What does this PR do?

Prevents compressed history that was already written into a newly split session from being appended again as live conversation history.

The bug had two related paths:

1. compress_context() created a new session and reset _last_flushed_db_idx to 0. Later _flush_messages_to_session_db() appended the entire compressed history to the new session as if it were new live output.
2. Gateway compression paths (session hygiene and /compress) wrote compressed messages with rewrite_transcript(), but the next agent instance still started with a flush cursor of 0, causing the compressed transcript to be appended a second time.

Since transcript replay prefers the source with more messages, the duplicate SQLite transcript could win and make compressed summaries / referenced old turns appear as valid live history.

Related Issue

Fixes #20293

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 🔒 Security fix
• 📝 Documentation update
• ✅ Tests (adding or improving test coverage)
• ♻️ Refactor (no behavior change)
• 🎯 New skill (bundled or hub)

Changes Made

• agent/conversation_compression.py — set agent._last_flushed_db_idx = len(compressed) after a compression session split.
• SessionEntry._prewritten_msg_count — add field with serialization/deserialization so gateway compression paths can persist how many messages were already written via rewrite_transcript().
• gateway/run.py:
  • hygiene compression records session_entry._prewritten_msg_count = len(_compressed)
  • /compress records session_entry._prewritten_msg_count = len(compressed)
  • _run_agent() accepts _prewritten_msg_count and advances the agent flush cursor before the turn runs
• Regression coverage for the source-level fix points, session-entry serialization compatibility, and flush-cursor behavior.

How to Test

1. python3 -m pytest -o 'addopts=' tests/compression/test_context_compaction_flush.py -q → 11 passed
2. Fail-without-fix proof:

   git checkout refs/remotes/upstream/main -- agent/conversation_compression.py gateway/run.py gateway/session.py
   python3 -m pytest -o 'addopts=' tests/compression/test_context_compaction_flush.py -q
   # 5 failed, 6 passed
   
   git checkout HEAD -- agent/conversation_compression.py gateway/run.py gateway/session.py
   python3 -m pytest -o 'addopts=' tests/compression/test_context_compaction_flush.py -q
   # 11 passed

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits (fix(scope):, feat(scope):, etc.)
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix/feature (no unrelated commits)
• I've run pytest tests/ -q and all tests pass
• I've added tests for my changes (required for bug fixes, strongly encouraged for features)
• I've tested on my platform: macOS 15 (Darwin 24.6.0)

Documentation & Housekeeping

• I've updated relevant documentation (README, docs/, docstrings) — or N/A
• I've updated cli-config.yaml.example if I added/changed config keys — or N/A
• I've updated CONTRIBUTING.md or AGENTS.md if I changed architecture or workflows — or N/A
• I've considered cross-platform impact (Windows, macOS) per the compatibility guide — or N/A
• I've updated tool descriptions/schemas if I changed tool behavior — or N/A

Screenshots / Logs

$ python3 -m pytest -o 'addopts=' tests/compression/test_context_compaction_flush.py -q
11 passed