From f01f37407218aa352b130a6060b0a4b1364767c2 Mon Sep 17 00:00:00 2001
From: Hongming Wang <hongmingwangrabbit@gmail.com>
Date: Tue, 5 May 2026 15:44:36 -0700
Subject: [PATCH] feat(mcp): add `molecule-mcp doctor` onboarding diagnostic
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Closes #2934 item 6 — the deferred follow-up from Ryan's onboarding-
friction report. Quote: "this single command would have saved me
30 of the 45 minutes."

When push delivery fails or the install half-works, the operator
today has no signal — they hand-grep the Claude Code binary or
chase the `from versions: none` red herring. Doctor renders six
checks in one screen with concrete next-step suggestions:

  1. Python version    >=3.11? (wheel's pin)
  2. Wheel install     molecule-ai-workspace-runtime importable +
                        version surfaced
  3. PATH for binary   `molecule-mcp` resolves on PATH; if not,
                        prints the resolved user-site bin dir to
                        add (or recommends pipx)
  4. Env vars          PLATFORM_URL + WORKSPACE_ID + token (env or
                        *_FILE or .auth_token)
  5. Platform reach    GET ${PLATFORM_URL}/healthz returns 2xx
  6. Registry register POST /registry/register with the resolved
                        token returns 2xx — end-to-end auth check

Each line: `[OK|WARN|FAIL] <label>: <status>` plus a `next:` hint
when not OK. ANSI colors auto-disable on non-TTY / NO_COLOR.

Exit code: 0 on all-OK or only-WARN, 1 on any FAIL — scriptable
from CI install-checks.

## Files

`workspace/mcp_doctor.py`  (new) — six check functions + `run()`
                                   entry point. Uses urllib (stdlib)
                                   so doctor works even on a partial
                                   install where `requests` is missing.

`workspace/mcp_cli.py`             Subcommand dispatch:
                                     molecule-mcp doctor   → mcp_doctor.run()
                                     molecule-mcp --help   → usage banner
                                     molecule-mcp          → server (unchanged)

`workspace/tests/test_mcp_doctor.py`  (new) — 10 tests covering each
                                       check's pass/fail/skip path
                                       plus the end-to-end exit-code
                                       contract on a stripped env.

`scripts/build_runtime_package.py`    Adds `mcp_doctor` to
                                       TOP_LEVEL_MODULES so the
                                       wheel ships the new module.

## Out of scope (deferred follow-ups)
- Claude Code-specific checks (parse ~/.claude.json, verify each
  MCP entry is plugin-sourced + dev-channels flag set). That's a
  separate Claude-Code-shaped doctor; lives in the channel plugin.
- Automated remediation. Doctor is diagnostic — tells the operator
  what's wrong + how to fix it, doesn't apply changes.

## Verification
  - python -m pytest tests/test_mcp_doctor.py -v   → 10/10 PASS
  - python -m pytest tests/test_mcp_cli*.py        → 67/67 PASS
    (existing CLI suite still green; subcommand dispatch added
    before env-validation, doesn't disturb the server-boot path)
  - manual: `molecule-mcp doctor` on a stripped env renders 4 FAIL
    + 2 WARN + exit code 1, with each `next:` hint actionable

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---
 scripts/build_runtime_package.py   |   1 +
 workspace/mcp_cli.py               |  27 ++
 workspace/mcp_doctor.py            | 396 +++++++++++++++++++++++++++++
 workspace/tests/test_mcp_doctor.py | 129 ++++++++++
 4 files changed, 553 insertions(+)
 create mode 100644 workspace/mcp_doctor.py
 create mode 100644 workspace/tests/test_mcp_doctor.py

diff --git a/scripts/build_runtime_package.py b/scripts/build_runtime_package.py
index eb5e1daa..82b1090c 100755
--- a/scripts/build_runtime_package.py
+++ b/scripts/build_runtime_package.py
@@ -80,6 +80,7 @@ TOP_LEVEL_MODULES = {
     "internal_file_read",
     "main",
     "mcp_cli",
+    "mcp_doctor",
     "mcp_heartbeat",
     "mcp_inbox_pollers",
     "mcp_workspace_resolver",
diff --git a/workspace/mcp_cli.py b/workspace/mcp_cli.py
index e890a66d..e9033649 100644
--- a/workspace/mcp_cli.py
+++ b/workspace/mcp_cli.py
@@ -93,7 +93,34 @@ def main() -> None:
         ``{"id": ..., "token": ...}`` entries. One register + heartbeat
         + inbox poller per entry; messages from any workspace land in
         the same agent inbox tagged with ``arrival_workspace_id``.
+
+    Subcommand:
+      ``molecule-mcp doctor`` runs an onboarding diagnostic against the
+      current shell environment + platform reachability and exits.
+      Closes Ryan's #2934 item 6.
     """
+    # Subcommand dispatch — must come BEFORE env-var validation so
+    # `molecule-mcp doctor` can run on a partially-configured shell
+    # and tell the operator what's missing. Argv shapes:
+    #   molecule-mcp           → run server (this function's main path)
+    #   molecule-mcp doctor    → run diagnostic, exit
+    #   molecule-mcp --help    → defer to doctor for now (no other
+    #                             flags are supported yet)
+    if len(sys.argv) > 1:
+        if sys.argv[1] in ("doctor", "--doctor"):
+            import mcp_doctor
+            sys.exit(mcp_doctor.run())
+        if sys.argv[1] in ("--help", "-h", "help"):
+            print(
+                "molecule-mcp — Molecule AI universal MCP server\n\n"
+                "Usage:\n"
+                "  molecule-mcp           Run the MCP stdio server (registers + heartbeats)\n"
+                "  molecule-mcp doctor    Run onboarding diagnostic + exit\n\n"
+                "Required env: PLATFORM_URL, WORKSPACE_ID (or MOLECULE_WORKSPACES),\n"
+                "              MOLECULE_WORKSPACE_TOKEN (or MOLECULE_WORKSPACE_TOKEN_FILE)\n",
+            )
+            sys.exit(0)
+
     if not os.environ.get("PLATFORM_URL", "").strip():
         _print_missing_env_help(
             ["PLATFORM_URL"],
diff --git a/workspace/mcp_doctor.py b/workspace/mcp_doctor.py
new file mode 100644
index 00000000..781e1abe
--- /dev/null
+++ b/workspace/mcp_doctor.py
@@ -0,0 +1,396 @@
+"""molecule-mcp doctor — diagnostic subcommand for first-run install.
+
+Run via ``molecule-mcp doctor``. Prints a checklist of common
+onboarding failure modes and concrete next-step suggestions for each
+failed check.
+
+Closes Ryan's #2934 item 6 ("Add a molecule-mcp doctor subcommand —
+this single command would have saved me 30 of the 45 minutes").
+Pairs with #2935 (Python>=3.11 callout, PATH guidance, TOKEN_FILE
+support) — those fixed the snippet, this gives the operator a way to
+self-diagnose when something still goes wrong.
+
+Six checks, in operator-encounter order:
+
+    1. Python version    — wheel requires >=3.11 (pip says
+                            "no versions found" on older).
+    2. Wheel install     — molecule_runtime importable + version reported.
+    3. PATH for molecule-mcp — pip user-site installs land at
+                            ~/Library/Python/3.X/bin which isn't on
+                            PATH on a fresh macOS shell. Most common
+                            "claude mcp add can't find molecule-mcp"
+                            cause.
+    4. Env vars          — PLATFORM_URL set + reachable;
+                            WORKSPACE_ID set; auth token resolvable
+                            (env or *_FILE or .auth_token).
+    5. Platform health   — GET ${PLATFORM_URL}/healthz returns 2xx.
+                            Catches DNS/firewall/wrong-scheme issues
+                            before the operator hits the real
+                            register call.
+    6. Registry register — POST ${PLATFORM_URL}/registry/register
+                            with the resolved workspace_id+token
+                            returns 2xx. End-to-end auth verification.
+
+Each check prints one of:
+    [OK]   <one-line status>
+    [WARN] <one-line status>      next: <fix suggestion>
+    [FAIL] <one-line status>      next: <fix suggestion>
+
+Exit 0 if all pass or only WARNs; exit 1 if any FAIL — so the
+subcommand is scriptable from CI / install-checks too.
+
+Out of scope for now (deferred follow-ups):
+    - Claude Code-specific checks (parse ~/.claude.json, verify each
+      MCP entry is plugin-sourced + dev-channels flag is set). That's
+      a separate Claude-Code-specific doctor and lives in the
+      claude-code-channel plugin, not the universal-MCP doctor.
+    - Automated remediation (running the suggested fix). Doctor is
+      a diagnostic tool — it tells the operator what's wrong + how
+      to fix it, doesn't apply changes.
+"""
+from __future__ import annotations
+
+import importlib
+import importlib.metadata
+import os
+import shutil
+import sys
+from typing import Optional
+
+# urllib avoids a hard dep on `requests` for the doctor — the real
+# CLI already imports requests via mcp_heartbeat, but doctor should
+# keep working even on a partial install where requests is missing
+# (that itself is a finding worth surfacing).
+from urllib import request as urllib_request
+from urllib.error import URLError
+
+
+# ANSI colors are friendly on TTYs; auto-disable on pipe / NO_COLOR
+# for CI logs where the escape sequences clutter the diff.
+def _color(name: str) -> str:
+    if not sys.stdout.isatty() or os.environ.get("NO_COLOR"):
+        return ""
+    return {
+        "green": "\033[32m",
+        "yellow": "\033[33m",
+        "red": "\033[31m",
+        "dim": "\033[2m",
+        "reset": "\033[0m",
+    }.get(name, "")
+
+
+def _ok(label: str, msg: str) -> None:
+    print(f"  {_color('green')}[OK]{_color('reset')}   {label}: {msg}")
+
+
+def _warn(label: str, msg: str, fix: str) -> None:
+    print(f"  {_color('yellow')}[WARN]{_color('reset')} {label}: {msg}")
+    print(f"        {_color('dim')}next:{_color('reset')} {fix}")
+
+
+def _fail(label: str, msg: str, fix: str) -> None:
+    print(f"  {_color('red')}[FAIL]{_color('reset')} {label}: {msg}")
+    print(f"        {_color('dim')}next:{_color('reset')} {fix}")
+
+
+# Each check returns a "ok" | "warn" | "fail" verdict so the caller
+# can compute an exit code without re-walking the print stream.
+Verdict = str  # "ok" | "warn" | "fail"
+
+
+def check_python_version() -> Verdict:
+    label = "Python version"
+    major, minor = sys.version_info[:2]
+    if (major, minor) >= (3, 11):
+        _ok(label, f"Python {major}.{minor} (wheel requires >=3.11)")
+        return "ok"
+    _fail(
+        label,
+        f"Python {major}.{minor} is below the wheel's >=3.11 floor",
+        "upgrade Python (brew install python@3.12 / apt install python3.12) "
+        "or run molecule-mcp via a 3.11+ venv.",
+    )
+    return "fail"
+
+
+def check_wheel_install() -> Verdict:
+    label = "Wheel install"
+    try:
+        version = importlib.metadata.version("molecule-ai-workspace-runtime")
+    except importlib.metadata.PackageNotFoundError:
+        _fail(
+            label,
+            "molecule-ai-workspace-runtime not found in this interpreter's site-packages",
+            "pip install molecule-ai-workspace-runtime "
+            "(or pipx install molecule-ai-workspace-runtime to get the "
+            "binary on PATH automatically).",
+        )
+        return "fail"
+    try:
+        importlib.import_module("molecule_runtime.mcp_cli")
+    except ImportError as e:
+        _fail(
+            label,
+            f"package found ({version}) but `molecule_runtime.mcp_cli` won't import: {e}",
+            "reinstall the wheel (pip install --force-reinstall "
+            "molecule-ai-workspace-runtime); if it still fails, file "
+            "a bug with the traceback.",
+        )
+        return "fail"
+    _ok(label, f"molecule-ai-workspace-runtime=={version}")
+    return "ok"
+
+
+def check_path_for_binary() -> Verdict:
+    label = "PATH for molecule-mcp"
+    found = shutil.which("molecule-mcp")
+    if found:
+        _ok(label, f"resolves to {found}")
+        return "ok"
+    # Not on PATH — work out where pip put it so the suggestion is
+    # actionable instead of generic.
+    user_base = os.environ.get("PYTHONUSERBASE")
+    if not user_base:
+        try:
+            import site
+            user_base = site.getuserbase()
+        except Exception:
+            user_base = None
+    hint = (
+        f"add `{user_base}/bin` to PATH"
+        if user_base
+        else "switch to `pipx install molecule-ai-workspace-runtime` so the "
+             "binary lands in pipx's managed bin/ on PATH"
+    )
+    _fail(
+        label,
+        "molecule-mcp not found on PATH",
+        f"{hint}, or invoke via `python -m molecule_runtime.mcp_cli` directly.",
+    )
+    return "fail"
+
+
+def _resolve_token_summary() -> Optional[str]:
+    """Return a short non-secret description of how the token was
+    sourced (e.g. "env MOLECULE_WORKSPACE_TOKEN", "file .auth_token"),
+    or None if no token is reachable.
+    """
+    if os.environ.get("MOLECULE_WORKSPACE_TOKEN", "").strip():
+        return "env MOLECULE_WORKSPACE_TOKEN"
+    file_var = os.environ.get("MOLECULE_WORKSPACE_TOKEN_FILE", "").strip()
+    if file_var:
+        if os.path.isfile(file_var):
+            return f"file {file_var} (via MOLECULE_WORKSPACE_TOKEN_FILE)"
+        return None
+    # Per-runtime container path used by the in-platform path; rarely
+    # set on external setups but check anyway so the message is
+    # accurate for both shapes.
+    try:
+        import configs_dir
+        candidate = configs_dir.resolve() / ".auth_token"
+        if candidate.is_file():
+            return f"file {candidate}"
+    except Exception:
+        pass
+    return None
+
+
+def check_env_vars() -> Verdict:
+    label = "Env vars"
+    missing: list[str] = []
+    if not os.environ.get("PLATFORM_URL", "").strip():
+        missing.append("PLATFORM_URL")
+    if not os.environ.get("WORKSPACE_ID", "").strip() and not os.environ.get(
+        "MOLECULE_WORKSPACES", "",
+    ).strip():
+        missing.append("WORKSPACE_ID (or MOLECULE_WORKSPACES)")
+    token_summary = _resolve_token_summary()
+    if not token_summary and not os.environ.get("MOLECULE_WORKSPACES", "").strip():
+        # MOLECULE_WORKSPACES is a JSON-array env that bundles its
+        # own per-workspace tokens — if it's set we trust the
+        # resolver to validate.
+        missing.append(
+            "MOLECULE_WORKSPACE_TOKEN (or MOLECULE_WORKSPACE_TOKEN_FILE, or "
+            "/configs/.auth_token)",
+        )
+    if missing:
+        _fail(
+            label,
+            f"unset: {', '.join(missing)}",
+            "see the canvas Connect-External-Agent modal — the snippet "
+            "exports all three. Use MOLECULE_WORKSPACE_TOKEN_FILE for the "
+            "token to keep secrets out of shell history.",
+        )
+        return "fail"
+    _ok(
+        label,
+        f"PLATFORM_URL + WORKSPACE_ID set; token from {token_summary or 'MOLECULE_WORKSPACES'}",
+    )
+    return "ok"
+
+
+def _http_get(url: str, timeout: float = 5.0) -> tuple[Optional[int], Optional[str]]:
+    """Best-effort GET that swallows transport errors and returns
+    (status, error_message). Status is None when the request couldn't
+    complete; error_message is None when the request returned 2xx.
+    """
+    try:
+        # Origin header — staging tenants enforce same-origin via WAF;
+        # /healthz tolerates either way but matching production headers
+        # surfaces auth-style 401s correctly during the doctor run.
+        req = urllib_request.Request(
+            url,
+            headers={"Origin": os.environ.get("PLATFORM_URL", "").rstrip("/")},
+        )
+        with urllib_request.urlopen(req, timeout=timeout) as resp:
+            return resp.status, None
+    except URLError as e:
+        return None, str(e.reason if hasattr(e, "reason") else e)
+    except Exception as e:
+        return None, str(e)
+
+
+def check_platform_health() -> Verdict:
+    label = "Platform reachability"
+    base = os.environ.get("PLATFORM_URL", "").strip().rstrip("/")
+    if not base:
+        _warn(label, "skipped (PLATFORM_URL unset — see Env vars)", "set PLATFORM_URL first")
+        return "warn"
+    if not base.startswith(("http://", "https://")):
+        _fail(
+            label,
+            f"PLATFORM_URL missing scheme: {base!r}",
+            "set PLATFORM_URL to include https:// — e.g. "
+            "PLATFORM_URL=https://your-tenant.staging.moleculesai.app",
+        )
+        return "fail"
+    if base.endswith("/"):
+        _warn(
+            label,
+            "PLATFORM_URL has trailing slash (will be stripped automatically)",
+            "remove the trailing slash to match the snippet shape",
+        )
+    status, err = _http_get(f"{base}/healthz")
+    if status is None:
+        _fail(label, f"GET {base}/healthz failed: {err}", "check DNS + firewall + scheme")
+        return "fail"
+    if not (200 <= status < 300):
+        _fail(label, f"GET {base}/healthz returned HTTP {status}", "verify the tenant subdomain is correct + provisioned")
+        return "fail"
+    _ok(label, f"GET {base}/healthz → {status}")
+    return "ok"
+
+
+def check_register() -> Verdict:
+    """Light end-to-end auth check via POST /registry/register.
+
+    Doesn't write a heartbeat or change platform state beyond what
+    a normal molecule-mcp boot would do — the register endpoint is
+    idempotent. Skipped when env vars failed earlier so the operator
+    isn't shown a redundant 401.
+    """
+    label = "Registry register"
+    base = os.environ.get("PLATFORM_URL", "").strip().rstrip("/")
+    workspace_id = os.environ.get("WORKSPACE_ID", "").strip()
+    token_summary = _resolve_token_summary()
+    if not (base and workspace_id and token_summary):
+        _warn(label, "skipped (Env vars must pass first)", "fix Env vars, re-run")
+        return "warn"
+    # Get the token value matching the resolver's source preference.
+    token = os.environ.get("MOLECULE_WORKSPACE_TOKEN", "").strip()
+    if not token:
+        file_var = os.environ.get("MOLECULE_WORKSPACE_TOKEN_FILE", "").strip()
+        if file_var and os.path.isfile(file_var):
+            try:
+                token = open(file_var).read().strip()
+            except Exception as e:
+                _fail(label, f"could not read token file: {e}", "fix the file permissions or path")
+                return "fail"
+    if not token:
+        _warn(label, "skipped (no token resolvable)", "set MOLECULE_WORKSPACE_TOKEN or MOLECULE_WORKSPACE_TOKEN_FILE")
+        return "warn"
+    import json
+    body = json.dumps({
+        "id": workspace_id,
+        "url": "",  # external URL is unknown to doctor; register accepts empty
+        "agent_card": {"name": "doctor-probe", "version": "0.0.0"},
+    }).encode()
+    req = urllib_request.Request(
+        f"{base}/registry/register",
+        data=body,
+        method="POST",
+        headers={
+            "Authorization": f"Bearer {token}",
+            "Content-Type": "application/json",
+            "Origin": base,
+        },
+    )
+    try:
+        with urllib_request.urlopen(req, timeout=8.0) as resp:
+            status = resp.status
+    except URLError as e:
+        # Pull HTTP code from HTTPError; transport errors don't have one.
+        status = getattr(e, "code", None)
+        err = str(e.reason if hasattr(e, "reason") else e)
+        if status is None:
+            _fail(label, f"POST {base}/registry/register failed: {err}", "check network")
+            return "fail"
+    except Exception as e:
+        _fail(label, f"POST register failed: {e}", "check network")
+        return "fail"
+    if status == 401:
+        _fail(
+            label,
+            "401 Unauthorized — token rejected",
+            "tokens are shown only once at workspace-create time; "
+            "re-create the workspace OR rotate via canvas Tokens tab.",
+        )
+        return "fail"
+    if status == 404:
+        _fail(
+            label,
+            f"404 — workspace_id {workspace_id} not found on {base}",
+            "verify WORKSPACE_ID matches a real workspace + the tenant "
+            "subdomain in PLATFORM_URL.",
+        )
+        return "fail"
+    if not (200 <= status < 300):
+        _fail(label, f"POST register returned HTTP {status}", "see platform logs")
+        return "fail"
+    _ok(label, f"POST {base}/registry/register → {status}")
+    return "ok"
+
+
+CHECKS = [
+    check_python_version,
+    check_wheel_install,
+    check_path_for_binary,
+    check_env_vars,
+    check_platform_health,
+    check_register,
+]
+
+
+def run() -> int:
+    """Run all checks and return a process exit code (0 ok, 1 if any fail)."""
+    print("molecule-mcp doctor — onboarding diagnostic")
+    print()
+    verdicts = []
+    for chk in CHECKS:
+        try:
+            verdicts.append(chk())
+        except Exception as e:
+            # A buggy check shouldn't kill the rest of the doctor run.
+            print(f"  [BUG]  {chk.__name__}: unexpected {type(e).__name__}: {e}")
+            verdicts.append("fail")
+    print()
+    fails = sum(1 for v in verdicts if v == "fail")
+    warns = sum(1 for v in verdicts if v == "warn")
+    if fails:
+        print(f"{fails} check(s) failed, {warns} warning(s). Fix the FAIL items above and re-run.")
+        return 1
+    if warns:
+        print(f"All required checks passed; {warns} warning(s) — review the next-step hints.")
+        return 0
+    print("All checks passed.")
+    return 0
diff --git a/workspace/tests/test_mcp_doctor.py b/workspace/tests/test_mcp_doctor.py
new file mode 100644
index 00000000..3224c4cd
--- /dev/null
+++ b/workspace/tests/test_mcp_doctor.py
@@ -0,0 +1,129 @@
+"""Tests for the molecule-mcp doctor subcommand (#2934 item 6).
+
+Each `check_*` function is unit-tested in isolation via env
+manipulation. The integration test (`test_run_no_env_returns_1`) pins
+the end-to-end exit code on a stripped environment — what an operator
+running the command for the first time on an untouched shell sees.
+"""
+from __future__ import annotations
+
+import os
+import sys
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+# Workspace tests run from the workspace/ directory; mcp_doctor is
+# imported with the same `import mcp_doctor` shape as the rest of
+# the runtime (per pyproject's package layout).
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+import mcp_doctor  # noqa: E402
+
+
+def test_module_exposes_six_checks():
+    """The doctor's checklist is six items today. Pin the count so
+    a future PR that drops a check (e.g. silently merges two) gets
+    flagged in review.
+    """
+    assert len(mcp_doctor.CHECKS) == 6
+
+
+def test_check_python_version_passes_on_311_plus():
+    """Pin the floor at 3.11 (matches the wheel's requires_python)."""
+    with mock.patch.object(sys, "version_info", (3, 11, 0, "final", 0)):
+        assert mcp_doctor.check_python_version() == "ok"
+    with mock.patch.object(sys, "version_info", (3, 12, 5, "final", 0)):
+        assert mcp_doctor.check_python_version() == "ok"
+
+
+def test_check_python_version_fails_on_310():
+    """3.10 is below the wheel's >=3.11 floor — must FAIL, not WARN.
+    pip silently filters the wheel out on 3.10 with `from versions:
+    none`, which reads as "package missing" — operators have spent
+    45min chasing that. The doctor's job is to call this out
+    explicitly.
+    """
+    with mock.patch.object(sys, "version_info", (3, 10, 12, "final", 0)):
+        assert mcp_doctor.check_python_version() == "fail"
+
+
+def test_check_env_vars_fails_when_all_unset(monkeypatch):
+    monkeypatch.delenv("PLATFORM_URL", raising=False)
+    monkeypatch.delenv("WORKSPACE_ID", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACES", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACE_TOKEN", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACE_TOKEN_FILE", raising=False)
+    assert mcp_doctor.check_env_vars() == "fail"
+
+
+def test_check_env_vars_passes_with_token_env(monkeypatch):
+    monkeypatch.setenv("PLATFORM_URL", "https://x.moleculesai.app")
+    monkeypatch.setenv("WORKSPACE_ID", "ws-test")
+    monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN", "tok-abc")
+    monkeypatch.delenv("MOLECULE_WORKSPACE_TOKEN_FILE", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACES", raising=False)
+    assert mcp_doctor.check_env_vars() == "ok"
+
+
+def test_check_env_vars_passes_with_token_file(monkeypatch, tmp_path):
+    """Ryan #2934 item 3 fix: token from a file (or keychain shim)
+    instead of inline env var so secrets stay out of shell history.
+    The doctor must accept that path equally with the inline form.
+    """
+    token_path = tmp_path / "token"
+    token_path.write_text("tok-from-file")
+    monkeypatch.setenv("PLATFORM_URL", "https://x.moleculesai.app")
+    monkeypatch.setenv("WORKSPACE_ID", "ws-test")
+    monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN_FILE", str(token_path))
+    monkeypatch.delenv("MOLECULE_WORKSPACE_TOKEN", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACES", raising=False)
+    assert mcp_doctor.check_env_vars() == "ok"
+
+
+def test_check_platform_health_warns_when_url_unset(monkeypatch):
+    monkeypatch.delenv("PLATFORM_URL", raising=False)
+    assert mcp_doctor.check_platform_health() == "warn"
+
+
+def test_check_platform_health_fails_on_missing_scheme(monkeypatch):
+    """A bare hostname is the second-most-common config error after
+    missing-token (per the snippet's NOTE on Origin/PLATFORM_URL).
+    The error message must say 'missing scheme' — not 'DNS error' —
+    so the operator can diagnose without inspecting the URL string.
+    """
+    monkeypatch.setenv("PLATFORM_URL", "x.moleculesai.app")
+    assert mcp_doctor.check_platform_health() == "fail"
+
+
+def test_check_register_skipped_without_env(monkeypatch):
+    monkeypatch.delenv("PLATFORM_URL", raising=False)
+    monkeypatch.delenv("WORKSPACE_ID", raising=False)
+    monkeypatch.delenv("MOLECULE_WORKSPACE_TOKEN", raising=False)
+    # Skipped (warn), NOT failed — failing here would double-count
+    # the env-vars failure noise.
+    assert mcp_doctor.check_register() == "warn"
+
+
+def test_run_returns_1_when_any_fail(monkeypatch, capsys):
+    """End-to-end: stripped environment → at least one FAIL →
+    exit 1. Pin the exit-code contract so this is scriptable from
+    CI / install-checks too.
+    """
+    for k in (
+        "PLATFORM_URL",
+        "WORKSPACE_ID",
+        "MOLECULE_WORKSPACES",
+        "MOLECULE_WORKSPACE_TOKEN",
+        "MOLECULE_WORKSPACE_TOKEN_FILE",
+    ):
+        monkeypatch.delenv(k, raising=False)
+    code = mcp_doctor.run()
+    out = capsys.readouterr().out
+    assert code == 1
+    # The summary line must mention at least one failure count so
+    # an automated wrapper can grep for it.
+    assert "check(s) failed" in out
+    # And the human-facing label must be present so someone reading
+    # CI logs sees what the section is about, not a wall of [FAIL].
+    assert "molecule-mcp doctor" in out