@heretek-ai/epistemic-swarm 0.7.25 → 1.0.2

package/runner/mcp_server.py

@@ -1,1447 +0,0 @@
-#!/usr/bin/env python3
-"""
-IUMBTEMS first-party MCP server: the canonical tool surface.
-
-Wraps the existing Python APIs in-process (no spawnSync, no shell-outs):
-- SwarmRunner  (runner/research_swarm.py)
-- SourceHasher  (skills/research_cache/hasher.py)
-- load_config / save_config  (skills/swarm_config/configure.py)
-- DesignTree  (skills/grilling/socratic_tree.py)
-
-Exposes the 7 canonical iumbtems_* tool names already registered by the
-OpenCode plugin and Pi extension, so harness adapters can thin out to a
-pointer at this server.
-
-Two entry points:
-  python3 runner/mcp_server.py                 # stdio MCP server
-  python3 runner/mcp_server.py call <tool> '{}' # one-shot dispatch (JSON out)
-
-Zero external dependencies by design: protocol loop is runner/mcp_protocol.py.
-"""
-
-import argparse
-import copy
-import io
-import json
-import os
-import sys
-from contextlib import redirect_stdout
-from pathlib import Path
-from typing import Any, Callable, Dict, List, Optional
-
-# Bootstrap imports when launched as `python3 runner/mcp_server.py`
-SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
-PROJECT_ROOT = os.path.abspath(os.path.join(SCRIPT_DIR, ".."))
-if PROJECT_ROOT not in sys.path:
-    sys.path.insert(0, PROJECT_ROOT)
-
-from runner.mcp_protocol import PROTOCOL_VERSION, StdioJsonRpcServer, ToolSpec  # noqa: E402
-
-SERVER_NAME = "iumbtems"
-SERVER_VERSION = "0.3.0"
-
-
-# ---------------------------------------------------------------------------
-# helpers
-# ---------------------------------------------------------------------------
-
-
-def _tool_text(payload: Any) -> str:
-    """Normalize a handler return into the MCP text content block body."""
-    if isinstance(payload, str):
-        return payload
-    return json.dumps(payload, indent=2, default=str)
-
-
-def _capture_stdout(fn: Callable[..., Any], *args: Any, **kwargs: Any) -> str:
-    """Run a print-based CLI function and return what it wrote to stdout."""
-    buf = io.StringIO()
-    with redirect_stdout(buf):
-        fn(*args, **kwargs)
-    return buf.getvalue()
-
-
-# ---------------------------------------------------------------------------
-# tool handlers
-# ---------------------------------------------------------------------------
-
-DEFAULT_RESEARCH_DIR = ".research"
-
-# `iumbtems_config` arguments that are not config keys.
-CONFIG_TOOL_CONTROL_ARGS = ("base_dir", "dir", "show", "expected_hash", "expectedHash")
-
-# Legacy aliases accepted for the corresponding canonical key (kept for the
-# slash-command/CLI vocabulary; the advertised schema uses canonical names).
-CONFIG_KEY_ALIASES = {
-    "engine": "search_engine",
-    "depth": "max_iterations",
-    "divergence": "divergence_threshold",
-}
-
-
-def config_tool_input_schema() -> Dict[str, Any]:
-    """Advertised `iumbtems_config` input schema, derived from the canonical CONFIG.
-
-    Generated from `runner.schemas.CONFIG` so the MCP surface cannot drift from
-    the persisted contract (a parity fixture asserts this).
-    """
-    from runner.schemas import CONFIG
-
-    props: Dict[str, Any] = {
-        "base_dir": {
-            "type": "string",
-            "description": "Path to .research workspace (default .research)",
-        },
-        "show": {
-            "type": "boolean",
-            "description": (
-                "Inspect only; equivalent to calling with no update keys "
-                "(reads are always safe). When true, the call is read-only "
-                "even if update keys are present: they are listed under "
-                "`ignored_updates` and nothing is written (the expected_hash "
-                "guard, including the dual-spelling conflict check, is not "
-                "evaluated)."
-            ),
-        },
-        "expected_hash": {
-            "type": "string",
-            "description": (
-                "Optimistic-concurrency guard: SHA-256 (or a unique prefix of at "
-                "least 8 hex chars) of the config file you read. A mismatch "
-                "returns a structured stale error with a fresh snapshot and "
-                "writes nothing. Empty/whitespace-only spellings count as absent. "
-                "Alias: `expectedHash`; if both spellings are "
-                "present they must be equal after normalization (strip + "
-                "lowercase) or the call is rejected."
-            ),
-        },
-        "expectedHash": {
-            "type": "string",
-            "description": "Alias of `expected_hash` (camelCase); must not conflict with it.",
-        },
-    }
-    for key, subschema in CONFIG["properties"].items():
-        props[key] = copy.deepcopy(subschema)
-    return {"type": "object", "properties": props}
-
-
-def _resolve_base_dir(args: Dict[str, Any]) -> Path:
-    raw = args.get("base_dir") or args.get("dir")
-    if raw:
-        return Path(os.path.realpath(str(raw)))
-    # Project root wins over process cwd: a relative ".research" resolved
-    # against the MCP server's cwd escapes the project (observed live:
-    # evidence landed in ~/.research instead of the project tree).
-    project = os.environ.get("IUMBTEMS_PROJECT_DIR", "").strip()
-    if project and Path(project).is_dir():
-        return Path(os.path.realpath(os.path.join(project, DEFAULT_RESEARCH_DIR)))
-    return Path(os.path.realpath(DEFAULT_RESEARCH_DIR))
-
-
-def _canonical_config_keys() -> List[str]:
-    from runner.schemas import CONFIG
-
-    return list(CONFIG["properties"].keys())
-
-
-def _allows_null(schema: Dict[str, Any]) -> bool:
-    types = schema.get("type")
-    if isinstance(types, list):
-        return "null" in types
-    return types == "null"
-
-
-def _normalize_hash_spelling(value: Any) -> str:
-    """Strip + lowercase a hash spelling for conflict comparison (H2).
-
-    Mirrors `normalize_expected_hash` in `skills/swarm_config/configure.py`
-    WITHOUT raising: malformed spellings still compare (so genuinely different
-    malformed guards conflict), and the single `save_config` writer later
-    validates the winner (malformed -> CONFIG_INVALID_EXPECTED_HASH).
-    Empty/whitespace-only spellings normalize to "" and are treated as absent
-    by the caller (R3: "" never conflicts).
-    """
-    return str(value).strip().lower()
-
-
-def _hash_spelling_present(value: Any) -> bool:
-    """True when an expected-hash spelling counts as provided (R3).
-
-    `None` and empty/whitespace-only strings mean "no guard" (mirroring
-    `normalize_expected_hash`); everything else is a guard spelling even if
-    malformed (malformed -> CONFIG_INVALID_EXPECTED_HASH on the write leg).
-    """
-    if value is None:
-        return False
-    return str(value).strip() != ""
-
-
-def _find_nested_null_violations(updates: Dict[str, Any]) -> List[str]:
-    """Dotted paths in `updates` carrying None where the schema bans null (H4).
-
-    The top-level loop in `_handle_config` already catches a direct
-    `{"mode": None}`; this extends the same `NULL_FOR_NON_NULLABLE_KEY` code
-    to nested nulls such as `{"verify": {"min_fuzzy_confidence": None}}`,
-    which previously surfaced as the generic `CONFIG_VALIDATION_FAILED`.
-    Contract: `NULL_FOR_NON_NULLABLE_KEY` wins for ANY caller-supplied null
-    at any depth; `CONFIG_VALIDATION_FAILED` covers every other schema
-    violation (including nulls already persisted on disk by a hand edit,
-    which the caller did not supply in this call).
-    """
-    from runner.schemas import CONFIG
-
-    found: List[str] = []
-
-    def walk(value: Any, subschema: Any, path: str) -> None:
-        if value is None:
-            if isinstance(subschema, dict) and not _allows_null(subschema):
-                found.append(path)
-            return
-        if isinstance(value, dict) and isinstance(subschema, dict):
-            props = subschema.get("properties") or {}
-            additional = subschema.get("additionalProperties")
-            for key, child in value.items():
-                if key in props:
-                    walk(child, props[key], f"{path}.{key}" if path else str(key))
-                elif isinstance(additional, dict):
-                    # e.g. `mcp_servers` values must be boolean; a null there
-                    # is a null-violation too, with the full dotted path.
-                    walk(
-                        child,
-                        additional,
-                        f"{path}.{key}" if path else str(key),
-                    )
-            # Unknown keys with no `additionalProperties` schema carry no
-            # nullability info; generic validation decides them (unknown
-            # object keys are preserved verbatim).
-            return
-        if isinstance(value, list) and isinstance(subschema, dict):
-            items = subschema.get("items")
-            if isinstance(items, dict):
-                for idx, child in enumerate(value):
-                    walk(child, items, f"{path}[{idx}]")
-
-    props = CONFIG.get("properties") or {}
-    for key, value in updates.items():
-        if value is None or not isinstance(value, (dict, list)):
-            continue  # top-level nulls are handled by the caller loop
-        canon = CONFIG_KEY_ALIASES.get(key, key)
-        if canon in props:
-            walk(value, props[canon], str(canon))
-    return sorted(found)
-
-
-def _config_updated_payload(
-    cfg_file: Path, candidate: Dict[str, Any], default_config: Dict[str, Any]
-) -> Dict[str, Any]:
-    """Success payload for the config write leg (H6).
-
-    `written_to` is ALWAYS an absolute path (via realpath, so symlinked
-    workspaces resolve to the true location). Both updated legs — the normal
-    single-read leg and the defensive branch where the just-written bytes
-    cannot be re-read — share this helper so the shape cannot diverge.
-    """
-    import hashlib
-
-    from skills.swarm_config.configure import _read_bounded_bytes, merge_config
-
-    abs_path = str(Path(os.path.realpath(str(cfg_file))))
-    try:
-        # Phase-08 R2 (W17): bounded re-read — the just-written file is
-        # regular by construction, but a single read primitive keeps the
-        # FIFO-hardening total (a concurrent swap can only fail into the
-        # defensive branch below, never hang the writer).
-        raw_bytes = _read_bounded_bytes(Path(cfg_file))
-    except OSError:
-        raw_bytes = None
-    if raw_bytes is None:
-        # A successful save always leaves bytes; keep the payload shape without
-        # a second read in this (unreachable) defensive branch.
-        return {
-            "status": "updated",
-            "config": candidate,
-            "written_to": abs_path,
-            "hash": None,
-        }
-    try:
-        parsed = json.loads(raw_bytes.decode("utf-8"))
-    except (ValueError, UnicodeDecodeError):
-        parsed = None
-    effective = (
-        merge_config(default_config, parsed)
-        if isinstance(parsed, dict)
-        else merge_config(default_config, {})
-    )
-    return {
-        "status": "updated",
-        "config": effective,
-        "written_to": abs_path,
-        "hash": hashlib.sha256(raw_bytes).hexdigest(),
-    }
-
-
-def _legacy_pin_migration_pending(base_dir: str) -> bool:
-    """Would the legacy-pin migration apply on the next write? (read-only)
-
-    Phase-04 R11: the `show` leg reports this WITHOUT persisting, so a read API
-    stays side-effect free. Mirrors `heal_config`'s decision — the on-disk file
-    carries a legacy ``["claude", "-p"]`` pin AND the would-be-persisted config
-    passes canonical validation (an invalid file is never healed, R1) — but
-    never writes.
-    """
-    try:
-        from skills.swarm_config.configure import (
-            _read_bounded_bytes,
-            load_config,
-            migrate_legacy_agent_backends,
-            validate_config,
-        )
-
-        cfg_file = Path(base_dir) / "config.json"
-        # Phase-08 R2 (W17): bounded pre-read — a FIFO here hung the show leg
-        # on a plain `read_bytes`. Unreadable/non-regular yields "no pending
-        # migration" (fail-open read, matching `load_config` defaults).
-        raw_bytes = _read_bounded_bytes(cfg_file)
-        if raw_bytes is None:
-            return False
-        raw = json.loads(raw_bytes.decode("utf-8"))
-        if not isinstance(raw, dict):
-            return False
-        if not migrate_legacy_agent_backends(raw):
-            return False
-        return not validate_config(load_config(base_dir))
-    except Exception:
-        return False
-
-
-def _handle_config(args: Dict[str, Any]) -> str:
-    """Inspect or modify swarm parameters in .research/config.json.
-
-    Every canonical key is accepted; invalid values, unknown keys, and `null`
-    for non-nullable keys are rejected with a structured error before anything
-    is written. Writes go through the single canonical writer (`save_config`:
-    locked, validated, atomic, unknown-key-preserving) with an optional
-    `expected_hash` guard (both `expected_hash` and `expectedHash` spellings).
-
-    Phase-05 H2 decisions: the two hash spellings compare NORMALIZED
-    (strip + lowercase, mirroring `normalize_expected_hash`), so
-    `"ABCDEF12"` vs `"abcdef12"` is one guard, not a conflict; empty or
-    whitespace-only spellings count as absent on both sides (R3), so `""`
-    never conflicts; and `show` forces the read-only leg even when update
-    keys are present (they are reported under `ignored_updates` and nothing
-    is written, without evaluating the guard or the dual-spelling conflict
-    check — R1 ordering).
-    """
-    from skills.swarm_config.configure import (
-        DEFAULT_CONFIG,
-        ConfigError,
-        load_config,
-        merge_config,
-        save_config,
-        validate_config,
-    )
-    from runner.schemas import CONFIG
-
-    base_dir = str(_resolve_base_dir(args))
-    cfg = load_config(base_dir)
-
-    snake = args.get("expected_hash")
-    camel = args.get("expectedHash")
-    snake_present = _hash_spelling_present(snake)
-    camel_present = _hash_spelling_present(camel)
-
-    accepted = _canonical_config_keys()
-    nullable = [key for key in accepted if _allows_null(CONFIG["properties"][key])]
-    unknown: List[str] = []
-    null_for_non_nullable: List[str] = []
-    updates: Dict[str, Any] = {}
-    for key, value in args.items():
-        if key in CONFIG_TOOL_CONTROL_ARGS:
-            continue
-        canon = CONFIG_KEY_ALIASES.get(key, key)
-        if canon not in accepted:
-            unknown.append(str(key))
-            continue
-        if value is None:
-            if _allows_null(CONFIG["properties"][canon]):
-                # Nullable key: explicit clear / follow-the-default-policy.
-                updates[canon] = None
-            else:
-                # R8: never mask a null for a non-nullable key as a no-op.
-                null_for_non_nullable.append(str(canon))
-            continue
-        updates[canon] = value
-
-    if unknown:
-        return _tool_text(
-            {
-                "status": "error",
-                "code": "UNKNOWN_CONFIG_KEY",
-                "written": False,
-                "errors": [f"unknown config key(s): {', '.join(sorted(unknown))}"],
-                "accepted_keys": accepted,
-            }
-        )
-    # H4: nested caller-supplied nulls share the top-level code, with dotted
-    # paths (e.g. `verify.min_fuzzy_confidence`).
-    null_for_non_nullable.extend(_find_nested_null_violations(updates))
-    if null_for_non_nullable:
-        return _tool_text(
-            {
-                "status": "error",
-                "code": "NULL_FOR_NON_NULLABLE_KEY",
-                "written": False,
-                "errors": [
-                    f"null is not accepted for non-nullable key(s): "
-                    f"{', '.join(sorted(set(null_for_non_nullable)))}; omit the key to "
-                    "leave it unchanged, or pass a valid value"
-                ],
-                "nullable_keys": nullable,
-                "accepted_keys": accepted,
-            }
-        )
-
-    if args.get("show") or not updates:
-        # R11/H2/R1: the show leg is strictly read-only — a settings panel reads
-        # through it, so it must never persist the legacy-pin migration nor
-        # evaluate the expected_hash guard (including the dual-spelling
-        # conflict check, which lives BELOW this return). Report whether a
-        # migration is pending; only the write leg below heals. When `show`
-        # overrides present update keys, name them so the caller knows nothing
-        # was written.
-        payload: Dict[str, Any] = {
-            "status": "current",
-            "config": cfg,
-            "migrated": _legacy_pin_migration_pending(base_dir),
-        }
-        if args.get("show") and updates:
-            payload["ignored_updates"] = sorted(updates)
-        return _tool_text(payload)
-
-    # R1 ordering: the dual-spelling conflict check lives BELOW the show
-    # early-return so the show leg is fully read-only. R4/H2: both spellings
-    # must agree AFTER normalization; never silently prefer one.
-    # Case/whitespace-only differences are one guard; empty/whitespace-only
-    # spellings count as absent (R3).
-    if (
-        snake_present
-        and camel_present
-        and _normalize_hash_spelling(snake) != _normalize_hash_spelling(camel)
-    ):
-        return _tool_text(
-            {
-                "status": "error",
-                "code": "CONFLICTING_EXPECTED_HASH",
-                "written": False,
-                "errors": [
-                    "expected_hash and expectedHash were both provided with "
-                    "different values; provide one spelling (or two equal values)."
-                ],
-                "expected_hash": str(snake),
-                "expectedHash": str(camel),
-            }
-        )
-    if snake_present:
-        expected: Any = snake
-    elif camel_present:
-        expected = camel
-    else:
-        expected = None
-
-    candidate = merge_config(cfg, updates)
-    problems = validate_config(candidate)
-    if problems:
-        return _tool_text(
-            {
-                "status": "error",
-                "code": "CONFIG_VALIDATION_FAILED",
-                "written": False,
-                "errors": problems,
-                "config": cfg,
-            }
-        )
-
-    # R12 (F1): do NOT heal before saving. The candidate is already migrated in
-    # memory (`load_config`) and `save_config` merges it over the on-disk bytes,
-    # so the legacy-pin migration persists as a side effect — while the caller's
-    # `expected_hash` guard still matches the bytes they read. A heal-before-save
-    # rewrote the file and turned a valid guarded write into a false `stale`.
-    try:
-        save_config(
-            candidate,
-            base_dir,
-            expected_hash=str(expected) if expected is not None else None,
-        )
-    except ConfigError as exc:
-        payload: Dict[str, Any] = {"status": "error", "written": False}
-        payload.update(exc.to_dict())
-        if exc.code == "CONFIG_STALE":
-            payload["status"] = "stale"
-            payload.update(exc.details)
-        return _tool_text(payload)
-
-    # R10 (single read): derive BOTH the effective config and the hash from ONE
-    # read of the just-published bytes, so the storage mirror and the `changed`
-    # event can never receive an era-A config paired with an era-B hash.
-    # `save_config` publishes a fully defaults-merged, validated object
-    # atomically, so the bytes on disk are already the effective config; the
-    # earlier `load_config()` + `config_hash()` were two independent reads.
-    # H6: the shared helper guarantees an absolute `written_to` on both legs.
-    cfg_file = Path(base_dir) / "config.json"
-    return _tool_text(_config_updated_payload(cfg_file, candidate, DEFAULT_CONFIG))
-
-
-def _run_swarm_mode(mode: Optional[str], args: Dict[str, Any]) -> str:
-    """Shared dispatch for the four swarm-shaped tools."""
-    from runner.research_swarm import SwarmRunner
-
-    objective = args.get("objective") or args.get("target") or args.get("feature")
-    if not objective:
-        raise ValueError("objective is required")
-
-    frontier = args.get("frontier") or args.get("frontier_file")
-    overrides = None
-    backend = (args.get("backend") or "").strip().lower()
-    if backend in ("claude", "opencode"):
-        argv = ["claude", "-p"] if backend == "claude" else ["opencode", "run"]
-        overrides = {"alpha": {"backend": argv}, "beta": {"backend": argv}}
-    runner = SwarmRunner(
-        base_dir=_resolve_base_dir(args),
-        mock_mode=bool(args.get("mock_claude") or args.get("mock_mode")),
-        mode=mode or args.get("mode"),
-        engine=args.get("engine"),
-        depth=args.get("depth"),
-        domain_pack=args.get("domain_pack"),
-        agent_overrides=overrides,
-        resume=bool(args.get("resume")),
-        dry_run=bool(args.get("dry_run")),
-    )
-    buf = io.StringIO()
-    status = None
-    with redirect_stdout(buf):
-        status = runner.run_swarm(
-            objective, frontier_file=Path(frontier) if frontier else None
-        )
-
-    mode_name = mode or args.get("mode") or "research"
-    log = buf.getvalue()[-4000:]
-
-    # Decide from the ACTUAL run outcome, not the raw gate verdict: mock and dry
-    # runs are exempt from the fail-fast halt (they complete/validate), and only
-    # a real halt sets `_halted`. Reading `_search_gate.action` alone mislabelled
-    # every blocked-but-exempt run as `halted`.
-    if status == "halted" or getattr(runner, "_halted", False):
-        gate = getattr(runner, "_search_gate", None) or {}
-        return _tool_text(
-            {
-                "status": "halted",
-                "mode": mode_name,
-                "reason": gate.get("reason"),
-                "message": gate.get("message"),
-                "log": log,
-            }
-        )
-    if status == "dry-run":
-        return _tool_text({"status": "dry-run", "mode": mode_name, "log": log})
-    if status == "incomplete":
-        return _tool_text({"status": "incomplete", "mode": mode_name, "log": log})
-
-    report = runner.base_dir / (
-        {
-            "audit": "code_audit_report.md",
-            "scout": "oss_scout_report.md",
-            "brainstorm": "brainstorm_report.md",
-            "darkharvest": "darkharvest_report.md",
-        }.get(mode_name, "final_synthesis.md")
-    )
-    return _tool_text(
-        {
-            "status": "completed",
-            "mode": mode_name,
-            "report": str(report),
-            "log": log,
-        }
-    )
-
-
-def _handle_swarm_research(args: Dict[str, Any]) -> str:
-    """Run the dialectic multi-agent research swarm (thesis vs antithesis)."""
-    return _run_swarm_mode(None, args)
-
-
-def _handle_code_audit(args: Dict[str, Any]) -> str:
-    """Run a dialectic codebase architecture & security audit."""
-    return _run_swarm_mode("audit", args)
-
-
-def _handle_oss_scout(args: Dict[str, Any]) -> str:
-    """Scout open-source software, libraries, and clean-room blueprints."""
-    return _run_swarm_mode("scout", args)
-
-
-def _handle_brainstorm(args: Dict[str, Any]) -> str:
-    """Run lateral brainstorming (feature vectors + paradigm moves + spikes)."""
-    return _run_swarm_mode("brainstorm", args)
-
-
-def _handle_darkharvest(args: Dict[str, Any]) -> str:
-    """Run product competitor teardown (seed + expand, harvest verdicts)."""
-    return _run_swarm_mode("darkharvest", args)
-
-
-def _handle_factory(args: Dict[str, Any]) -> str:
-    """Drive factory run state (init / phase-add / qa-record / expansion / stop / gate).
-
-    Wraps skills/factory/scripts/factory.py so agents never need a filesystem
-    path to the helper: the npm-installed toolchain lives outside the project,
-    and relative `skills/...` paths broke in consuming projects (observed
-    live: the manager agent ran `find / -name factory.py`).
-
-    Phase-08 R4 (W6): the `gate` command forwards `--run/--phase/--action`
-    (+ optional `--reason`) to the helper's `gate` subcommand. Before this
-    fix the handler accepted `gate` but forwarded no gate args, so the helper
-    exited 2 (missing required `--run/--phase/--action`) and gate was
-    unreachable through the tool surface.
-    """
-    import subprocess
-
-    command = str(args.get("command") or "").strip()
-    if command not in ("init", "phase-add", "qa-record", "expansion", "stop", "gate"):
-        raise ValueError(
-            "command must be one of: init, phase-add, qa-record, expansion, stop, gate"
-        )
-    script = Path(PROJECT_ROOT) / "skills" / "factory" / "scripts" / "factory.py"
-    if not script.is_file():
-        raise FileNotFoundError(f"factory helper not found at {script}")
-
-    project = (
-        args.get("project_dir") or os.environ.get("IUMBTEMS_PROJECT_DIR") or os.getcwd()
-    )
-    cmd = [sys.executable, str(script), command, "--project-dir", str(project)]
-    if command == "init":
-        cmd += ["--run", str(args.get("run") or "")]
-    elif command == "phase-add":
-        cmd += [
-            "--run",
-            str(args.get("run") or ""),
-            "--phase",
-            str(args.get("phase") or ""),
-            "--goal",
-            str(args.get("goal") or ""),
-            "--accept",
-            str(args.get("accept") or ""),
-        ]
-    elif command == "qa-record":
-        cmd += [
-            "--run",
-            str(args.get("run") or ""),
-            "--phase",
-            str(args.get("phase") or ""),
-            "--seat",
-            str(args.get("seat") or ""),
-            "--verdict",
-            str(args.get("verdict") or ""),
-        ]
-        if args.get("reason"):
-            cmd += ["--reason", str(args["reason"])]
-    elif command == "expansion":
-        cmd += [
-            "--run",
-            str(args.get("run") or ""),
-            "--loops",
-            str(int(args.get("loops") or 1)),
-        ]
-        if args.get("max_loops"):
-            cmd += ["--max-loops", str(int(args["max_loops"]))]
-    elif command == "stop":
-        cmd += ["--run", str(args.get("run") or "")]
-    elif command == "gate":
-        cmd += [
-            "--run",
-            str(args.get("run") or ""),
-            "--phase",
-            str(args.get("phase") or ""),
-            "--action",
-            str(args.get("action") or ""),
-        ]
-        if args.get("reason"):
-            cmd += ["--reason", str(args["reason"])]
-
-    proc = subprocess.run(
-        cmd,
-        capture_output=True,
-        text=True,
-        shell=False,
-        stdin=subprocess.DEVNULL,
-        cwd=str(project),
-    )
-    payload = {
-        "status": "ok" if proc.returncode == 0 else "error",
-        "command": command,
-        "returncode": proc.returncode,
-        "project_dir": str(project),
-        "output": (proc.stdout or proc.stderr or "").strip()[-4000:],
-    }
-    if proc.returncode == 2:
-        payload["status"] = "escalated"
-    return _tool_text(payload)
-
-
-def _verify_min_fuzzy_confidence(cfg: Any) -> Any:
-    """Configured `verify.min_fuzzy_confidence`, defaulting to 0.88 (H5).
-
-    SINGLE-ENFORCEMENT-POINT CONTRACT: this returns the configured value
-    UNTOUCHED (no `float()` parse, no clamp) and `SourceHasher.verify_quote`
-    enforces it via `coerce_min_fuzzy_confidence` at call time. The persisted
-    schema stays strict (`type: number`); coercion exists only for
-    hand-edited files and direct library callers. The response echoes the
-    EFFECTIVE threshold (`coerce_min_fuzzy_confidence(configured)`), so the
-    reported value is always the one that governed the decision.
-    """
-    verify = cfg.get("verify") if isinstance(cfg, dict) else None
-    raw = verify.get("min_fuzzy_confidence") if isinstance(verify, dict) else None
-    return 0.88 if raw is None else raw
-
-
-def _handle_verify_quote(args: Dict[str, Any]) -> str:
-    """Verify a verbatim quote against the content-addressed source cache."""
-    from skills.research_cache.hasher import (
-        SourceHasher,
-        coerce_min_fuzzy_confidence,
-    )
-    from skills.swarm_config.configure import load_config
-
-    content_hash = (
-        args.get("hash") or args.get("content_hash") or args.get("source_hash")
-    )
-    quote = args.get("quote")
-    if not content_hash or quote is None:
-        raise ValueError("hash and quote are required")
-
-    base_dir = _resolve_base_dir(args)
-    configured = _verify_min_fuzzy_confidence(load_config(str(base_dir)))
-    hasher = SourceHasher(base_dir)
-    is_verified, confidence, message = hasher.verify_quote(
-        content_hash, quote, min_fuzzy_confidence=configured
-    )
-    return _tool_text(
-        {
-            "verified": bool(is_verified),
-            "confidence": float(confidence),
-            "message": message,
-            "content_hash": content_hash,
-            "min_fuzzy_confidence": coerce_min_fuzzy_confidence(configured),
-        }
-    )
-
-
-def _handle_report_retraction(args: Dict[str, Any]) -> str:
-    """Record a RETRACTED/REVISED event for a cached source (Living Dossiers)."""
-    from runner.living_dossiers import write_retraction
-
-    source_hash = args.get("hash") or args.get("source_hash")
-    event = args.get("event")
-    if not source_hash or not event:
-        raise ValueError("hash and event are required")
-    base_dir = _resolve_base_dir(args)
-    path = write_retraction(
-        base_dir,
-        source_hash,
-        str(event).upper(),
-        note=args.get("note") or "",
-        supersedes=args.get("supersedes"),
-    )
-    return _tool_text({"status": "recorded", "path": str(path)})
-
-
-def _handle_check_staleness(args: Dict[str, Any]) -> str:
-    """Run one claim-degradation pass (retractions -> STALE/SUSPECT + requeue)."""
-    from runner.living_dossiers import check_staleness
-
-    base_dir = _resolve_base_dir(args)
-    scope_ids = args.get("scope_ids")
-    return _tool_text(check_staleness(base_dir, scope_ids=scope_ids))
-
-
-def _handle_set_domain_pack(args: Dict[str, Any]) -> str:
-    """Activate a Regulated Domain Pack (epistemic constitution) in config.
-
-    H3: surrounding whitespace is stripped before resolving — a blank or
-    whitespace-only id is rejected (the canonical schema additionally rejects
-    blank/padded ids at validation, so a padded id can never persist).
-    """
-    from runner.refinement import load_domain_pack
-    from skills.swarm_config.configure import load_config, save_config
-
-    raw_pack = args.get("pack") or args.get("domain_pack") or args.get("pack_id")
-    pack = raw_pack.strip() if isinstance(raw_pack, str) else raw_pack
-    if not pack or (isinstance(pack, str) and not pack.strip()):
-        raise ValueError("pack is required (blank/whitespace-only ids are rejected)")
-    constitution = load_domain_pack(pack)  # raises if unknown — fail loudly
-    base_dir = str(_resolve_base_dir(args))
-    cfg = load_config(base_dir)
-    cfg["domain_pack"] = pack
-    save_config(cfg, base_dir)
-    return _tool_text(
-        {
-            "status": "activated",
-            "domain_pack": pack,
-            "accept_threshold": constitution.accept_threshold,
-            "retraction_policy": constitution.retraction_policy,
-            "banned_domains": constitution.banned_domains,
-        }
-    )
-
-
-def _handle_export_brief(args: Dict[str, Any]) -> str:
-    """Export a proof-carrying research brief (signed, self-contained bundle)."""
-    from runner.pcrb import export_brief
-
-    base_dir = _resolve_base_dir(args)
-    key = args.get("key")
-    key_path = Path(args["key_file"]) if args.get("key_file") else None
-    path = export_brief(
-        base_dir,
-        out_path=Path(args["out"]) if args.get("out") else None,
-        scope_ids=args.get("scope_ids"),
-        objective=args.get("objective"),
-        key=key,
-        key_path=key_path,
-        key_id=args.get("key_id") or "local",
-    )
-    return _tool_text({"status": "exported", "path": str(path)})
-
-
-def _handle_verify_brief(args: Dict[str, Any]) -> str:
-    """Verify a proof-carrying brief against its bundled sources (no trust in the LLM)."""
-    import os
-
-    from runner.pcrb import ENV_KEY
-    from runner.pcrb_verify import verify_brief
-
-    brief = args.get("brief") or args.get("path")
-    if not brief:
-        raise ValueError("brief path is required")
-    p = Path(os.path.realpath(str(brief)))
-    if not p.exists():
-        raise FileNotFoundError(f"no such brief: {p}")
-    bundle = json.loads(p.read_text(encoding="utf-8"))
-
-    key = None
-    if args.get("key"):
-        key = args["key"].encode("utf-8")
-    elif args.get("key_file"):
-        kf = Path(os.path.realpath(str(args["key_file"])))
-        # An explicit key_file that cannot be read must surface as an error, not
-        # a silent fallthrough to `alg: "none"`.
-        if not kf.is_file():
-            raise ValueError(f"key file is not a readable file: {args['key_file']!r}")
-        key = kf.read_bytes().strip()
-    elif os.environ.get(ENV_KEY):
-        key = os.environ[ENV_KEY].encode("utf-8")
-
-    return _tool_text(verify_brief(bundle, key=key))
-
-
-def _handle_reindex_claims(args: Dict[str, Any]) -> str:
-    """Rebuild the derived claims.sqlite index from .research flat files."""
-    from runner.claim_store import reindex
-
-    base_dir = _resolve_base_dir(args)
-    return _tool_text(reindex(base_dir))
-
-
-def _handle_doctor(args: Dict[str, Any]) -> str:
-    """Preflight for the resolved workspace: backend, engine, write test, version."""
-    from runner.preflight import format_report, host_websearch_provider, preflight
-    from skills.swarm_config.configure import load_config
-
-    base_dir = _resolve_base_dir(args)
-    cfg = load_config(str(base_dir))
-    report = preflight(
-        base_dir,
-        mode=args.get("mode") or cfg.get("mode") or "research",
-        config=cfg,
-        # Never spawn in a health check; report resolution only.
-        mock_mode=True,
-        probe=bool(args.get("probe", True)),
-        # Feed the same host-reported provider/since the run path uses, or the
-        # doctor names a different provider than the run banner (observed:
-        # IUMBTEMS_WEBSEARCH_PROVIDER=tavily -> doctor said duckduckgo).
-        host_provider=host_websearch_provider(cfg),
-        since=args.get("since"),
-    )
-    return _tool_text({"report": report, "text": format_report(report)})
-
-
-def _handle_test(args: Dict[str, Any]) -> str:
-    """Run the packaged test suite in a subprocess (timeout-bounded)."""
-    import subprocess
-
-    timeout = float(os.environ.get("IUMBTEMS_TEST_TIMEOUT", "300"))
-    try:
-        result = subprocess.run(
-            [sys.executable, "-m", "unittest", "discover", "-s", "runner/tests"],
-            cwd=str(PROJECT_ROOT),
-            capture_output=True,
-            text=True,
-            timeout=timeout,
-            stdin=subprocess.DEVNULL,
-        )
-    except subprocess.TimeoutExpired:
-        return _tool_text({"status": "timeout", "timeout_s": timeout})
-    tail = "\n".join((result.stderr or "").strip().splitlines()[-12:])
-    passed = result.returncode == 0
-    return _tool_text(
-        {
-            "status": "pass" if passed else "fail",
-            "returncode": result.returncode,
-            "tail": tail,
-        }
-    )
-
-
-def _handle_socratic_frontier(args: Dict[str, Any]) -> str:
-    """Inspect, add to, settle, or export the Socratic decision-tree frontier."""
-    from skills.grilling.socratic_tree import (
-        DecisionNode,
-        DesignTree,
-        frontier_transaction,
-    )
-
-    file_path = Path(
-        args.get("file") or args.get("frontier_file") or ".research/frontier.json"
-    )
-    action = str(args.get("action") or "").strip().lower()
-    node_spec = args.get("node") if isinstance(args.get("node"), dict) else {}
-    objective = args.get("objective", "")
-
-    # Authoring: add a node (tool-drivable, previously hand-written JSON only).
-    # Mutations run as a locked read-modify-write so concurrent add/settle calls
-    # are serialized across processes instead of racing on a bare open("w").
-    if action == "add" or node_spec:
-        if not node_spec.get("id") or not node_spec.get("question"):
-            return _tool_text(
-                {"status": "error", "message": "'node' needs 'id' and 'question'"}
-            )
-        with frontier_transaction(file_path, objective) as tree:
-            tree.add_node(
-                DecisionNode(
-                    node_id=node_spec["id"],
-                    title=node_spec.get("title") or node_spec["id"],
-                    question=node_spec["question"],
-                    recommended=node_spec.get("recommended", ""),
-                    options=node_spec.get("options") or [],
-                    prerequisites=node_spec.get("depends_on") or [],
-                )
-            )
-        return _tool_text(
-            {"status": "added", "node_id": node_spec["id"], "file": str(file_path)}
-        )
-
-    if action == "export":
-        with frontier_transaction(file_path, objective):
-            pass
-        return _tool_text({"status": "exported", "file": str(file_path)})
-
-    if args.get("settle"):
-        node_id, answer = args["settle"][0], args["settle"][1]
-        with frontier_transaction(file_path, objective) as tree:
-            tree.settle_node(node_id, answer)
-        return _tool_text(
-            {"status": "settled", "node_id": node_id, "file": str(file_path)}
-        )
-
-    if not file_path.exists():
-        return _tool_text(
-            {
-                "status": "no_frontier",
-                "message": f"No frontier file at {file_path}. Run /grilling first.",
-                "file": str(file_path),
-            }
-        )
-
-    tree = DesignTree.load_from_json(file_path)
-    frontier = tree.compute_frontier()
-    return _tool_text(
-        {
-            "status": "frontier",
-            "objective": tree.objective,
-            "is_complete": tree.is_complete(),
-            "total_nodes": len(tree.nodes),
-            "settled": sum(1 for n in tree.nodes.values() if n.is_settled()),
-            "frontier": [
-                {"node_id": n.node_id, "question": n.question} for n in frontier
-            ],
-            "file": str(file_path),
-        }
-    )
-
-
-# ---------------------------------------------------------------------------
-# registry
-# ---------------------------------------------------------------------------
-
-
-def build_tools() -> List[ToolSpec]:
-    """The 7 canonical iumbtems_* tools, in-process wrappers only."""
-    return [
-        ToolSpec(
-            name="iumbtems_config",
-            description=(
-                "Inspect or modify the active Epistemic Swarm configuration "
-                "(.research/config.json). Accepts every canonical key; writes are "
-                "schema-validated, locked, atomic, and preserve unknown keys. "
-                "null is accepted only for nullable keys (it clears them / "
-                "follows the default policy); null for a non-nullable key is "
-                "rejected. Pass expected_hash (alias expectedHash; min 8 hex "
-                "chars) to guard against a stale write."
-            ),
-            input_schema=config_tool_input_schema(),
-            handler=_handle_config,
-        ),
-        ToolSpec(
-            name="iumbtems_swarm_research",
-            description="Dispatch the dialectic researcher pair (Agent Alpha thesis vs Agent Beta antithesis) with epistemic auditing. Long-running; blocks until the swarm completes.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "objective": {
-                        "type": "string",
-                        "description": "Research question or objective",
-                    },
-                    "base_dir": {"type": "string"},
-                    "frontier_file": {
-                        "type": "string",
-                        "description": "Settled frontier.json from grilling",
-                    },
-                    "engine": {
-                        "type": "string",
-                        "enum": ["duckduckgo", "brave", "firecrawl", "searxng"],
-                    },
-                    "depth": {"type": "integer"},
-                    "mock_claude": {
-                        "type": "boolean",
-                        "description": "Synthetic run, zero API cost",
-                    },
-                    "backend": {
-                        "type": "string",
-                        "enum": ["auto", "claude", "opencode"],
-                        "description": "Agent runtime backend (default auto = host-native)",
-                    },
-                },
-                "required": ["objective"],
-            },
-            handler=_handle_swarm_research,
-        ),
-        ToolSpec(
-            name="iumbtems_code_audit",
-            description="Dispatch a dialectic codebase review (structural architect vs vulnerability red-team).",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "target": {
-                        "type": "string",
-                        "description": "Codebase target or audit focus",
-                    },
-                    "base_dir": {"type": "string"},
-                    "frontier_file": {
-                        "type": "string",
-                        "description": "Settled frontier.json from /grilling",
-                    },
-                    "mock_claude": {"type": "boolean"},
-                    "backend": {
-                        "type": "string",
-                        "enum": ["auto", "claude", "opencode"],
-                    },
-                },
-                "required": ["target"],
-            },
-            handler=_handle_code_audit,
-        ),
-        ToolSpec(
-            name="iumbtems_oss_scout",
-            description="Scout open-source libraries, audit licenses, and build clean-room blueprints.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "feature": {
-                        "type": "string",
-                        "description": "Feature or library to scout",
-                    },
-                    "base_dir": {"type": "string"},
-                    "frontier_file": {
-                        "type": "string",
-                        "description": "Settled frontier.json from /grilling",
-                    },
-                    "mock_claude": {"type": "boolean"},
-                    "backend": {
-                        "type": "string",
-                        "enum": ["auto", "claude", "opencode"],
-                    },
-                },
-                "required": ["feature"],
-            },
-            handler=_handle_oss_scout,
-        ),
-        ToolSpec(
-            name="iumbtems_brainstorm",
-            description="Lateral ideation portfolio (feature vectors + paradigm moves + falsifiable spikes). Never bug fixes.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "objective": {
-                        "type": "string",
-                        "description": "Ambiguous prompt to ideate on",
-                    },
-                    "base_dir": {"type": "string"},
-                    "frontier_file": {
-                        "type": "string",
-                        "description": "Settled frontier.json from /grilling",
-                    },
-                    "mock_claude": {"type": "boolean"},
-                    "backend": {
-                        "type": "string",
-                        "enum": ["auto", "claude", "opencode"],
-                    },
-                },
-                "required": ["objective"],
-            },
-            handler=_handle_brainstorm,
-        ),
-        ToolSpec(
-            name="iumbtems_darkharvest",
-            description="Product competitor teardown: seed inspirations plus prompt, expand to adjacents, emit per-feature depend/vendor/clean-room/skip verdicts with SPDX attribution. Permissive-only vendoring; GPL/AGPL spec-rebuild only.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "objective": {
-                        "type": "string",
-                        "description": "Product arena to tear down (e.g. Paseo-class agent harness competitor)",
-                    },
-                    "seeds": {
-                        "type": "array",
-                        "items": {"type": "string"},
-                        "description": "Seed inspiration repo URLs",
-                    },
-                    "maxRepos": {
-                        "type": "integer",
-                        "description": "Cap on total competitors (default 10)",
-                    },
-                    "depth": {"type": "integer", "description": "Dialectic depth 1-4"},
-                    "base_dir": {"type": "string"},
-                    "frontier_file": {
-                        "type": "string",
-                        "description": "Settled frontier.json from /grilling",
-                    },
-                    "mock_claude": {"type": "boolean"},
-                    "backend": {
-                        "type": "string",
-                        "enum": ["auto", "claude", "opencode"],
-                    },
-                },
-                "required": ["objective"],
-            },
-            handler=_handle_darkharvest,
-        ),
-        ToolSpec(
-            name="iumbtems_factory",
-            description="Drive factory run state: init / phase-add / qa-record / expansion / stop / gate. State goes to <project>/.factory and <project>/.roadmap; no filesystem path to helper scripts required.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "command": {
-                        "type": "string",
-                        "enum": [
-                            "init",
-                            "phase-add",
-                            "qa-record",
-                            "expansion",
-                            "stop",
-                            "gate",
-                        ],
-                    },
-                    "action": {
-                        "type": "string",
-                        "enum": [
-                            "open",
-                            "settle",
-                            "approve",
-                            "waive",
-                            "escalate",
-                            "count",
-                        ],
-                        "description": "Gate action (with command: gate)",
-                    },
-                    "run": {"type": "string", "description": "Factory run name"},
-                    "phase": {
-                        "type": "string",
-                        "description": "Phase id (e.g. 01-auth)",
-                    },
-                    "goal": {"type": "string"},
-                    "accept": {
-                        "type": "string",
-                        "description": "Semicolon-separated acceptance criteria",
-                    },
-                    "seat": {"type": "string", "description": "QA seat (qa-a | qa-b)"},
-                    "verdict": {
-                        "type": "string",
-                        "enum": ["pass", "fail", "conditional"],
-                    },
-                    "reason": {"type": "string"},
-                    "loops": {
-                        "type": "integer",
-                        "description": "Expansion loop count (1-10)",
-                    },
-                    "max_loops": {"type": "integer"},
-                    "project_dir": {
-                        "type": "string",
-                        "description": "Project root (default: IUMBTEMS_PROJECT_DIR or cwd)",
-                    },
-                },
-                "required": ["command"],
-            },
-            handler=_handle_factory,
-        ),
-        ToolSpec(
-            name="iumbtems_verify_quote",
-            description="Audit a verbatim citation against the SHA-256 source cache (.research/sources/<hash>.md).",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "hash": {
-                        "type": "string",
-                        "description": "Content-addressed SHA-256 of the cached source",
-                    },
-                    "quote": {
-                        "type": "string",
-                        "description": "Verbatim quote to verify",
-                    },
-                    "base_dir": {"type": "string"},
-                },
-                "required": ["hash", "quote"],
-            },
-            handler=_handle_verify_quote,
-        ),
-        ToolSpec(
-            name="iumbtems_reindex_claims",
-            description="Rebuild the derived claims.sqlite index from .research flat files (idempotent; flat files are source of truth).",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "base_dir": {
-                        "type": "string",
-                        "description": "Path to .research workspace",
-                    },
-                },
-            },
-            handler=_handle_reindex_claims,
-        ),
-        ToolSpec(
-            name="iumbtems_report_retraction",
-            description="Record a RETRACTED/REVISED event for a cached source; dependent VERIFIED claims degrade to STALE/SUSPECT on the next audit (Living Dossiers).",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "hash": {
-                        "type": "string",
-                        "description": "Content-addressed SHA-256 of the affected source",
-                    },
-                    "event": {"type": "string", "enum": ["RETRACTED", "REVISED"]},
-                    "note": {
-                        "type": "string",
-                        "description": "Why the source was retracted/revised",
-                    },
-                    "base_dir": {"type": "string"},
-                },
-                "required": ["hash", "event"],
-            },
-            handler=_handle_report_retraction,
-        ),
-        ToolSpec(
-            name="iumbtems_check_staleness",
-            description="Run one claim-degradation pass: join claims against retraction events, write the status ledger, and queue re-runs for degraded scopes. Never mutates dossiers.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "base_dir": {"type": "string"},
-                    "scope_ids": {
-                        "type": "array",
-                        "items": {"type": "string"},
-                        "description": "Limit the pass to specific scopes",
-                    },
-                },
-            },
-            handler=_handle_check_staleness,
-        ),
-        ToolSpec(
-            name="iumbtems_set_domain_pack",
-            description="Activate a Regulated Domain Pack (biopharma/quant/legal epistemic constitution) for subsequent audits.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "pack": {
-                        "type": "string",
-                        "description": "Pack id: biopharma | quant | legal (or a path)",
-                    },
-                    "base_dir": {"type": "string"},
-                },
-                "required": ["pack"],
-            },
-            handler=_handle_set_domain_pack,
-        ),
-        ToolSpec(
-            name="iumbtems_export_brief",
-            description="Export a proof-carrying research brief (PCRB): self-contained signed bundle of synthesis, claims, quote witnesses, and full source texts.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "base_dir": {"type": "string"},
-                    "out": {
-                        "type": "string",
-                        "description": "Output path (default <base_dir>/brief.pcrb.json)",
-                    },
-                    "objective": {"type": "string"},
-                    "key": {
-                        "type": "string",
-                        "description": "HMAC key (prefer key_file or env IUMBTEMS_PCRB_KEY)",
-                    },
-                    "key_file": {"type": "string"},
-                },
-            },
-            handler=_handle_export_brief,
-        ),
-        ToolSpec(
-            name="iumbtems_verify_brief",
-            description="Verify a proof-carrying brief against its BUNDLED sources: manifest integrity, HMAC signature, and every quote re-checked. Exit-fail semantics; no trust in the producing LLM.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "brief": {
-                        "type": "string",
-                        "description": "Path to brief.pcrb.json",
-                    },
-                    "key": {"type": "string"},
-                    "key_file": {"type": "string"},
-                },
-                "required": ["brief"],
-            },
-            handler=_handle_verify_brief,
-        ),
-        ToolSpec(
-            name="iumbtems_socratic_frontier",
-            description="Inspect or advance the Socratic decision-tree frontier (.research/frontier.json).",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "file": {"type": "string", "description": "Path to frontier.json"},
-                    "objective": {"type": "string"},
-                    "action": {
-                        "type": "string",
-                        "enum": ["inspect", "add", "settle", "export"],
-                        "description": "inspect (default) | add a node | settle a node | export the file",
-                    },
-                    "node": {
-                        "type": "object",
-                        "description": "Node to add: {id, question, title?, recommended?, depends_on?[]}",
-                    },
-                    "settle": {
-                        "type": "array",
-                        "items": {"type": "string"},
-                        "description": "Two-element [node_id, answer] to settle a frontier node",
-                    },
-                },
-            },
-            handler=_handle_socratic_frontier,
-        ),
-        ToolSpec(
-            name="iumbtems_doctor",
-            description="Preflight health check for the resolved workspace: plugin version, backend binary, search-engine reachability, and workspace writability. Run this first when anything looks wrong.",
-            input_schema={
-                "type": "object",
-                "properties": {
-                    "base_dir": {"type": "string"},
-                    "mode": {"type": "string"},
-                    "probe": {
-                        "type": "boolean",
-                        "description": "Run a live 1-query search probe (default true)",
-                    },
-                },
-            },
-            handler=_handle_doctor,
-        ),
-        ToolSpec(
-            name="iumbtems_test",
-            description="Run the packaged IUMBTEMS test suite (subprocess, timeout-bounded) and report pass/fail with the tail of the output.",
-            input_schema={"type": "object", "properties": {}},
-            handler=_handle_test,
-        ),
-    ]
-
-
-def build_server() -> StdioJsonRpcServer:
-    return StdioJsonRpcServer(
-        server_name=SERVER_NAME,
-        version=SERVER_VERSION,
-        tools=build_tools(),
-        protocol_version=PROTOCOL_VERSION,
-        log_prefix="[iumbtems-mcp]",
-    )
-
-
-# ---------------------------------------------------------------------------
-# entry points
-# ---------------------------------------------------------------------------
-
-
-def call_once(tool_name: str, arguments: Dict[str, Any]) -> int:
-    """One-shot dispatch: run a single tool and print its text payload."""
-    server = build_server()
-    spec = server._by_name.get(tool_name)
-    if spec is None:
-        json.dump(
-            {
-                "error": f"Tool {tool_name} not found",
-                "available": [t.name for t in server.tools],
-            },
-            sys.stdout,
-            indent=2,
-        )
-        sys.stdout.write("\n")
-        return 1
-    try:
-        text = spec.handler(arguments)
-    except Exception as exc:  # noqa: BLE001 - surface as a JSON error payload
-        json.dump({"error": f"{type(exc).__name__}: {exc}"}, sys.stdout, indent=2)
-        sys.stdout.write("\n")
-        return 1
-    sys.stdout.write(text if text.endswith("\n") else text + "\n")
-    return 0
-
-
-def main(argv: Optional[List[str]] = None) -> int:
-    parser = argparse.ArgumentParser(description="IUMBTEMS MCP server")
-    sub = parser.add_subparsers(dest="command")
-
-    call_p = sub.add_parser("call", help="One-shot tool dispatch (JSON out)")
-    call_p.add_argument("tool", help="Tool name, e.g. iumbtems_verify_quote")
-    call_p.add_argument("arguments", help="JSON object of tool arguments")
-
-    sub.add_parser("serve", help="Run stdio MCP server (default)")
-
-    args = parser.parse_args(argv)
-
-    if args.command == "call":
-        try:
-            arguments = json.loads(args.arguments) if args.arguments else {}
-        except json.JSONDecodeError as exc:
-            print(json.dumps({"error": f"arguments must be valid JSON: {exc}"}))
-            return 1
-        return call_once(args.tool, arguments)
-
-    build_server().serve_forever()
-    return 0
-
-
-if __name__ == "__main__":
-    sys.exit(main())