notes: add collections feature (col-create, col-add); store collections in collections_data; update storage and CLI

Author: openhands-agent

prototype/agingbench/registry/suts/claude_code/claude_code_opus46_s7.yaml

@@ -0,0 +1,16 @@
+sut_id: claude_code_opus46_s7
+description: "Claude Code CLI + Opus 4.6 (premium reasoning) on S7+ Research-Notes CLI."
+
+model:
+  provider: litellm
+  model: claude-opus-4-6
+  max_tokens: 2048
+
+adapter:
+  type: claude_code
+  model: claude-opus-4-6
+  max_turns: 50
+  cli_path: claude
+  isolated_workspace: true
+
+seed: 42

prototype/agingbench/registry/suts/claude_code/claude_code_opus48_s7.yaml

@@ -0,0 +1,16 @@
+sut_id: claude_code_opus48_s7
+description: "Claude Code CLI + Opus 4.8 (premium reasoning) on S7+ Research-Notes CLI."
+
+model:
+  provider: litellm
+  model: claude-opus-4-8
+  max_tokens: 2048
+
+adapter:
+  type: claude_code
+  model: claude-opus-4-8
+  max_turns: 50
+  cli_path: claude
+  isolated_workspace: true
+
+seed: 42

prototype/agingbench/registry/suts/claude_code/claude_code_sonnet45_s7.yaml

@@ -0,0 +1,16 @@
+sut_id: claude_code_sonnet45_s7
+description: "Claude Code CLI + Sonnet 4.5 on S7 Research-Notes CLI (calibrated-suite re-run)."
+
+model:
+  provider: litellm
+  model: claude-sonnet-4-5
+  max_tokens: 2048
+
+adapter:
+  type: claude_code
+  model: claude-sonnet-4-5
+  max_turns: 50
+  cli_path: claude
+  isolated_workspace: true
+
+seed: 42

prototype/agingbench/registry/suts/claude_code/claude_code_sonnet46_s7_seed45.yaml

@@ -0,0 +1,16 @@
+sut_id: claude_code_sonnet46_s7_seed45
+description: "Claude Code CLI + Sonnet 4.6 (latest sonnet) on S7+ Research-Notes CLI."
+
+model:
+  provider: litellm
+  model: claude-sonnet-4-6
+  max_tokens: 2048
+
+adapter:
+  type: claude_code
+  model: claude-sonnet-4-6
+  max_turns: 50
+  cli_path: claude
+  isolated_workspace: true
+
+seed: 45

prototype/experiments/results/s1_research_literature/haiku45_lossy_compress/trace.jsonl

@@ -0,0 +1,3 @@
+{"event": "run_start", "span_id": "2ea9b7a016054556", "parent_span_id": "f8d8e7c417b44c2c", "timestamp": 1778962150.1761088, "sut_id": "haiku45_lossy_compress", "scenario": "s1_research_literature", "seed": 42, "n_cycles": 2, "policy": "SummarizeStorePolicy", "oracle_mode": false, "gen_ai.request.model": "claude-haiku-4-5-20251001"}
+{"event": "cycle_start", "span_id": "cb42b82b5c874787", "parent_span_id": "2ea9b7a016054556", "timestamp": 1778962150.1762664, "cycle": 0}
+{"event": "probe_batch", "span_id": "31cbbf1045b94e8b", "parent_span_id": "cb42b82b5c874787", "timestamp": 1778962150.1763382, "cycle": 0, "probe_scores": [1, 1, 1, 0, 0, 0], "m": 0.8333, "n_probes": 6, "memory_bloat": 30, "t_writes": 0}