fix: unnecessary restore prompt, wrong checkpoint on tree nav, and leaf position persistence

[LiusCraft]

Background

When using pi agent's Tree navigation (double Esc → select a previous turn), two issues occurred:

Issue 1: Unnecessary restore prompt + wrong checkpoint restored

Two facets to this bug:

1. Navigating to a turn that made no file changes still showed "Restore files to that point".
2. If the user chose to restore, files were rolled back to an older checkpoint than expected — not the state at the navigated turn.

Root cause: Checkpoints are created at turn_end, with timestamps after the user message in the same turn. The original handleTreeRestore used sorted.find(c => c.timestamp <= targetTs) to locate a checkpoint for the target entry. This lookup always missed the current turn's checkpoint (its timestamp is too recent) and found one from an earlier turn instead. This caused two symptoms:

• cp !== latestCp was always true, so the restore prompt always appeared
• When the user accepted, the restore targeted that earlier checkpoint, not the navigated turn's state

Issue 2: Navigation position not persisted

After navigating back via the tree and exiting pi, running pi -c resumed at the latest conversation tail instead of the previously navigated position.

Root cause (surface): SessionManager._buildIndex() always sets leafId to the last entry when loading from disk — navigateTree only changes leafId in memory, never persisted.

Root cause (deeper): The original leaf file was keyed by ephemeral session UUID (leaf-{sessionId}.json). Since pi -c starts a new process with a new session UUID, the saved leaf was never found on resume.

Changes

commands.ts

• handleForkRestore: Compute hasFileChanges by comparing target vs latest checkpoint; only show file-restore options when real changes exist. Remove the no-op if (!target && state.resumeCheckpoint) stub.
• handleTreeRestore: Accept oldLeafId in event type; compare old-leaf checkpoint vs target-leaf checkpoint to decide whether file restore is needed. Variable names consolidated.

index.ts

• Add leaf-position persistence (leafFilePath/saveLeafId/loadLeafId/clearLeafId) — keyed by repo root path (stable across session restarts), saved to ~/.pi/agent/pi-rewind/leaf-{repoKey}.json.
• session_tree listener: save leaf on tree navigation.
• before_agent_start (new): clear saved leaf on new turn.
• initSession: restore saved leaf unconditionally on session start (no reason guard, so it works for pi -c too).

[LiusCraft]

@arpagon This PR fixes three issues with Tree navigation in pi-rewind:

Issue 1: Unnecessary restore prompt + wrong checkpoint restored

• Restore prompt appeared even when no files changed
• If accepted, files rolled back to an older checkpoint than expected

Root cause: checkpoint timestamps are at turn_end (after user message), so the lookup always missed the current turn's checkpoint.

Issue 2: Navigation position not persisted
After navigating back via the tree and re-launching pi, the session resumed at the latest conversation tail. Root cause: leafId only lives in memory.

Issue 3 (new): pi update --extensions wiped the saved leaf
initSession consumed the leaf unconditionally; now guarded by reason === "resume".

Full details in the PR description. Would appreciate a review. Thanks!