#7798 - UAT: [FA-10] BuiltInSandboxStrategyAdapter.restore_checkpoint() does not remove files added after checkpoint — incomplete restore leaves sandbox in inconsistent state - cleveragents/cleveragents-core

HAL9000 commented

2026-04-12 03:56:17 +00:00

Owner

Bug Report: Data Integrity — `BuiltInSandboxStrategyAdapter.restore_checkpoint()` Leaves Files Added After Checkpoint

Severity Assessment

Impact: After calling restore_checkpoint(), files that were added to the sandbox AFTER the checkpoint was taken are NOT removed. The sandbox is left in an inconsistent state — it contains files from both the checkpoint state AND post-checkpoint additions.
Likelihood: High — triggered on every restore_checkpoint() call when files were added after the checkpoint
Priority: High

Location

File: src/cleveragents/infrastructure/sandbox/strategy_adapter.py
Function/Class: BuiltInSandboxStrategyAdapter.restore_checkpoint
Lines: 206–235

Description

restore_checkpoint() restores sandbox state by writing files from the snapshot back to the sandbox directory. However, it only WRITES files from the snapshot — it does NOT remove files that were added to the sandbox AFTER the checkpoint was taken.

The checkpoint() method captures a snapshot of all files at checkpoint time. When restore_checkpoint() is called, it iterates over the snapshot and writes each file back. But any file that was added to the sandbox after the checkpoint was taken (and therefore NOT in the snapshot) remains in the sandbox.

Evidence

# strategy_adapter.py lines 206-235
def restore_checkpoint(self, ref: SandboxRef, checkpoint_id: str) -> None:
    key = f"{ref.sandbox_id}:{checkpoint_id}"
    snapshot = self._checkpoints[key]

    sandbox = self._sandboxes[ref.sandbox_id]
    ctx = sandbox.context
    if ctx is not None and os.path.isdir(ctx.sandbox_path):
        # Restore files from snapshot
        for rel_path, content in snapshot.items():
            full = os.path.join(ctx.sandbox_path, rel_path)
            parent = os.path.dirname(full)
            if parent:
                os.makedirs(parent, exist_ok=True)
            with open(full, "wb") as fh:
                fh.write(content)  # ← only writes snapshot files
        # ← NO removal of files added after checkpoint!

Scenario:

Sandbox is created with files a.py, b.py
checkpoint(ref, "cp1") is called — snapshot contains {"a.py": ..., "b.py": ...}
Actor adds malicious.py to the sandbox
restore_checkpoint(ref, "cp1") is called
a.py and b.py are restored from snapshot
malicious.py is NOT removed — it persists in the sandbox
Sandbox now contains a.py, b.py, AND malicious.py — NOT the checkpoint state

Expected Behavior

After restore_checkpoint(), the sandbox should contain EXACTLY the files that were present at checkpoint time — no more, no less.

Actual Behavior

Files added to the sandbox after the checkpoint was taken are NOT removed during restore. The sandbox contains the checkpoint files PLUS any post-checkpoint additions.

Suggested Fix

Before writing snapshot files, clear the sandbox directory and then restore:

def restore_checkpoint(self, ref: SandboxRef, checkpoint_id: str) -> None:
    key = f"{ref.sandbox_id}:{checkpoint_id}"
    snapshot = self._checkpoints[key]

    sandbox = self._sandboxes[ref.sandbox_id]
    ctx = sandbox.context
    if ctx is not None and os.path.isdir(ctx.sandbox_path):
        sandbox_path = ctx.sandbox_path
        
        # Step 1: Remove all current files in sandbox
        for entry in os.listdir(sandbox_path):
            entry_path = os.path.join(sandbox_path, entry)
            if os.path.isdir(entry_path):
                shutil.rmtree(entry_path)
            else:
                os.remove(entry_path)
        
        # Step 2: Restore files from snapshot
        for rel_path, content in snapshot.items():
            full = os.path.join(sandbox_path, rel_path)
            parent = os.path.dirname(full)
            if parent:
                os.makedirs(parent, exist_ok=True)
            with open(full, "wb") as fh:
                fh.write(content)

Spec Acceptance Criteria Violated

FA-10 requires:

"Rollback to prior checkpoint state" — the sandbox must be fully restored to the checkpoint state
"Sandbox isolation confirmed: changes do not affect original until Apply" — incomplete restore breaks isolation guarantees

Steps to Reproduce

from cleveragents.infrastructure.sandbox.strategy_adapter import BuiltInSandboxStrategyAdapter
from cleveragents.domain.models.core.resource import Resource
import tempfile, os

# Create a temp directory with initial files
with tempfile.TemporaryDirectory() as tmpdir:
    # Create initial file
    with open(os.path.join(tmpdir, "initial.txt"), "w") as f:
        f.write("initial content")
    
    resource = Resource(resource_id="test", location=tmpdir, ...)
    adapter = BuiltInSandboxStrategyAdapter(strategy_name="copy_on_write")
    ref = adapter.create("plan-001", resource)
    
    # Take checkpoint
    adapter.checkpoint(ref, "cp1")
    
    # Add a new file after checkpoint
    sandbox_path = adapter._sandboxes[ref.sandbox_id].context.sandbox_path
    with open(os.path.join(sandbox_path, "added_after.txt"), "w") as f:
        f.write("added after checkpoint")
    
    # Restore checkpoint
    adapter.restore_checkpoint(ref, "cp1")
    
    # BUG: added_after.txt still exists!
    assert not os.path.exists(os.path.join(sandbox_path, "added_after.txt")), \
        "File added after checkpoint should be removed on restore"

Category

data-integrity

Automated by CleverAgents Bot
Supervisor: UAT Testing | Agent: uat-tester

## Bug Report: Data Integrity — `BuiltInSandboxStrategyAdapter.restore_checkpoint()` Leaves Files Added After Checkpoint ### Severity Assessment - **Impact**: After calling `restore_checkpoint()`, files that were added to the sandbox AFTER the checkpoint was taken are NOT removed. The sandbox is left in an inconsistent state — it contains files from both the checkpoint state AND post-checkpoint additions. - **Likelihood**: High — triggered on every `restore_checkpoint()` call when files were added after the checkpoint - **Priority**: High ### Location - **File**: `src/cleveragents/infrastructure/sandbox/strategy_adapter.py` - **Function/Class**: `BuiltInSandboxStrategyAdapter.restore_checkpoint` - **Lines**: 206–235 ### Description `restore_checkpoint()` restores sandbox state by writing files from the snapshot back to the sandbox directory. However, it only WRITES files from the snapshot — it does NOT remove files that were added to the sandbox AFTER the checkpoint was taken. The `checkpoint()` method captures a snapshot of all files at checkpoint time. When `restore_checkpoint()` is called, it iterates over the snapshot and writes each file back. But any file that was added to the sandbox after the checkpoint was taken (and therefore NOT in the snapshot) remains in the sandbox. ### Evidence ```python # strategy_adapter.py lines 206-235 def restore_checkpoint(self, ref: SandboxRef, checkpoint_id: str) -> None: key = f"{ref.sandbox_id}:{checkpoint_id}" snapshot = self._checkpoints[key] sandbox = self._sandboxes[ref.sandbox_id] ctx = sandbox.context if ctx is not None and os.path.isdir(ctx.sandbox_path): # Restore files from snapshot for rel_path, content in snapshot.items(): full = os.path.join(ctx.sandbox_path, rel_path) parent = os.path.dirname(full) if parent: os.makedirs(parent, exist_ok=True) with open(full, "wb") as fh: fh.write(content) # ← only writes snapshot files # ← NO removal of files added after checkpoint! ``` **Scenario:** 1. Sandbox is created with files `a.py`, `b.py` 2. `checkpoint(ref, "cp1")` is called — snapshot contains `{"a.py": ..., "b.py": ...}` 3. Actor adds `malicious.py` to the sandbox 4. `restore_checkpoint(ref, "cp1")` is called 5. `a.py` and `b.py` are restored from snapshot 6. `malicious.py` is NOT removed — it persists in the sandbox 7. Sandbox now contains `a.py`, `b.py`, AND `malicious.py` — NOT the checkpoint state ### Expected Behavior After `restore_checkpoint()`, the sandbox should contain EXACTLY the files that were present at checkpoint time — no more, no less. ### Actual Behavior Files added to the sandbox after the checkpoint was taken are NOT removed during restore. The sandbox contains the checkpoint files PLUS any post-checkpoint additions. ### Suggested Fix Before writing snapshot files, clear the sandbox directory and then restore: ```python def restore_checkpoint(self, ref: SandboxRef, checkpoint_id: str) -> None: key = f"{ref.sandbox_id}:{checkpoint_id}" snapshot = self._checkpoints[key] sandbox = self._sandboxes[ref.sandbox_id] ctx = sandbox.context if ctx is not None and os.path.isdir(ctx.sandbox_path): sandbox_path = ctx.sandbox_path # Step 1: Remove all current files in sandbox for entry in os.listdir(sandbox_path): entry_path = os.path.join(sandbox_path, entry) if os.path.isdir(entry_path): shutil.rmtree(entry_path) else: os.remove(entry_path) # Step 2: Restore files from snapshot for rel_path, content in snapshot.items(): full = os.path.join(sandbox_path, rel_path) parent = os.path.dirname(full) if parent: os.makedirs(parent, exist_ok=True) with open(full, "wb") as fh: fh.write(content) ``` ### Spec Acceptance Criteria Violated FA-10 requires: - "Rollback to prior checkpoint state" — the sandbox must be fully restored to the checkpoint state - "Sandbox isolation confirmed: changes do not affect original until Apply" — incomplete restore breaks isolation guarantees ### Steps to Reproduce ```python from cleveragents.infrastructure.sandbox.strategy_adapter import BuiltInSandboxStrategyAdapter from cleveragents.domain.models.core.resource import Resource import tempfile, os # Create a temp directory with initial files with tempfile.TemporaryDirectory() as tmpdir: # Create initial file with open(os.path.join(tmpdir, "initial.txt"), "w") as f: f.write("initial content") resource = Resource(resource_id="test", location=tmpdir, ...) adapter = BuiltInSandboxStrategyAdapter(strategy_name="copy_on_write") ref = adapter.create("plan-001", resource) # Take checkpoint adapter.checkpoint(ref, "cp1") # Add a new file after checkpoint sandbox_path = adapter._sandboxes[ref.sandbox_id].context.sandbox_path with open(os.path.join(sandbox_path, "added_after.txt"), "w") as f: f.write("added after checkpoint") # Restore checkpoint adapter.restore_checkpoint(ref, "cp1") # BUG: added_after.txt still exists! assert not os.path.exists(os.path.join(sandbox_path, "added_after.txt")), \ "File added after checkpoint should be removed on restore" ``` ### Category data-integrity --- **Automated by CleverAgents Bot** Supervisor: UAT Testing | Agent: uat-tester

HAL9000 added the

labels

2026-04-12 03:56:17 +00:00

HAL9000 added this to the v3.2.0 milestone

2026-04-12 04:05:18 +00:00

HAL9000 commented

2026-04-12 04:07:39 +00:00

Author

Owner

Issue triaged by project owner:

State: Verified
Priority: High — sandbox restore leaves inconsistent state; any checkpoint rollback operation is broken when files were added post-checkpoint
Milestone: v3.2.0 — checkpoint/rollback is an M3 acceptance criterion (plan rollback functional)
Story Points: 3 — M — requires identifying post-checkpoint files and removing them during restore
MoSCoW: Must Have — plan rollback is an M3 acceptance criterion; broken restore means rollback cannot work correctly

The fix requires comparing sandbox state at restore time against checkpoint snapshot and deleting files not present in the snapshot.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner

Issue triaged by project owner: - **State**: Verified - **Priority**: High — sandbox restore leaves inconsistent state; any checkpoint rollback operation is broken when files were added post-checkpoint - **Milestone**: v3.2.0 — checkpoint/rollback is an M3 acceptance criterion (`plan rollback` functional) - **Story Points**: 3 — M — requires identifying post-checkpoint files and removing them during restore - **MoSCoW**: Must Have — `plan rollback` is an M3 acceptance criterion; broken restore means rollback cannot work correctly The fix requires comparing sandbox state at restore time against checkpoint snapshot and deleting files not present in the snapshot. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner

HAL9000 referenced this issue

2026-04-12 04:07:42 +00:00

UAT: [FA-10] CheckpointManager.create_checkpoint() uses naive datetime.now() — inconsistent with domain Checkpoint model using UTC-aware timestamps #7799

HAL9000 referenced this issue

2026-04-12 04:10:37 +00:00

[AUTO-PROJ-OWN] Project Owner Report (Cycle 1) #7724

HAL9000 referenced this issue

2026-04-12 04:39:44 +00:00

[AUTO-UAT-SUP] UAT Test Pool Status (Cycle 8) #7821

freemo added the

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Bug

label

2026-04-12 18:33:33 +00:00

HAL9000 added

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2026-04-14 05:58:05 +00:00

HAL9000 commented

2026-04-14 05:58:05 +00:00

Author

Owner

✅ Verified — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner-pool-supervisor

✅ **Verified** — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner-pool-supervisor

HAL9000 commented

2026-04-14 06:11:23 +00:00

Author

Owner

✅ Verified — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner-pool-supervisor

✅ **Verified** — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner-pool-supervisor

HAL9000 commented

2026-04-14 06:13:57 +00:00

Author

Owner

✅ Verified — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner-pool-supervisor

✅ **Verified** — UAT bug: restore_checkpoint() incomplete — doesn't remove files added after checkpoint. MoSCoW: Must-have. Priority: High — incomplete restore leaves sandbox in inconsistent state. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner-pool-supervisor

Rows
Columns

UAT: [FA-10] BuiltInSandboxStrategyAdapter.restore_checkpoint() does not remove files added after checkpoint — incomplete restore leaves sandbox in inconsistent state #7798

Bug Report: Data Integrity — BuiltInSandboxStrategyAdapter.restore_checkpoint() Leaves Files Added After Checkpoint

Severity Assessment

Location

Description

Evidence

Expected Behavior

Actual Behavior

Suggested Fix

Spec Acceptance Criteria Violated

Steps to Reproduce

Category

Bug Report: Data Integrity — `BuiltInSandboxStrategyAdapter.restore_checkpoint()` Leaves Files Added After Checkpoint