adding more integration / e2e tests for different scenarios

[Soph]

Adding more integration / e2e tests to make both test the same scenarios and added some more.

[cursor]

PR Summary

Low Risk
Test-only changes that expand coverage around checkpoint condensation/carry-forward and git-hook behavior; low risk to production code but may increase CI runtime/flakiness due to more scenarios.

Overview
Expands checkpoint workflow coverage in both E2E and integration suites, focusing on carry-forward edge cases and ensuring checkpoint trailers always correspond to metadata condensed onto entire/checkpoints/v1.

Adds new scenarios for ENDED sessions (commits after agent exit / session-end hook), deleted files committed via git rm, agent mid-turn commits followed by user committing remaining files, and opt-out behavior when users remove the Entire-Checkpoint: trailer. Multiple existing E2E scenarios now also assert that no unexpected entire/* shadow branches remain once all touched files are committed (with noted exceptions for still-stashed files).

Enhances test harnesses with helpers to git rm, commit already-staged changes while still running prepare-commit-msg/post-commit hooks (GitCommitStagedWithShadowHooks), remove trailers before committing (GitCommitWithTrailerRemoved), and simulate the session-end hook (SimulateSessionEnd).

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[Copilot]

Pull request overview

This PR adds comprehensive integration and end-to-end tests for different checkpoint and file management scenarios in the shadow branching system. The tests focus on edge cases like session ending, file deletions, carry-forward behavior, and trailer removal.

Changes:

• Added helper methods for git operations (GitRm, GitCommitStagedWithShadowHooks, GitCommitWithTrailerRemoved)
• Added SimulateSessionEnd hook simulation for testing ENDED session phase
• Added three new integration tests covering ended sessions, deleted files, and modified file carry-forward scenarios
• Added five new E2E tests validating checkpoint workflows for ended sessions, file deletions, mid-turn commits, trailer removal, and session depletion

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
cmd/entire/cli/integration_test/testenv.go	Added git operation helpers (GitRm, GitCommitStagedWithShadowHooks) for testing file deletions and staged commits with hooks
cmd/entire/cli/integration_test/hooks.go	Added SimulateSessionEnd method to test session-end hook behavior
cmd/entire/cli/integration_test/deferred_finalization_test.go	Added integration tests for ended sessions, deleted files, and carry-forward with modified files
cmd/entire/cli/e2e_test/testenv.go	Added git operation helpers (GitRm, GitCommitStagedWithShadowHooks, GitCommitWithTrailerRemoved) for E2E testing
cmd/entire/cli/e2e_test/scenario_checkpoint_workflows_test.go	Added E2E tests for various checkpoint scenarios and shadow branch cleanup validations