diff --git a/tests/hermes_cli/test_checkpoints_prune.py b/tests/hermes_cli/test_checkpoints_prune.py
new file mode 100644
index 000000000000..d597bc86f9c2
--- /dev/null
+++ b/tests/hermes_cli/test_checkpoints_prune.py
@@ -0,0 +1,208 @@
+"""Tests for `hermes checkpoints prune`'s orphan confirmation flow.
+
+Covers the P1 raised on PR #69141: the confirmation preview must cover
+BOTH v2 projects (`store_status()["projects"]`) and pre-v2 shadow repos
+(`store_status()["pre_v2_projects"]`), since `prune_checkpoints()` deletes
+orphans from both layouts. Exercises decline / accept / --force across
+pre-v2-only and mixed (v2 + pre-v2) stores.
+"""
+
+from __future__ import annotations
+
+import argparse
+
+import pytest
+
+
+def _ns(**kwargs) -> argparse.Namespace:
+    defaults = {"retention_days": 7, "max_size_mb": 500, "keep_orphans": False, "force": False}
+    defaults.update(kwargs)
+    return argparse.Namespace(**defaults)
+
+
+def _prune_result(**kwargs) -> dict:
+    result = {"scanned": 0, "deleted_orphan": 0, "deleted_stale": 0, "errors": 0, "bytes_freed": 0}
+    result.update(kwargs)
+    return result
+
+
+_V2_ORPHAN_ONLY_STATUS = {
+    "projects": [],
+    "pre_v2_projects": [],
+}
+
+_PRE_V2_ONLY_STATUS = {
+    "projects": [],
+    "pre_v2_projects": [
+        {"path": "/home/user/.hermes/checkpoints/deadbeefcafebabe", "workdir": None, "exists": False},
+    ],
+}
+
+_MIXED_STATUS = {
+    "projects": [
+        {"hash": "abc123", "workdir": "/gone/v2-project", "exists": False, "commits": 4},
+    ],
+    "pre_v2_projects": [
+        {"path": "/home/user/.hermes/checkpoints/deadbeefcafebabe", "workdir": "/gone/pre-v2-project", "exists": False},
+    ],
+}
+
+
+def _patch_checkpoint_manager(monkeypatch, status: dict, prune_calls: list):
+    import tools.checkpoint_manager as ckpt_mgr
+
+    monkeypatch.setattr(ckpt_mgr, "store_status", lambda *a, **k: status)
+
+    def _fake_prune(**kwargs):
+        prune_calls.append(kwargs)
+        return _prune_result(
+            deleted_orphan=len(status["projects"]) + len(status["pre_v2_projects"]),
+        )
+
+    monkeypatch.setattr(ckpt_mgr, "prune_checkpoints", _fake_prune)
+
+
+# ─── pre-v2-only store ──────────────────────────────────────────────────────
+
+
+def test_pre_v2_only_decline_aborts_without_deleting(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "n")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 1
+    assert prune_calls == []
+    out = capsys.readouterr().out
+    assert "pre-v2 shadow repo" in out
+    assert "Aborted" in out
+
+
+def test_pre_v2_only_accept_deletes(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "y")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is True
+
+
+def test_pre_v2_only_force_skips_prompt(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _PRE_V2_ONLY_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --force is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(force=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+
+
+# ─── mixed store (v2 + pre-v2) ──────────────────────────────────────────────
+
+
+def test_mixed_store_decline_aborts_without_deleting(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "n")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 1
+    assert prune_calls == []
+    out = capsys.readouterr().out
+    # Both layouts must appear in the preview, not just the v2 one.
+    assert "/gone/v2-project" in out
+    assert "/gone/pre-v2-project" in out
+    assert "This will permanently delete 2 orphan checkpoint project(s)" in out
+
+
+def test_mixed_store_accept_deletes_both_layouts(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+    monkeypatch.setattr("builtins.input", lambda _prompt: "y")
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    out = capsys.readouterr().out
+    assert "Deleted orphan:  2" in out
+
+
+def test_mixed_store_force_skips_prompt_deletes_both(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _MIXED_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --force is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(force=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is True
+
+
+# ─── --keep-orphans skips the prompt entirely, on either layout ───────────
+
+
+@pytest.mark.parametrize("status", [_PRE_V2_ONLY_STATUS, _MIXED_STATUS], ids=["pre_v2_only", "mixed"])
+def test_keep_orphans_skips_prompt(monkeypatch, capsys, status):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, status, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when --keep-orphans is passed")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns(keep_orphans=True))
+
+    assert rc == 0
+    assert len(prune_calls) == 1
+    assert prune_calls[0]["delete_orphans"] is False
+
+
+# ─── no orphans present: never prompts even without --force ───────────────
+
+
+def test_no_orphans_skips_prompt(monkeypatch, capsys):
+    import hermes_cli.checkpoints as checkpoints_cli
+
+    prune_calls: list = []
+    _patch_checkpoint_manager(monkeypatch, _V2_ORPHAN_ONLY_STATUS, prune_calls)
+
+    def _unexpected_input(_prompt):
+        raise AssertionError("input() must not be called when there are no orphans")
+
+    monkeypatch.setattr("builtins.input", _unexpected_input)
+
+    rc = checkpoints_cli.cmd_prune(_ns())
+
+    assert rc == 0
+    assert len(prune_calls) == 1