_stage.compute_md5()
+    new_stage.dump()
+    if stage != new_stage:
+        stage.dvcfile.remove()
+        self.scm_context.track_file(stage.dvcfile.relpath)
+    return stage, new_stage
@@ -32,7 +32,7 @@ logger = logger.getChild(__name__)


 def onerror_collect(result: dict, exception: Exception, *args, **kwargs):
-    logger.debug("", exc_info=True)
+    logger.debug("", exc_info=True)  # noqa: LOG014
    result["error"] = exception


@@ -346,14 +346,14 @@ def _get_data_targets(definitions: dict):


 def infer_data_sources(plot_id, config=None):
-    y = config.get("y", None)
+    y = config.get("y", None) if config else None

    if isinstance(y, dict):
        sources = list(y.keys())
    else:
        sources = [plot_id]

-    x = config.get("x", None)
+    x = config.get("x", None) if config else None
    if isinstance(x, dict):
        sources.append(first(x.keys()))

@@ -507,7 +507,7 @@ def _collect_pipeline_files(repo, targets: list[str], props, onerror=None):
@error_handler
 def _collect_definitions(
    repo: "Repo",
-    targets=None,
+    targets: list[str],
    props: Optional[dict] = None,
    onerror: Optional[Callable] = None,
    **kwargs,
@@ -39,7 +39,7 @@ def pull(  # noqa: PLR0913
        run_cache=run_cache,
    )
    try:
-        stats = self.checkout(
+        result = self.checkout(
            targets=expanded_targets,
            with_deps=with_deps,
            force=force,
@@ -47,8 +47,10 @@ def pull(  # noqa: PLR0913
            allow_missing=allow_missing,
        )
    except CheckoutError as exc:
-        exc.stats["fetched"] = processed_files_count
+        # put fetched counts first
+        exc.result["stats"] = {"fetched": processed_files_count} | exc.result["stats"]
        raise
-
-    stats["fetched"] = processed_files_count
-    return stats
+    else:
+        # put fetched counts first
+        result["stats"] = {"fetched": processed_files_count} | result["stats"]
+    return result
@@ -152,10 +152,12 @@ def push(  # noqa: PLR0913
    finally:
        ws_idx = indexes.get("workspace")
        if ws_idx is not None:
+            from dvc.repo.index import IndexView
+
+            _index = ws_idx.index if isinstance(ws_idx, IndexView) else ws_idx
            _update_meta(
-                self.index,
+                _index,
                targets=glob_targets(targets, glob=glob),
-                remote=remote,
                with_deps=with_deps,
                recursive=recursive,
            )
@@ -41,10 +41,12 @@ class SCMContext:
    def add(self, paths: Union[str, Iterable[str]]) -> None:
        from scmrepo.exceptions import UnsupportedIndexFormat

+        from dvc.scm import add_no_submodules
+
        try:
-            return self.scm.add(paths)
+            add_no_submodules(self.scm, paths)
        except UnsupportedIndexFormat:
-            link = "https://github.com/iterative/dvc/issues/610"
+            link = "https://github.com/treeverse/dvc/issues/610"
            add_cmd = self._make_git_add_cmd([relpath(path) for path in paths])
            logger.info("")
            msg = (
@@ -56,7 +58,7 @@ class SCMContext:
    def track_changed_files(self) -> None:
        """Stage files that have changed."""
        if not self.files_to_track:
-            return
+            return None
        logger.debug("Staging files: %s", self.files_to_track)
        return self.add(self.files_to_track)

@@ -74,6 +76,7 @@ class SCMContext:
            logger.debug("Added '%s' to gitignore file.", path)
            self.track_file(relpath(gitignore_file))
            return self.ignored_paths.append(path)
+        return None

    def ignore_remove(self, path: str) -> None:
        from scmrepo.exceptions import FileNotInRepoError
@@ -88,6 +91,7 @@ class SCMContext:

        if gitignore_file:
            return self.track_file(relpath(gitignore_file))
+        return None

    @contextmanager
    def __call__(
@@ -130,7 +130,7 @@ def status(  # noqa: PLR0913
            remote=remote,
            all_tags=all_tags,
            all_commits=all_commits,
-            recursive=True,
+            recursive=recursive,
        )

    ignored = list(
@@ -152,7 +152,7 @@ def _merge_push_meta(  # noqa: C901
    else:
        if entry.hash_info:
            out.hash_info = entry.hash_info
-        if out.meta.version_id is None:
+        if out.meta is None or out.meta.version_id is None:
            out.meta = entry.meta
    if out.meta:
        out.meta.remote = remote
@@ -181,7 +181,7 @@ def _update_worktree_out(
 ):
    from dvc_data.index import build

-    remote_name = out.remote or out.meta.remote
+    remote_name = out.remote or (out.meta.remote if out.meta is not None else None)
    if not remote_name:
        logger.warning("Could not update '%s', it was never pushed to a remote", out)
        return
@@ -212,11 +212,12 @@ def _update_worktree_out(
        logger.warning("Could not update '%s', directory is empty in the remote", out)
        return

-    _fetch_out_changes(out, local_index, remote_index, remote)
+    _fetch_out_changes(repo, out, local_index, remote_index, remote)
    _update_out_meta(repo, out, local_index, remote_index, remote)


 def _fetch_out_changes(
+    repo: "Repo",
    out: "Output",
    local_index: Union["DataIndex", "DataIndexView"],
    remote_index: Union["DataIndex", "DataIndexView"],
@@ -242,7 +243,7 @@ def _fetch_out_changes(
        cb.set_size(total)
        apply(
            diff,
-            out.repo.root_dir,
+            repo.root_dir,
            out.fs,
            update_meta=False,
            storage="data",
@@ -1,17 +1,18 @@
 """Manages source control systems (e.g. Git)."""

 import os
-from collections.abc import Iterator, Mapping
+from collections.abc import Iterable, Iterator, Mapping
 from contextlib import contextmanager
 from functools import partial
 from typing import TYPE_CHECKING, Literal, Optional, Union, overload

 from funcy import group_by
-from scmrepo.base import Base  # noqa: F401
+from scmrepo.base import Base  # noqa: TC002
 from scmrepo.git import Git
 from scmrepo.noscm import NoSCM

 from dvc.exceptions import DvcException
+from dvc.log import logger
 from dvc.progress import Tqdm

 if TYPE_CHECKING:
@@ -19,6 +20,8 @@ if TYPE_CHECKING:

    from dvc.fs import FileSystem

+logger = logger.getChild(__name__)
+

 class SCMError(DvcException):
    """Base class for source control management errors."""
@@ -42,7 +45,7 @@ class NoSCMError(SCMError):
        super().__init__(msg)


-class InvalidRemoteSCMRepo(SCMError):
+class InvalidRemoteSCMRepo(SCMError):  # noqa: N818
    pass


@@ -283,3 +286,35 @@ def lfs_prefetch(fs: "FileSystem", paths: list[str]):
            include=[(path if path.startswith("/") else f"/{path}") for path in paths],
            progress=pbar.update_git,
        )
+
+
+def add_no_submodules(
+    scm: "Base",
+    paths: Union[str, Iterable[str]],
+    **kwargs,
+) -> None:
+    """Stage paths to Git, excluding those inside submodules."""
+
+    if isinstance(paths, str):
+        paths = [paths]
+
+    submodule_roots = {os.path.join(scm.root_dir, sub) for sub in scm.list_submodules()}
+
+    repo_paths: list[str] = []
+    skipped_paths: list[str] = []
+
+    for p in paths:
+        abs_path = os.path.abspath(p)
+        if any(
+            abs_path == root or abs_path.startswith(root + os.sep)
+            for root in submodule_roots
+        ):
+            skipped_paths.append(p)
+        else:
+            repo_paths.append(p)
+
+    if skipped_paths:
+        msg = "Skipping staging for path(s) inside submodules: %s"
+        logger.debug(msg, ", ".join(skipped_paths))
+
+    scm.add(repo_paths, **kwargs)
@@ -32,7 +32,7 @@ from .utils import (
 )

 if TYPE_CHECKING:
-    from dvc.dependency import ParamsDependency
+    from dvc.dependency import Dependency, ParamsDependency
    from dvc.dvcfile import ProjectFile, SingleStageFile
    from dvc.output import Output
    from dvc.repo import Repo
@@ -121,7 +121,7 @@ def restore_fields(stage: "Stage") -> None:

    old_outs = {out.def_path: out for out in old.outs}
    for out in stage.outs:
-        old_out = old_outs.get(out.def_path, None)
+        old_out = old_outs.get(out.def_path)
        if old_out is not None:
            out.restore_fields(old_out)

@@ -153,8 +153,8 @@ class Stage(params.StageParams):
        self._path = path
        self.cmd = cmd
        self.wdir = wdir
-        self.outs = outs
-        self.deps = deps
+        self.outs: list[Output] = outs
+        self.deps: list[Dependency] = deps
        self.md5 = md5
        self.frozen = locked or frozen
        self.always_changed = always_changed
@@ -509,34 +509,20 @@ class Stage(params.StageParams):
                if not allow_missing:
                    raise

-    def get_versioned_outs(self) -> dict[str, "Output"]:
-        from .exceptions import StageFileDoesNotExistError, StageNotFound
-
-        try:
-            old = self.reload()
-        except (StageFileDoesNotExistError, StageNotFound):
-            return {}
-
-        return {
-            out.def_path: out
-            for out in old.outs
-            if out.files is not None
-            or (out.meta is not None and out.meta.version_id is not None)
-        }
-
    def save_outs(self, allow_missing: bool = False):
        from dvc.output import OutputDoesNotExistError

-        old_versioned_outs = self.get_versioned_outs()
        for out in self.outs:
+            # old state just before saving so to merge them later
+            old_state = out._get_versioned_meta()
            try:
                out.save()
            except OutputDoesNotExistError:
                if not allow_missing:
                    raise

-            if old_out := old_versioned_outs.get(out.def_path):
-                out.merge_version_meta(old_out)
+            if old_state:
+                out.merge_version_meta(*old_state)

    def ignore_outs(self) -> None:
        for out in self.outs:
@@ -579,8 +565,9 @@ class Stage(params.StageParams):
        from dvc.output import OutputDoesNotExistError

        link_failures = []
-        old_versioned_outs = self.get_versioned_outs()
        for out in self.filter_outs(filter_info):
+            # old state just before saving so to merge them later
+            old_state = out._get_versioned_meta()
            try:
                out.add(filter_info, **kwargs)
            except (FileNotFoundError, OutputDoesNotExistError):
@@ -589,8 +576,8 @@ class Stage(params.StageParams):
            except CacheLinkError:
                link_failures.append(filter_info or out.fs_path)

-            if old_out := old_versioned_outs.get(out.def_path):
-                out.merge_version_meta(old_out)
+            if old_state:
+                out.merge_version_meta(*old_state)

        if link_failures:
            raise CacheLinkError(link_failures)
@@ -82,7 +82,7 @@ class DataSourceChanged(DvcException):
        super().__init__(f"data source changed: {path}")


-class StageNotFound(DvcException, KeyError):
+class StageNotFound(DvcException, KeyError):  # noqa: N818
    def __init__(self, file, name):
        self.file = file.relpath
        self.name = name
@@ -51,7 +51,7 @@ def _warn_if_fish(executable):
        "Be aware that it might cause problems by overwriting "
        "your current environment variables with values defined "
        "in 'config.fish', which might affect your command. See "
-        "https://github.com/iterative/dvc/issues/1307. "
+        "https://github.com/treeverse/dvc/issues/1307. "
    )


@@ -99,7 +99,7 @@ def prepare_kwargs(stage, run_env=None):
    #
    # [1] https://github.com/python/cpython/blob/3.7/Lib/subprocess.py
    #                                                            #L1426
-    # [2] https://github.com/iterative/dvc/issues/2506
+    # [2] https://github.com/treeverse/dvc/issues/2506
    #                                           #issuecomment-535396799
    kwargs["shell"] = os.name == "nt"
    return kwargs
@@ -168,6 +168,7 @@ def to_single_stage_lockfile(stage: "Stage", **kwargs) -> dict:
                    for f in _serialize_tree_obj_to_files(obj)
                ]
        else:
+            assert item.meta is not None
            meta_d = item.meta.to_dict()
            meta_d.pop("isdir", None)
            ret.update(_serialize_hi_to_dict(item.hash_info))
@@ -177,7 +178,7 @@ def to_single_stage_lockfile(stage: "Stage", **kwargs) -> dict:
    res = OrderedDict([("cmd", stage.cmd)])
    params, deps = split_params_deps(stage)
    deps, outs = (
-        [_dumpd(item) for item in sorted(items, key=attrgetter("def_path"))]
+        [_dumpd(item) for item in sorted(items, key=attrgetter("def_path"))]  # type: ignore[call-overload]
        for items in [deps, stage.outs]
    )
    params = _serialize_params_values(params)
@@ -4,7 +4,7 @@ dvc.testing.benchmarks
 ======================

 Benchmark test definitions are now part of ``dvc.testing``.
-For CLI usage and `bench.dvc.org <https://bench.dvc.org>`_ details see `dvc-bench <https://github.com/iterative/dvc-bench>`_.
+For CLI usage and `bench.dvc.org <https://bench.dvc.org>`_ details see `dvc-bench <https://github.com/treeverse/dvc-bench>`_.

 ``dvc.testing.benchmarks`` structure:

--- a/Show More
+++ b/Show More