Merge pull request #2935 from Molecule-AI/fix/onboarding-friction-2934
fix(onboarding): address Claude Code MCP onboarding friction (#2934)
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Hongming Wang
GitHub
commit
1ad107cc15
@ -290,10 +290,37 @@ directory** by the `publish-runtime` GitHub Actions workflow on every
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Operators running an agent outside the platform's container fleet
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(any runtime that supports MCP stdio — Claude Code, hermes, codex,
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etc.) can install this wheel and run the universal MCP server
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locally:
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locally.
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### Requirements
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* **Python ≥3.11.** The wheel sets `requires-python = ">=3.11"`. On
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older interpreters `pip install` returns the cryptic
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`Could not find a version that satisfies the requirement` — that
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message is pip filtering this wheel out, NOT the package missing
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from PyPI. Upgrade with `brew install python@3.12` /
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`apt install python3.12` / `pyenv install 3.12` first.
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* **`pipx` recommended over `pip`.** `pipx install` puts
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`molecule-mcp` on PATH automatically and isolates the runtime's
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deps from your system Python. Plain `pip install --user` works
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but the binary lands in `~/.local/bin` (Linux) or
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`~/Library/Python/3.X/bin` (macOS) which is often not on PATH on
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a fresh shell — `claude mcp add molecule -- molecule-mcp` then
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fails with "command not found" at first use.
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### Install
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```sh
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# Recommended:
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pipx install molecule-ai-workspace-runtime
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# Alternative (manage PATH yourself):
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pip install --user molecule-ai-workspace-runtime
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```
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### Run
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```sh
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pip install molecule-ai-workspace-runtime
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WORKSPACE_ID=<uuid> \\
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PLATFORM_URL=https://<tenant>.staging.moleculesai.app \\
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MOLECULE_WORKSPACE_TOKEN=<bearer> \\
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@ -306,10 +333,64 @@ runtimes already get via the workspace's auto-spawned MCP. Register
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the binary in your agent's MCP config (e.g. Claude Code's
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`claude mcp add molecule -- molecule-mcp` with the env above).
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### Keeping the token out of shell history
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Inline `MOLECULE_WORKSPACE_TOKEN=<bearer>` ends up in `~/.zsh_history`
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and (when registered via `claude mcp add`) plaintext in
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`~/.claude.json`. To avoid that, write the token to a 0600 file and
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point `MOLECULE_WORKSPACE_TOKEN_FILE` at it:
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```sh
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umask 077
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printf '%s' "<bearer>" > ~/.config/molecule/token
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WORKSPACE_ID=<uuid> \\
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PLATFORM_URL=https://<tenant>.staging.moleculesai.app \\
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MOLECULE_WORKSPACE_TOKEN_FILE=$HOME/.config/molecule/token \\
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molecule-mcp
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```
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Token resolution order: `MOLECULE_WORKSPACE_TOKEN` (inline env) →
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`MOLECULE_WORKSPACE_TOKEN_FILE` (path) → `${CONFIGS_DIR}/.auth_token`
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(in-container default).
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The token comes from the canvas → Tokens tab. Restarting an external
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workspace from the canvas no longer revokes the token (PR #2412), so
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operator tokens persist across status nudges.
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### Push vs poll delivery (Claude Code specifics)
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By default the inbox runs in **poll mode** — every turn the agent
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calls `wait_for_message`, which blocks up to ~60s on
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`/activity?since_id=…`. Real-time push delivery is also supported,
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but on Claude Code it requires THREE conditions, ALL of which must
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hold:
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1. **The MCP server declares `experimental.claude/channel`** — this
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wheel does (see `_build_initialize_result`). Nothing for you to
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do.
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2. **Claude Code installs the server as a marketplace plugin** — a
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plain `claude mcp add molecule -- molecule-mcp` produces a
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non-plugin-sourced server, which Claude Code rejects with
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`channel_enable requires a marketplace plugin`. Until the
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official `moleculesai/claude-code-plugin` marketplace lands
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(issue #2934 follow-up), operators who want push must scaffold
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their own local marketplace under
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`~/.claude/marketplaces/molecule-local/` containing a
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`marketplace.json` + `plugin.json` that points at this wheel.
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3. **Claude Code is launched with the dev-channels flag** — pass
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`--dangerously-load-development-channels plugin:molecule@<marketplace>`
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on the `claude` invocation. Without this flag the channel
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capability is silently ignored.
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Symptom of any condition failing: messages arrive but only via the
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poll path (every ~1–60s), not real-time. There's currently no
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diagnostic surfaced — `molecule-mcp doctor` (issue #2934 follow-up)
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is planned.
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If you don't need real-time push, the default poll path works
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universally with no extra setup; both modes converge on the same
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`inbox_pop` ack so messages never duplicate.
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See [`docs/workspace-runtime-package.md`](https://github.com/Molecule-AI/molecule-core/blob/main/docs/workspace-runtime-package.md)
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for the publish flow and architecture.
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"""
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@ -425,7 +425,16 @@ def _build_initialize_result() -> dict:
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"tools": {"listChanged": False},
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"experimental": {"claude/channel": {}},
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},
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"serverInfo": {"name": "a2a-delegation", "version": "1.0.0"},
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# Identifier convention: this server is what users register with
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# `claude mcp add molecule -- molecule-mcp` (and similar across
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# other MCP hosts), so the canonical name is "molecule". Earlier
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# versions reported "a2a-delegation" — accurate to the original
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# purpose but a mismatch with how operators actually name it.
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# Mismatch is harmless on tool routing (all MCP hosts dispatch
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# by the user-supplied registration name, NOT serverInfo.name)
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# but matters for any future Claude Code allowlist that gates
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# channel push by hardcoded server name (issue #2934).
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"serverInfo": {"name": "molecule", "version": "1.0.0"},
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# Built per-call (not the module-level constant) so an operator
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# who sets MOLECULE_MCP_POLL_TIMEOUT_SECS after import — e.g.
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# via a wrapper script that exports then re-imports — sees
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@ -35,9 +35,15 @@ def resolve_workspaces() -> tuple[list[tuple[str, str]], list[str]]:
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N workspaces). When set, ``WORKSPACE_ID`` / ``MOLECULE_WORKSPACE_TOKEN``
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are IGNORED — the JSON is the source of truth.
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2. Single-workspace fallback — ``WORKSPACE_ID`` env var + token from
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``MOLECULE_WORKSPACE_TOKEN`` or ``${CONFIGS_DIR}/.auth_token``.
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This is the pre-existing path; back-compat exact.
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2. Single-workspace fallback — ``WORKSPACE_ID`` env var + token
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resolved in this order:
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a. ``MOLECULE_WORKSPACE_TOKEN`` (inline env — convenient but
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leaks into shell history + plaintext MCP-host config).
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b. ``MOLECULE_WORKSPACE_TOKEN_FILE`` (path to a file holding
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the token — operator can keep it 0600 in their home dir;
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survives shell-history scrubs).
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c. ``${CONFIGS_DIR}/.auth_token`` (in-container runtimes —
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the platform writes this on provision).
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Returns ``(workspaces, errors)``:
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* ``workspaces``: list of ``(workspace_id, token)`` — non-empty
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@ -98,16 +104,47 @@ def resolve_workspaces() -> tuple[list[tuple[str, str]], list[str]]:
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wsid = os.environ.get("WORKSPACE_ID", "").strip()
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if not wsid:
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return [], ["WORKSPACE_ID (or MOLECULE_WORKSPACES) is required"]
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# Token resolution order (#2934): inline env → file path → CONFIGS_DIR
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# default. The file-path option exists so operators can keep the
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# bearer out of shell history and out of MCP-host config plaintext
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# (e.g. ~/.claude.json) — set MOLECULE_WORKSPACE_TOKEN_FILE to a
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# 0600 file containing the token. The CONFIGS_DIR/.auth_token
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# fallback predates this and stays for in-container runtimes.
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tok = os.environ.get("MOLECULE_WORKSPACE_TOKEN", "").strip()
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if not tok:
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tok = _read_token_from_file_env()
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if not tok:
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tok = read_token_file()
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if not tok:
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return [], [
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"MOLECULE_WORKSPACE_TOKEN (or CONFIGS_DIR/.auth_token) is required"
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"MOLECULE_WORKSPACE_TOKEN, MOLECULE_WORKSPACE_TOKEN_FILE, or "
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"CONFIGS_DIR/.auth_token is required"
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]
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return [(wsid, tok)], []
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def _read_token_from_file_env() -> str:
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"""Read the token from the file path in MOLECULE_WORKSPACE_TOKEN_FILE.
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Returns "" on:
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- env var unset / blank
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- file not found, unreadable, or empty
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- any OSError on read
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Empty-on-failure (rather than raising) lets the resolver fall through
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to the CONFIGS_DIR fallback. The caller surfaces the combined "no
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token" error if every source is empty.
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"""
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path = os.environ.get("MOLECULE_WORKSPACE_TOKEN_FILE", "").strip()
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if not path:
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return ""
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try:
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with open(path, encoding="utf-8") as fh:
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return fh.read().strip()
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except OSError:
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return ""
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def print_missing_env_help(missing: list[str], have_token_file: bool) -> None:
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print("molecule-mcp: missing required environment.\n", file=sys.stderr)
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print("Set the following before running molecule-mcp:", file=sys.stderr)
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@ -123,6 +160,16 @@ def print_missing_env_help(missing: list[str], have_token_file: bool) -> None:
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"(canvas → Tokens tab)",
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file=sys.stderr,
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)
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print(
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" OR set MOLECULE_WORKSPACE_TOKEN_FILE"
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" to a path that holds the token",
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file=sys.stderr,
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)
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print(
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" (keeps the secret out of shell"
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" history and MCP-host config plaintext)",
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file=sys.stderr,
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)
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print("", file=sys.stderr)
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print(f"Currently missing: {', '.join(missing)}", file=sys.stderr)
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@ -229,3 +229,87 @@ class TestResolveWorkspacesDirect:
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out, errors = mcp_workspace_resolver.resolve_workspaces()
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assert out == [("ws-a", "a"), ("ws-b", "b")]
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assert errors == []
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# ============== Token-from-file env var (issue #2934) ==============
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class TestTokenFileEnv:
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"""``MOLECULE_WORKSPACE_TOKEN_FILE`` lets operators keep the bearer
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out of shell history and out of MCP-host config plaintext (e.g.
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~/.claude.json). Resolution order: inline TOKEN env > TOKEN_FILE
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env > ${CONFIGS_DIR}/.auth_token.
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"""
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@pytest.fixture(autouse=True)
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def _isolate(self, monkeypatch, tmp_path):
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for v in (
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"WORKSPACE_ID",
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"MOLECULE_WORKSPACE_TOKEN",
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"MOLECULE_WORKSPACE_TOKEN_FILE",
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"MOLECULE_WORKSPACES",
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):
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monkeypatch.delenv(v, raising=False)
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# Point CONFIGS_DIR at an empty tmp_path so the .auth_token
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# fallback returns "" — keeps the test cases unambiguous.
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monkeypatch.setenv("CONFIGS_DIR", str(tmp_path))
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yield tmp_path
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def test_token_file_env_resolves(self, monkeypatch, tmp_path):
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token_path = tmp_path / "token.txt"
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token_path.write_text("file-tok-123\n") # trailing newline must strip
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monkeypatch.setenv("WORKSPACE_ID", "ws-1")
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monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN_FILE", str(token_path))
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out, errors = mcp_workspace_resolver.resolve_workspaces()
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assert out == [("ws-1", "file-tok-123")]
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assert errors == []
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def test_inline_token_takes_precedence_over_file(self, monkeypatch, tmp_path):
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# If both env vars are set, inline wins — matches the docstring's
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# documented order. (Operators sometimes set both during a
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# rotation; we want predictable behavior.)
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token_path = tmp_path / "token.txt"
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token_path.write_text("file-tok")
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monkeypatch.setenv("WORKSPACE_ID", "ws-1")
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monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN", "inline-tok")
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monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN_FILE", str(token_path))
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out, _ = mcp_workspace_resolver.resolve_workspaces()
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assert out == [("ws-1", "inline-tok")]
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def test_missing_file_falls_through_to_error(self, monkeypatch, tmp_path):
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# Pointed at a non-existent path — resolver should return the
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# combined "no token" error, NOT crash.
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monkeypatch.setenv("WORKSPACE_ID", "ws-1")
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monkeypatch.setenv(
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"MOLECULE_WORKSPACE_TOKEN_FILE", str(tmp_path / "does-not-exist")
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)
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out, errors = mcp_workspace_resolver.resolve_workspaces()
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assert out == []
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assert any("MOLECULE_WORKSPACE_TOKEN_FILE" in e for e in errors)
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def test_empty_file_falls_through_to_error(self, monkeypatch, tmp_path):
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# File exists but is blank — same shape as no token at all.
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token_path = tmp_path / "empty.txt"
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token_path.write_text("")
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monkeypatch.setenv("WORKSPACE_ID", "ws-1")
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monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN_FILE", str(token_path))
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out, errors = mcp_workspace_resolver.resolve_workspaces()
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assert out == []
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assert errors # at least one combined error message
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def test_blank_env_var_treated_as_unset(self, monkeypatch):
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# Empty string is treated as "not set" — common pitfall when
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# users export an unset shell var.
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monkeypatch.setenv("WORKSPACE_ID", "ws-1")
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monkeypatch.setenv("MOLECULE_WORKSPACE_TOKEN_FILE", "")
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out, errors = mcp_workspace_resolver.resolve_workspaces()
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assert out == []
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assert errors
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def test_help_message_advertises_token_file(self, capsys):
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# Help text must mention TOKEN_FILE so a first-run operator
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# learns about the safer option without grepping the source.
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mcp_workspace_resolver.print_missing_env_help(
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["WORKSPACE_ID", "MOLECULE_WORKSPACE_TOKEN"], have_token_file=False
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)
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err = capsys.readouterr().err
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assert "MOLECULE_WORKSPACE_TOKEN_FILE" in err
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