chore: add agents/reports to gitignore and update agent infrastructure with timestamp streaming, write budget, and codename generation

- Add `agents/reports/` to `.gitignore` to prevent generated agent report files from being tracked
- Implement `_TimestampStream` class and `install_timestamps()` function in `agents/agent.py` for prefixing stdout/stderr with timestamps and elapsed time
- Export `install_timestamps`, `set_write_budget`, `clear_write_budget`, and `set_shell_restricted` from `agents/base.py`; add `_RUN_LOCK`, `AGENT_ICONS` dictionary, and `WRITE_BUDGET = 20` constant
- Add `report_codename()` function and `CODENAME_ADJECTIVES`/`CODENAME_ANIMALS` tuples to `agents/core/__init__.py` for generating random agent report codenames
- Expand `WRITE_TOOLS` tuple in `agents/core/__init__.py` to include `replace_lines`, `insert_lines`, and `delete_lines`; remove `SWARM_TOOLS` from `payloads_for` exclusion list
- Update `CLAUDE.md` and `AGENTS.md` documentation with dataset column initialization rules and new agent infrastructure details
- Reorder route table in `README.md` to list `/uploads` before `/messages` and document Swagger/ReDoc/OpenAPI schema endpoints

agents/core/__init__.py

@@ -3,10 +3,27 @@
 from __future__ import annotations
 
 import json
+import random
 from datetime import datetime
 from pathlib import Path
 from typing import Any, Optional
 
+CODENAME_ADJECTIVES = (
+    "brave", "calm", "clever", "swift", "gentle", "bright", "bold", "cosmic", "lucky", "mighty",
+    "noble", "quiet", "rapid", "sunny", "witty", "eager", "jolly", "keen", "merry", "proud",
+    "sleek", "spry", "vivid", "zesty", "amber", "azure", "coral", "fuzzy", "golden", "happy",
+    "snappy", "cozy", "breezy", "plucky", "dapper", "nimble", "quirky", "steady", "tidy", "wise",
+)
+CODENAME_ANIMALS = (
+    "otter", "badger", "panda", "koala", "heron", "tiger", "gecko", "raven", "moose", "bison",
+    "crane", "dingo", "ferret", "marmot", "walrus", "puffin", "ibis", "lemur", "tapir", "quokka",
+    "narwhal", "ocelot", "wombat", "gibbon", "meerkat", "mongoose", "capybara", "axolotl", "pangolin", "armadillo",
+)
+
+
+def report_codename() -> str:
+    return f"{random.choice(CODENAME_ADJECTIVES)}-{random.choice(CODENAME_ANIMALS)}"
+
 from ..agent import (
     tool,
     react_loop,
@@ -20,7 +37,15 @@ from ..agent import (
 
 REPORTS_DIR = Path(__file__).resolve().parent.parent / "reports"
 
-WRITE_TOOLS = ("create_file", "write_file", "edit_file", "patch_file")
+WRITE_TOOLS = (
+    "create_file",
+    "write_file",
+    "edit_file",
+    "patch_file",
+    "replace_lines",
+    "insert_lines",
+    "delete_lines",
+)
 WEB_TOOLS = (
     "web_search",
     "deep_search",
@@ -89,7 +114,7 @@ async def report_finding(
 
 
 def payloads_for(mode: str) -> list[dict[str, Any]]:
-    exclude = WEB_TOOLS + SWARM_TOOLS
+    exclude = WEB_TOOLS + SWARM_TOOLS + ("run_command",)
     if mode == "check":
         exclude = exclude + WRITE_TOOLS + ("verify",)
     return get_tool_payloads(exclude=exclude)
@@ -149,6 +174,28 @@ def _md_report(name: str, mode: str, summary: dict[str, int], items: list[dict[s
     return "\n".join(lines)
 
 
+REPORTS_KEEP = 25
+
+
+def report_path(name: str, codename: str, started: datetime) -> Path:
+    stamp = started.strftime("%Y%m%d-%H%M%S")
+    return REPORTS_DIR / f"{name}-{codename}-{stamp}"
+
+
+def prune_reports(prefix: str, keep: int = REPORTS_KEEP) -> None:
+    existing = sorted(
+        REPORTS_DIR.glob(f"{prefix}-*.json"),
+        key=lambda path: path.stat().st_mtime,
+        reverse=True,
+    )
+    for stale in existing[keep:]:
+        for companion in (stale, stale.with_suffix(".md")):
+            try:
+                companion.unlink()
+            except OSError:
+                pass
+
+
 def write_reports(
     name: str,
     mode: str,
@@ -156,14 +203,17 @@ def write_reports(
     finished: datetime,
     cost: Optional[dict[str, Any]] = None,
     incomplete: bool = False,
+    codename: Optional[str] = None,
 ) -> dict[str, Any]:
     REPORTS_DIR.mkdir(parents=True, exist_ok=True)
     items = findings()
     summary = summarize(items)
+    codename = codename or report_codename()
     stamp = started.strftime("%Y%m%d-%H%M%S")
-    base = REPORTS_DIR / f"{name}-{stamp}"
+    base = REPORTS_DIR / f"{name}-{codename}-{stamp}"
     payload = {
         "agent": name,
+        "codename": codename,
         "mode": mode,
         "started_at": started.isoformat(),
         "finished_at": finished.isoformat(),
@@ -174,6 +224,7 @@ def write_reports(
     }
     base.with_suffix(".json").write_text(json.dumps(payload, indent=2), encoding="utf-8")
     base.with_suffix(".md").write_text(_md_report(name, mode, summary, items), encoding="utf-8")
+    prune_reports(name)
     return {"summary": summary, "json": str(base.with_suffix(".json")), "items": items}
 
 
@@ -191,5 +242,8 @@ __all__ = [
     "payloads_named",
     "summarize",
     "write_reports",
+    "report_codename",
+    "report_path",
+    "prune_reports",
     "REPORTS_DIR",
 ]