Make E2E pass and add some more tests

[Soph]

Follow up to #336 and #325

• E2E suite passes now
• Added more tests
• Updated how we consider a change to belong to the last session after partial commits
• E2E suite also working for Gemini

[Copilot]

Pull request overview

This PR is a follow-up to PRs #336 (E2E tests) and #325 (1:1 checkpoint model). It fixes issues that prevented the E2E test suite from passing and adds comprehensive test coverage for various checkpoint scenarios.

Changes:

• Enhanced content-aware overlap detection with significant line comparison to handle partial staging scenarios
• Updated CondenseSession signature to accept committedFiles parameter for accurate 1:1 checkpoint-to-commit filtering
• Improved E2E test infrastructure with better git stash handling and helper functions
• Added comprehensive E2E tests for subagent checkpoints, existing file modifications, and complex workflow scenarios

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
manual_commit_test.go	Updated all test calls to CondenseSession with new signature (added nil parameter)
manual_commit_hooks.go	Enhanced sessionHasNewContent logic to handle carry-forward and partial staging scenarios; pass committedFiles to condensation
manual_commit_condensation.go	Added committedFiles parameter to CondenseSession and filtering logic to ensure 1:1 checkpoint-to-commit mapping
content_overlap.go	Added sophisticated content overlap detection with hasSignificantContentOverlap, extractSignificantLines, and isTrivialLine functions to distinguish partial staging from revert-and-replace
auto_commit.go	Pass transcript path to checkpoint store for content hash generation
e2e_test/testenv.go	Added GitAddAll, GetLatestCheckpointID helpers; changed GitStash to use -u flag; commit config files after entire enable
e2e_test/scenario_subagent_test.go	New comprehensive tests for subagent/task checkpoint creation and commit flows
e2e_test/scenario_rewind_test.go	Updated rewind tests to verify that shadow branch IDs become invalid after commit (logs-only points have different IDs)
e2e_test/scenario_checkpoint_workflows_test.go	Removed transcript content validation (too flaky); added extensive tests for existing file modification scenarios
e2e_test/scenario_checkpoint_test.go	Enhanced auto-commit test with better assertions and checkpoint validation
e2e_test/prompts.go	Added PromptUseTaskTool template for testing subagent functionality
CLAUDE.md	Added comprehensive E2E test documentation with warnings about API costs and environment variables

[Soph]

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