Fix: Add incremental parsing to SystemIntegrity handler

[anutron]

Summary

Resolves performance issue where Stop hooks take 1-2 minutes to complete in long sessions.

Problem

The SystemIntegrity handler parses the entire transcript on every Stop event. In long sessions (1000+ lines), this adds 1-2 minutes of overhead per Stop event. The transcript is reparsed from line 0 every time, creating unnecessary CPU overhead that compounds as sessions grow.

Solution

This PR implements incremental parsing by tracking the last parsed line number in the integrity state:

1. Track last_parsed_line in integrity-state.json
2. Only parse new lines since the last check
3. Update state after each parse with the new last_parsed_line

Changes

change-detection.ts

• Added last_parsed_line?: number to IntegrityState interface
• Modified parseToolUseBlocks() to accept startLine parameter for incremental parsing
• Changed return type from FileChange[] to { changes: FileChange[]; lastLine: number }

SystemIntegrity.ts

• Import readIntegrityState from change-detection
• Read last_parsed_line from state before parsing
• Pass startLine to parseToolUseBlocks()
• Update state with new lastLine after parsing

Performance Impact

• Before: O(n) where n = total transcript lines
• After: O(m) where m = new lines since last check
• In 953-line session: ~950 lines saved per Stop event

This eliminates the transcript re-parsing overhead and makes Stop hooks complete much faster in long sessions.

Testing

Tested locally in long session. Stop hook performance improved significantly - no longer waiting 1-2 minutes for SystemIntegrity to complete.

Backwards Compatibility

Fully backwards compatible. If last_parsed_line is missing from state (fresh install or existing state file), it defaults to 0 and parses the entire transcript on first run.