molecule-core/workspace
Hongming Wang f01f374072 feat(mcp): add molecule-mcp doctor onboarding diagnostic
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>
2026-05-05 15:44:36 -07:00
..
adapters fix: comprehensive a2a-sdk 1.x migration sweep across workspace/ 2026-04-27 09:42:57 -07:00
builtin_tools feat(harness): coordinator phase-boundary instrumentation for RFC #2251 2026-04-28 20:11:46 -07:00
lib feat(workspace): pre-stop serialization for pause/resume (closes #1386) 2026-04-21 12:40:44 +00:00
molecule_audit chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
platform_tools feat(mcp): multi-workspace routing for memory + chat_history + workspace_info 2026-05-04 14:17:58 -07:00
plugins_registry feat(plugin): implement MCPServerAdaptor (issue #847) 2026-04-24 01:42:13 +00:00
policies feat(platform): single-source-of-truth tool registry — adapters consume, no drift 2026-04-28 17:11:36 -07:00
scripts fix(git-token-helper): close TOCTOU window + stop swallowing chmod errors (closes #1552) 2026-04-26 08:22:29 -07:00
skill_loader feat(skills): per-skill runtime compatibility (#119, hermes pattern) 2026-04-27 01:57:43 -07:00
tests feat(mcp): add molecule-mcp doctor onboarding diagnostic 2026-05-05 15:44:36 -07:00
.coveragerc test(workspace): centralize pytest-cov config + 92% floor (closes #1817) 2026-04-26 06:21:22 -07:00
a2a_cli.py fix(runtime): use lowercase wire role for v0.3 JSON-RPC compat layer 2026-04-27 12:40:11 -07:00
a2a_client.py perf(a2a): bound + LRU-evict _peer_metadata cache (#2482) 2026-05-05 01:39:07 -07:00
a2a_executor.py fix(a2a): route terminal Message via TaskUpdater.complete/failed in task mode 2026-05-03 04:06:45 -07:00
a2a_mcp_server.py fix(onboarding): address Claude Code MCP onboarding friction (#2934) 2026-05-05 14:19:09 -07:00
a2a_tools_delegation.py refactor(workspace): extract delegation handlers from a2a_tools.py to a2a_tools_delegation.py (RFC #2873 iter 4b) 2026-05-05 05:00:52 -07:00
a2a_tools_inbox.py refactor(workspace): extract inbox tools from a2a_tools.py (RFC #2873 iter 4e) 2026-05-05 14:28:58 -07:00
a2a_tools_memory.py refactor(workspace): extract memory tools from a2a_tools.py to a2a_tools_memory.py (RFC #2873 iter 4c) 2026-05-05 09:50:39 -07:00
a2a_tools_messaging.py refactor(workspace): extract messaging tools from a2a_tools.py to a2a_tools_messaging.py (RFC #2873 iter 4d) 2026-05-05 09:50:47 -07:00
a2a_tools_rbac.py refactor(workspace): extract RBAC helpers from a2a_tools.py to a2a_tools_rbac.py (RFC #2873 iter 4a) 2026-05-05 04:43:16 -07:00
a2a_tools.py refactor(workspace): extract inbox tools from a2a_tools.py (RFC #2873 iter 4e) 2026-05-05 14:28:58 -07:00
adapter_base.py feat: drop shared_context — use memory v2 team namespace instead 2026-05-04 16:30:26 -07:00
agent.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
agents_md.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
boot_routes.py test(runtime): pin PR #2756's card-vs-setup decoupling with build_routes helper 2026-05-04 14:59:56 -07:00
build-all.sh fix: update workspace script comments for workspace-template → workspace rename 2026-04-18 01:48:05 -07:00
card_helpers.py fix(runtime): isolate card-skill enrichment + transcript handler from adapter shape mismatch 2026-05-04 14:15:27 -07:00
config.py feat: drop shared_context — use memory v2 team namespace instead 2026-05-04 16:30:26 -07:00
configs_dir.py fix(runtime): auto-fallback CONFIGS_DIR for non-container hosts (closes #2458) 2026-05-01 13:07:55 -07:00
consolidation.py fix: apply #1124 env-var defaults + scrub F1088 credentials from INCIDENT_LOG.md (#1347) 2026-04-21 08:11:44 +00:00
coordinator.py feat: drop shared_context — use memory v2 team namespace instead 2026-05-04 16:30:26 -07:00
Dockerfile feat(workspace): 45-min gh-token refresh daemon + credential helper cache 2026-04-22 19:52:46 -07:00
entrypoint.sh fix(workspace): credential helper security hardening (#1797) 2026-04-23 18:14:55 +00:00
event_log.py feat(workspace): event_log module + EventLogConfig (#119 PR-2) 2026-05-03 00:17:12 -07:00
events.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
executor_helpers.py docs(a2a): correct misleading v1-tolerance comments 2026-05-02 02:33:00 -07:00
heartbeat.py feat(workspace): wire observability config into heartbeat + uvicorn (#119 PR-3a) 2026-05-03 01:01:57 -07:00
inbox_uploads.py fix(inbox-uploads): cancel BatchFetcher futures on wait_all timeout 2026-05-05 12:34:41 -07:00
inbox.py fix(inbox): drop unused batch_fetcher = None after end-of-batch drain 2026-05-05 11:56:54 -07:00
initial_prompt.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
internal_chat_uploads.py fix(workspace): surface errno + path on chat-upload mkdir failure 2026-05-01 11:47:53 -07:00
internal_file_read.py feat(chat_files): rewrite Download as HTTP-forward (RFC #2312, PR-D) 2026-04-29 15:19:02 -07:00
main.py test(runtime): pin PR #2756's card-vs-setup decoupling with build_routes helper 2026-05-04 14:59:56 -07:00
mcp_cli.py feat(mcp): add molecule-mcp doctor onboarding diagnostic 2026-05-05 15:44:36 -07:00
mcp_doctor.py feat(mcp): add molecule-mcp doctor onboarding diagnostic 2026-05-05 15:44:36 -07:00
mcp_heartbeat.py refactor(workspace): split mcp_cli.py (626 LOC) into focused modules (RFC #2873 iter 3) 2026-05-05 04:33:06 -07:00
mcp_inbox_pollers.py refactor(workspace): split mcp_cli.py (626 LOC) into focused modules (RFC #2873 iter 3) 2026-05-05 04:33:06 -07:00
mcp_workspace_resolver.py mcp: surface specific TOKEN_FILE errors + link follow-ups (#2934) 2026-05-05 15:07:15 -07:00
molecule_ai_status.py fix(runtime): replace remaining /app/ legacy paths in agent prompts + docstrings 2026-04-27 11:22:00 -07:00
not_configured_handler.py fix(runtime): redact secret-shaped tokens from JSON-RPC error.data 2026-05-04 15:07:53 -07:00
platform_auth.py feat(mcp): cross-workspace delegation routing (multi-ws PR-2) 2026-05-04 08:32:24 -07:00
platform_inbound_auth.py fix(runtime): auto-fallback CONFIGS_DIR for non-container hosts (closes #2458) 2026-05-01 13:07:55 -07:00
plugins.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
preflight.py fix(preflight): downgrade required_env + auth_token failures to warnings 2026-05-04 12:20:34 -07:00
prompt.py feat: drop shared_context — use memory v2 team namespace instead 2026-05-04 16:30:26 -07:00
pytest.ini feat(preflight): replace SUPPORTED_RUNTIMES static list with adapter discovery 2026-04-27 00:44:51 -07:00
rebuild-runtime-images.sh fix: update workspace script comments for workspace-template → workspace rename 2026-04-18 01:48:05 -07:00
requirements.txt chore(deps)(deps): update starlette requirement in /workspace 2026-05-03 01:36:45 +00:00
runtime_wedge.py chore(workspace): drop claude_sdk_executor — Phase 2 of #87 2026-04-27 00:52:55 -07:00
secret_redactor.py fix(runtime): redact secret-shaped tokens from JSON-RPC error.data 2026-05-04 15:07:53 -07:00
shared_runtime.py feat(platform): single-source-of-truth tool registry — adapters consume, no drift 2026-04-28 17:11:36 -07:00
smoke_mode.py chore(smoke): runtime_wedge follow-ups from PR #2473 review 2026-05-01 18:01:51 -07:00
transcript_auth.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
watcher.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00