feat: add persistent memory system + SQLite session store

Two-part implementation:

Part A - Curated Bounded Memory:
- New memory tool (tools/memory_tool.py) with MEMORY.md + USER.md stores
- Character-limited (2200/1375 chars), § delimited entries
- Frozen snapshot injected into system prompt at session start
- Model manages pruning via replace/remove with substring matching
- Usage indicator shown in system prompt header

Part B - SQLite Session Store:
- New hermes_state.py with SessionDB class, FTS5 full-text search
- Gateway session.py rewritten to dual-write SQLite + legacy JSONL
- Compression-triggered session splitting with parent_session_id chains
- New session_search tool with Gemini Flash summarization of matched sessions
- CLI session lifecycle (create on launch, close on exit)

Also:
- System prompt now cached per session, only rebuilt on compression
  (fixes prefix cache invalidation from date/time changes every turn)
- Config version bumped to 3, hermes doctor checks for new artifacts
- Disabled in batch_runner and RL environments

batch_runner.py

@@ -277,6 +277,7 @@ def _process_single_prompt(
             reasoning_config=config.get("reasoning_config"),
             prefill_messages=config.get("prefill_messages"),
             skip_context_files=True,  # Don't pollute trajectories with SOUL.md/AGENTS.md
+            skip_memory=True,  # Don't use persistent memory in batch runs
         )
 
         # Run the agent with task_id to ensure each task gets its own isolated VM