fix: make shadow branches worktree-specific to prevent false conflicts

[khaong]

Summary

• Fixes false positive "Shadow branch conflict detected" errors when starting Claude in a new terminal or different worktree
• Changes shadow branch naming from entire/<commit[:7]> to entire/<commit[:7]>-<hash(worktreeID)[:6]>
• Each git worktree now gets its own shadow branch namespace, eliminating cross-worktree conflicts

Changes

• paths package: Added GetWorktreeID() to extract internal git worktree identifier
• checkpoint package: Added HashWorktreeID() and updated ShadowBranchNameForCommit() to include worktree hash
• strategy package: Updated all shadow branch operations to pass WorktreeID through the call chain
• Removed dead code: ShadowBranchConflictError and cross-worktree conflict detection (now impossible)
• Kept: SessionIDConflictError for same-worktree, different-session conflicts (still valid)

Test plan

• All unit tests pass
• All integration tests pass (with race detection)
• Updated integration tests to use new shadow branch format
• Updated CLAUDE.md documentation

🤖 Generated with Claude Code

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Note

Medium Risk
Touches core checkpoint/session persistence and cleanup logic; mistakes could strand or delete shadow branches or prevent rewinds, though changes are contained and covered by updated tests.

Overview
Manual-commit shadow branches are now worktree-scoped to avoid cross-worktree collisions: naming changes from entire/<commit[:7]> to entire/<commit[:7]>-<hash(worktreeID)[:6]>, and WorktreeID is stored in session state and threaded through checkpoint read/write/list paths.

Adds paths.GetWorktreeID() plus hashing/parsing helpers in checkpoint (HashWorktreeID, ParseShadowBranchName) and refactors callers to use branch names directly where available. Removes the old cross-worktree ShadowBranchConflictError flow and updates orphan/session cleanup matching to the new naming, alongside broad unit/integration test updates and documentation refresh in CLAUDE.md.

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[Copilot]

Pull request overview

This PR makes shadow branches worktree-specific to eliminate false cross-worktree conflicts and threads a stable worktree identifier through session and checkpoint handling.

Changes:

• Add paths.GetWorktreeID and checkpoint.HashWorktreeID/ShadowBranchNameForCommit(baseCommit, worktreeID) to derive worktree-aware shadow branch names (entire/<commit[:7]>-<hash(worktreeID)[:6]>).
• Propagate WorktreeID through session state, manual-commit strategy code paths, and checkpoint storage APIs, updating unit and integration tests plus documentation accordingly.
• Remove cross-worktree shadow branch conflict handling, keeping only same-worktree SessionIDConflictError logic.

Reviewed changes

Copilot reviewed 26 out of 26 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/strategy.go	Removes the now-impossible ShadowBranchConflictError used for cross-worktree conflicts.
cmd/entire/cli/strategy/manual_commit_types.go	Extends SessionState with a WorktreeID field for worktree-aware session tracking.
cmd/entire/cli/strategy/manual_commit_test.go	Updates shadow branch naming expectations and adds tests for worktree-specific naming, including main vs linked worktrees.
cmd/entire/cli/strategy/manual_commit_session.go	Derives WorktreeID via paths.GetWorktreeID during initialization and uses it when resolving shadow branch names.
cmd/entire/cli/strategy/manual_commit_rewind.go	Passes WorktreeID into ListTemporaryCheckpoints and uses worktree-specific shadow branch names during rewinds.
cmd/entire/cli/strategy/manual_commit_reset.go	Uses current worktree’s WorktreeID to reset only that worktree’s shadow branch.
cmd/entire/cli/strategy/manual_commit_logs.go	Uses worktree-specific shadow branch names when reporting current and additional sessions and reading descriptions.
cmd/entire/cli/strategy/manual_commit_hooks.go	Wires WorktreeID into session initialization, shadow-branch migration, condensation, prompt attribution, and last-prompt retrieval; keeps only SessionIDConflictError for same-worktree conflicts.
cmd/entire/cli/strategy/manual_commit_git.go	Propagates WorktreeID into ShadowBranchNameForCommit, ShadowBranchExists, and WriteTemporary/WriteTemporaryTask options.
cmd/entire/cli/strategy/manual_commit_condensation.go	Uses WorktreeID when resolving shadow branch names during session condensation.
cmd/entire/cli/strategy/manual_commit.go	Maps WorktreeID between session.State and strategy SessionState.
cmd/entire/cli/session/state.go	Adds WorktreeID to persisted session state (backed by .git/entire-sessions/*).
cmd/entire/cli/paths/worktree.go	Introduces GetWorktreeID to parse the internal git worktree identifier from .git (directory vs gitdir file cases).
cmd/entire/cli/paths/worktree_test.go	Provides unit tests for GetWorktreeID across main worktree, linked worktrees, and error conditions.
cmd/entire/cli/integration_test/testenv.go	Adds helpers to compute the current worktree’s shadow branch name (for HEAD or arbitrary commit).
cmd/entire/cli/integration_test/subagent_checkpoints_test.go	Switches shadow branch detection in tests to the new worktree-specific naming via TestEnv.
cmd/entire/cli/integration_test/session_conflict_test.go	Updates conflict tests to use worktree-specific shadow names and clarifies they represent same-worktree concurrent sessions, not cross-worktree.
cmd/entire/cli/integration_test/manual_commit_workflow_test.go	Adapts workflow tests to validate worktree-specific shadow branch names and existence.
cmd/entire/cli/integration_test/manual_commit_untracked_files_test.go	Uses GetShadowBranchNameForCommit for new naming when asserting shadow branch creation.
cmd/entire/cli/integration_test/last_checkpoint_id_test.go	Updates cleanup expectations to the new shadow branch naming format.
cmd/entire/cli/hooks_claudecode_handlers.go	Removes user-facing handling of ShadowBranchConflictError; keeps only SessionIDConflictError messaging.
cmd/entire/cli/explain.go	Switches reachable-checkpoint discovery to list by explicit branch name via ListCheckpointsForBranch.
cmd/entire/cli/checkpoint/temporary.go	Adds worktree-aware hashing/naming (HashWorktreeID, ShadowBranchNameForCommit), threads WorktreeID through write/read/list helpers, and generalizes listing by branch name.
cmd/entire/cli/checkpoint/temporary_test.go	Tests HashWorktreeID properties and the new ShadowBranchNameForCommit behavior.
cmd/entire/cli/checkpoint/checkpoint.go	Extends the Store interface and write options to accept WorktreeID.
CLAUDE.md	Updates strategy documentation to describe worktree-specific shadow branch naming and behaviors.

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