fix: clean up staging ODB after dvc add --out transfer

[BALOGUN-DAVID]

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Fix Staging ODB Cleanup for dvc add --out

📝 Description

When running dvc add --out, DVC copies source files into the cache via a staging mechanism but fails to clean up the temporary staging ODB (stored in memfs) and temporary upload files after the transfer completes.
This causes lingering temporary files and memfs bloat.
This issue was confirmed as a bug by DVC maintainers.

Approach:
This PR adds a staging.clear() call inside the Output.transfer() method in dvc/output.py, directly after otransfer() successfully moves the objects from the staging area to the cache ODB.

Impact:
Prevents memory leaks and disk space accumulation by properly freeing up temporary memfs staging files and caching artifacts upon successful completion of the dvc add --out command.

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✅ Test Results

• Added a new test test_add_with_out_cleans_up_staging in tests/func/test_add.py that uses a mocker spy on ObjectDB.clear to ensure the cleanup function is triggered.
• Validated that all existing tests related to add --out pass smoothly (e.g.,
  test_add_with_out, test_add_force_overwrite_out, test_add_to_cache_different_name).

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🧩 Visual Evidence — output.py Changes

# dvc/output.py # (Showing lines 1059-1066)
                 callback=cb,
             )

             staging.clear()  # <- ADDED THIS LINE

         self.hash_info = obj.hash_info
         self.files = None
         return obj

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🧪 Visual Evidence — Test Changes

# tests/func/test_add.py # (Showing lines 896-905)
def test_add_with_out_cleans_up_staging(tmp_dir, dvc, mocker):
    """Test that 'dvc add --out' cleans up the staging ODB after transfer."""
    from dvc_objects.db import ObjectDB

    tmp_dir.gen({"foo": "foo"})
    clear_spy = mocker.spy(ObjectDB, "clear")
    dvc.add("foo", out="out_foo")

    assert (tmp_dir / "out_foo").read_text() == "foo"
    assert clear_spy.call_count >= 1  # <- ADDED ASSERTION

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📋 Checklist

• [x ] ❗ I have followed the Contributing to DVC checklist.

• 📖 If this PR requires documentation updates, I have created a separate PR (or issue, at least) in dvc.org and linked it here.

Thank you for the contribution - we'll try to review it as soon as possible. 🙏

[CLAassistant]

All committers have signed the CLA.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.98%. Comparing base (2431ec6) to head (a4ac06c).
⚠️ Report is 194 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main   #11008      +/-   ##
==========================================
+ Coverage   90.68%   90.98%   +0.30%     
==========================================
  Files         504      505       +1     
  Lines       39795    41111    +1316     
  Branches     3141     3258     +117     
==========================================
+ Hits        36087    37404    +1317     
- Misses       3042     3069      +27     
+ Partials      666      638      -28     

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[BALOGUN-DAVID]

Hi @skshetry, I’ve just opened this PR to address #10783 . When you have a moment, I would really appreciate your review and feedback on the implementation. Thank you!