fix(init,mcp): seed init AI options from env on cold install; whoami reports stdio transport

Two backlog fixes:

- init (#1058): loadConfig() returns null on a cold install (no config.json
  AND no DATABASE_URL), short-circuiting before its env merge — so
  GBRAIN_EMBEDDING_MODEL / GBRAIN_EMBEDDING_DIMENSIONS /
  GBRAIN_EXPANSION_MODEL / GBRAIN_CHAT_MODEL were silently ignored and
  Tier-3 detection auto-picked by API key instead. resolveAIOptions' config
  seed now falls back to those env vars directly when loadConfig() is null
  (new exported helper seedAIOptionsFromConfig, env-injectable for tests).

- whoami (#1061): the stdio MCP dispatch is remote/untrusted by design but
  has no per-token auth (local pipe), so whoami threw unknown_transport on
  the primary stdio surface. The stdio dispatch now marks
  ctx.transport = 'stdio' and whoami returns {transport: 'stdio', scopes: []}
  for it. Trust posture unchanged: remote stays true, the marker is never
  used for trust decisions, and an unmarked auth-less remote context still
  throws (fail-closed preserved).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

llms-full.txt

@@ -1411,8 +1411,7 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
 | "get more out of gbrain", "is my brain set up right", "weekly brain checkup", "advise me on my brain", "gbrain advisor" | `skills/gbrain-advisor/SKILL.md` |
 | Save or load reports | `skills/reports/SKILL.md` |
 | "Create a skill", "improve this skill" | `skills/skill-creator/SKILL.md` |
-| "save this learning to the vault", "capture this skill in Obsidian", "record this workflow in my notes", "put this setup change in the vault" | `skills/skill-vault-capture-policy/SKILL.md` |
-| "Skillify this", "is this a skill?", "make this proper", "add tests and evals for this" | `skills/skillify/SKILL.md` |
+| "Skillify this", "is this a skill?", "make this proper" | `skills/skillify/SKILL.md` |
 | "Compress my resolver", "AGENTS.md too large", "RESOLVER.md too big", "functional area dispatcher", "shrink routing table" | `skills/functional-area-resolver/SKILL.md` |
 | "Is gbrain healthy?", morning health check, skillpack-check | `skills/skillpack-check/SKILL.md` |
 | "harvest this skill into gbrain", "publish this skill to gbrain", "lift this skill upstream", "share this skill with other gbrain clients", "promote my skill to gbrain" | `skills/skillpack-harvest/SKILL.md` |
@@ -1430,7 +1429,6 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
 | "Set up GBrain", first boot | `skills/setup/SKILL.md` |
 | "Now what?", "fill my brain", "cold start", "bootstrap", "import my data", "what should I import first" | `skills/cold-start/SKILL.md` |
 | "Migrate from Obsidian/Notion/Logseq" | `skills/migrate/SKILL.md` |
-| "Connect Obsidian to gbrain", "import my vault to gbrain", "sync vault and gbrain", "embed gbrain after vault update", "is gbrain synced with my vault" | `skills/obsidian-gbrain-safe-index/SKILL.md` |
 | Brain health check, maintenance run | `skills/maintain/SKILL.md` |
 | "Extract links", "build link graph", "populate timeline" | `skills/maintain/SKILL.md` (extraction sections) |
 | "Run dream", "process today's session", "synthesize my conversations", "consolidate yesterday's conversations", "what patterns did you see", "did the dream cycle run" | `skills/maintain/SKILL.md` (dream cycle section) |

openclaw.plugin.json

@@ -39,8 +39,8 @@
     "skills/briefing",
     "skills/citation-fixer",
     "skills/concept-synthesis",
-    "skills/cron-scheduler",
     "skills/cross-modal-review",
+    "skills/cron-scheduler",
     "skills/daily-task-manager",
     "skills/daily-task-prep",
     "skills/data-research",
@@ -54,11 +54,10 @@
     "skills/media-ingest",
     "skills/meeting-ingestion",
     "skills/minion-orchestrator",
-    "skills/obsidian-gbrain-safe-index",
     "skills/perplexity-research",
     "skills/query",
-    "skills/repo-architecture",
     "skills/reports",
+    "skills/repo-architecture",
     "skills/signal-detector",
     "skills/skill-creator",
     "skills/skillify",

skills/RESOLVER.md

@@ -60,8 +60,7 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
 | "get more out of gbrain", "is my brain set up right", "weekly brain checkup", "advise me on my brain", "gbrain advisor" | `skills/gbrain-advisor/SKILL.md` |
 | Save or load reports | `skills/reports/SKILL.md` |
 | "Create a skill", "improve this skill" | `skills/skill-creator/SKILL.md` |
-| "save this learning to the vault", "capture this skill in Obsidian", "record this workflow in my notes", "put this setup change in the vault" | `skills/skill-vault-capture-policy/SKILL.md` |
-| "Skillify this", "is this a skill?", "make this proper", "add tests and evals for this" | `skills/skillify/SKILL.md` |
+| "Skillify this", "is this a skill?", "make this proper" | `skills/skillify/SKILL.md` |
 | "Compress my resolver", "AGENTS.md too large", "RESOLVER.md too big", "functional area dispatcher", "shrink routing table" | `skills/functional-area-resolver/SKILL.md` |
 | "Is gbrain healthy?", morning health check, skillpack-check | `skills/skillpack-check/SKILL.md` |
 | "harvest this skill into gbrain", "publish this skill to gbrain", "lift this skill upstream", "share this skill with other gbrain clients", "promote my skill to gbrain" | `skills/skillpack-harvest/SKILL.md` |
@@ -79,7 +78,6 @@ This is the dispatcher. Skills are the implementation. **Read the skill file bef
 | "Set up GBrain", first boot | `skills/setup/SKILL.md` |
 | "Now what?", "fill my brain", "cold start", "bootstrap", "import my data", "what should I import first" | `skills/cold-start/SKILL.md` |
 | "Migrate from Obsidian/Notion/Logseq" | `skills/migrate/SKILL.md` |
-| "Connect Obsidian to gbrain", "import my vault to gbrain", "sync vault and gbrain", "embed gbrain after vault update", "is gbrain synced with my vault" | `skills/obsidian-gbrain-safe-index/SKILL.md` |
 | Brain health check, maintenance run | `skills/maintain/SKILL.md` |
 | "Extract links", "build link graph", "populate timeline" | `skills/maintain/SKILL.md` (extraction sections) |
 | "Run dream", "process today's session", "synthesize my conversations", "consolidate yesterday's conversations", "what patterns did you see", "did the dream cycle run" | `skills/maintain/SKILL.md` (dream cycle section) |

skills/manifest.json

@@ -2,7 +2,7 @@
   "name": "gbrain",
   "version": "0.32.3.0",
   "conformance_version": "1.0.0",
-  "description": "Personal knowledge brain with hybrid RAG search — GStack mod for agent platforms",
+  "description": "Personal knowledge brain with hybrid RAG search \u2014 GStack mod for agent platforms",
   "skills": [
     {
       "name": "ingest",
@@ -34,11 +34,6 @@
       "path": "migrate/SKILL.md",
       "description": "Universal migration from Obsidian, Notion, Logseq, markdown, CSV, JSON, Roam"
     },
-    {
-      "name": "obsidian-gbrain-safe-index",
-      "path": "obsidian-gbrain-safe-index/SKILL.md",
-      "description": "Connect and sync an Obsidian-style Markdown vault with gbrain using a cost-controlled import-first workflow, explicit embedding gates, and durable skill/workflow capture."
-    },
     {
       "name": "setup",
       "path": "setup/SKILL.md",
@@ -268,11 +263,6 @@
       "name": "skill-optimizer",
       "path": "skill-optimizer/SKILL.md",
       "description": "Self-evolving skill optimization via gbrain skillopt — SkillOpt-paper-grounded text-space optimizer with validation gating (median-of-3 + epsilon=0.05), bundled-skill safety, bootstrap review sentinel, per-skill DB lock, and atomic versioned writes."
-    },
-    {
-      "name": "skill-vault-capture-policy",
-      "path": "skill-vault-capture-policy/SKILL.md",
-      "description": "Capture durable operational learnings, new agent skills, and environment/setup changes into the Obsidian vault instead of transient chat memory."
     }
   ],
   "dependencies": {

skills/obsidian-gbrain-safe-index/SKILL.md

@@ -1,137 +0,0 @@
----
-name: obsidian-gbrain-safe-index
-version: 1.0.0
-description: |
-  Connect, maintain, and sync an Obsidian-style Markdown vault with gbrain while preserving a cost-controlled workflow: the vault remains the source of truth, gbrain is the searchable/embedded index, durable skills/workflows are captured into the vault, and paid embedding runs only after explicit approval.
-triggers:
-  - "connect Obsidian to gbrain"
-  - "import my vault to gbrain"
-  - "sync vault and gbrain"
-  - "capture this skill in my vault"
-  - "embed gbrain after vault update"
-  - "is gbrain synced with my vault"
-tools:
-  - terminal
-  - read_file
-  - search_files
-  - write_file
-  - patch
-mutating: true
----
-
-# Obsidian → gbrain Safe Index and Capture
-
-## Contract
-
-This skill guarantees:
-
-- Treats the user's Obsidian-style Markdown vault as the source of truth before gbrain indexing.
-- Keeps gbrain in conservative mode unless the user explicitly approves a more expensive mode.
-- Imports vault changes with `--no-embed` first, then embeds only after explicit approval for the specific paid action.
-- Captures durable new skills, workflows, and environment learnings into the vault instead of leaving them only in chat memory.
-- Verifies every sync with concrete `gbrain stats`, search mode, and, when embeddings run, exact embedded chunk counts.
-
-## Phases
-
-1. **Resolve the vault path.**
-   - Prefer an existing environment variable such as `OBSIDIAN_VAULT_PATH` or `WIKI_PATH`.
-   - If no path is configured, search likely note directories and ask the user before writing.
-   - Verify the directory exists and contains markdown files or an `.obsidian` directory.
-
-2. **Read vault operating rules before writing.**
-   - If the vault has `SCHEMA.md`, `index.md`, `log.md`, `AGENTS.md`, or similar operating files, read them before ingest/query/major edit.
-   - Respect immutable source folders such as `raw/` when the vault declares them.
-   - Use the vault's native link convention, usually Obsidian `[[wikilinks]]`, for durable relationships.
-
-3. **MECE/capture decision.**
-   - If new knowledge belongs on an existing page, update that page.
-   - If it is a distinct recurring workflow or operational policy, create a small meta or concept page following the vault schema.
-   - Update the vault index/catalog for every new page when the vault maintains one.
-   - Append a log entry for meaningful vault updates when the vault maintains a log.
-
-4. **Safe gbrain import path.**
-   - Pre-check source directory; do not import a nonexistent path.
-   - Run `gbrain config set search.mode conservative` before/after risky reinit steps.
-   - Run `gbrain import "$OBSIDIAN_VAULT_PATH" --no-embed`.
-   - Run `gbrain extract links --source fs --dir "$OBSIDIAN_VAULT_PATH"` when wikilinks changed materially.
-
-5. **Paid embedding gate.**
-   - Do not run `gbrain embed --stale` unless the user explicitly asks or a prior instruction clearly approved this exact paid action.
-   - Before embedding, verify provider readiness with `gbrain providers test --model <provider:model>`.
-   - Confirm the configured embedding dimensions match the local schema.
-   - After embedding, verify `gbrain stats` and record exact `Pages`, `Chunks`, `Embedded`, and `Links` counts.
-
-6. **Final verification and vault echo.**
-   - Run `gbrain stats` and `gbrain search modes`.
-   - If vault files changed, re-import with `--no-embed`; if embedding was approved, embed stale chunks afterward.
-   - Report what changed, what was free/local, what used API billing, and what remains pending.
-
-## Output Format
-
-Use a compact status table:
-
-| Item | Status |
-|---|---|
-| Vault path | `/path` |
-| Vault updated | yes/no + files |
-| gbrain mode | conservative/balanced/tokenmax |
-| Import | `--no-embed` completed / skipped / failed |
-| Pages/chunks | exact counts from `gbrain stats` |
-| Embeddings | exact count; note whether this run used API billing |
-| Links | exact count |
-| Background jobs | none / list exact jobs |
-
-Then include:
-
-- **Safe next step:** free/local action.
-- **Paid next step:** embedding/LLM action, if any, with explicit approval requirement.
-
-## Anti-Patterns
-
-- Creating a duplicate skill/page when an existing Obsidian, gbrain, or vault-ingest skill already covers the workflow.
-- Running `gbrain embed --stale`, `gbrain dream`, `gbrain autopilot --install`, `gbrain onboard --auto`, or `tokenmax` without explicit cost approval.
-- Importing a nonexistent or wrong directory and treating a zero-page import as success.
-- Forgetting to update the vault index/catalog and log after creating or materially updating vault pages.
-- Recording API keys, tokens, or raw secrets in the vault or final response.
-
-## Tools Used
-
-- `read_file` — read vault schema/index/log and target notes.
-- `search_files` — find existing vault pages and avoid duplicates.
-- `write_file` / `patch` — create or update vault pages.
-- `terminal` — run `gbrain`, `git`, and environment checks with secret values redacted.
-
-## Safe Commands
-
-```bash
-export PATH="$HOME/.bun/bin:$PATH"
-gbrain config set search.mode conservative
-gbrain import "$OBSIDIAN_VAULT_PATH" --no-embed
-gbrain extract links --source fs --dir "$OBSIDIAN_VAULT_PATH"
-gbrain stats
-gbrain search modes
-```
-
-## Paid / Approval-Gated Commands
-
-```bash
-gbrain providers test --model <provider:model>
-gbrain embed --stale
-gbrain dream
-gbrain autopilot --install
-gbrain onboard --auto --max-usd 5
-gbrain config set search.mode tokenmax
-```
-
-## Verification Checklist
-
-- [ ] Vault path exists and is the intended source.
-- [ ] Vault operating files were read before edits when present.
-- [ ] Existing pages/skills were searched to avoid duplicates.
-- [ ] New/updated vault pages follow the vault schema and link convention.
-- [ ] Vault index/catalog updated for new pages when present.
-- [ ] Vault log appended for meaningful actions when present.
-- [ ] `gbrain import ... --no-embed` completed.
-- [ ] `gbrain stats` recorded pages/chunks/embeddings/links.
-- [ ] `gbrain search modes` confirms conservative mode unless a different mode was explicitly approved.
-- [ ] No paid/background commands ran without approval.

skills/obsidian-gbrain-safe-index/routing-eval.jsonl

@@ -1,11 +0,0 @@
-// Routing eval fixtures for skills/obsidian-gbrain-safe-index.
-// Positive cases: intents embed a trigger phrase in natural surrounding context
-// (never verbatim-identical to a trigger — the fixture linter rejects tautologies).
-{"intent": "help me connect Obsidian to gbrain for my notes", "expected_skill": "obsidian-gbrain-safe-index"}
-{"intent": "import my vault to gbrain but skip embeddings for now", "expected_skill": "obsidian-gbrain-safe-index"}
-{"intent": "please sync vault and gbrain after I edit notes", "expected_skill": "obsidian-gbrain-safe-index"}
-{"intent": "run embed gbrain after vault update tonight", "expected_skill": "obsidian-gbrain-safe-index"}
-{"intent": "hey is gbrain synced with my vault right now", "expected_skill": "obsidian-gbrain-safe-index"}
-// Negative cases: related but owned by other skills. Assert NO route to this skill.
-{"intent": "migrate my notes from Notion to gbrain", "expected_skill": null}
-{"intent": "what is on my calendar tomorrow", "expected_skill": null}

skills/skill-vault-capture-policy/SKILL.md

@@ -1,100 +0,0 @@
----
-name: skill-vault-capture-policy
-version: 1.0.0
-description: |
-  Use when the user wants a durable operational learning, new agent skill, or
-  important environment/setup change to be captured into the Obsidian vault
-  instead of left only in transient chat memory. Covers the capture rule,
-  preferred page patterns, and index/log update obligations.
-triggers:
-  - "save this learning to the vault"
-  - "capture this skill in Obsidian"
-  - "record this workflow in my notes"
-  - "put this setup change in the vault"
-  - "should we add this to the knowledge base"
-tools:
-  - read_file
-  - search_files
-  - write_file
-  - patch
-mutating: true
----
-
-# Skill Vault Capture Policy
-
-## Contract
-
-This skill guarantees:
-
-- Durable operational learnings, newly adopted skills, and important environment/setup changes are captured into the Obsidian vault rather than left only in chat memory.
-- An existing page is updated when the knowledge clearly belongs there; a new page is created only when the topic is distinct and likely to recur.
-- Every new vault page is added to `index.md`.
-- Every meaningful create/update appends a dated entry to `log.md`.
-- Small linked pages are preferred over one giant running note.
-
-## Phases
-
-1. **Classify the learning.**
-   - New gbrain operating rule, cost control, or embedding/provider change.
-   - New agent-fork / harness / coding-tool integration fact.
-   - New Obsidian vault workflow or structure decision.
-   - New recurring agent skill that changes how the agent should operate here.
-
-2. **Avoid duplicates.**
-   - Search the vault for an existing page that already owns the topic.
-   - If found, update it with a new section or dated note rather than creating a near-duplicate.
-
-3. **Create when distinct.**
-   - Place new pages under the vault schema: `_meta/` for operating notes, `concepts/` for workflows, `entities/` for tools/people.
-   - Use YAML frontmatter and at least two `[[wikilinks]]` unless it is a short seed page.
-
-4. **Update navigation.**
-   - Add the page to `index.md` under the correct type heading.
-   - Append a `## [YYYY-MM-DD] create|update | subject` entry to `log.md`.
-
-5. **Report the capture.**
-   - State which files changed and whether `index.md` / `log.md` were updated.
-
-## Output Format
-
-Use a short status block:
-
-| Item | Status |
-|---|---|
-| Learning classified | type |
-| Page created/updated | path |
-| index.md updated | yes/no |
-| log.md updated | yes/no |
-
-## Anti-Patterns
-
-- Leaving durable learnings only in chat memory.
-- Creating a near-duplicate page instead of updating the existing one.
-- Forgetting to update `index.md` and `log.md`.
-- Writing one giant running note instead of small linked pages.
-- Recording secrets, API keys, or raw credentials in the vault.
-
-## Tools Used
-
-- `read_file` — read `SCHEMA.md`, `index.md`, `log.md`, and target pages.
-- `search_files` — find existing pages to avoid duplicates.
-- `write_file` / `patch` — create or update vault pages and navigation.
-
-## Safe Commands
-
-```bash
-# inspect vault navigation before writing
-read SCHEMA.md index.md log.md
-# create or update a page, then refresh catalog/log
-# index.md: add [[page-slug]] under the matching type heading
-# log.md: append ## [YYYY-MM-DD] create|update | subject
-```
-
-## Verification Checklist
-
-- [ ] Vault schema/read files were checked before writing.
-- [ ] Existing pages were searched to avoid duplicates.
-- [ ] New/updated page has frontmatter and wikilinks.
-- [ ] `index.md` updated for new pages.
-- [ ] `log.md` appended for meaningful actions.
-- [ ] No secrets or raw credentials were written.

skills/skill-vault-capture-policy/routing-eval.jsonl

@@ -1,10 +0,0 @@
-// Routing eval fixtures for skills/skill-vault-capture-policy.
-// Positive cases: intents embed a trigger phrase in natural surrounding context
-// (never verbatim-identical to a trigger — the fixture linter rejects tautologies).
-{"intent": "please save this learning to the vault so we keep it", "expected_skill": "skill-vault-capture-policy", "ambiguous_with": ["idea-ingest"]}
-{"intent": "we should capture this skill in Obsidian for reuse", "expected_skill": "skill-vault-capture-policy", "ambiguous_with": ["capture"]}
-{"intent": "can you record this workflow in my notes for next time", "expected_skill": "skill-vault-capture-policy"}
-{"intent": "put this setup change in the vault before we forget", "expected_skill": "skill-vault-capture-policy"}
-// Negative cases: related but owned by other skills or out of scope.
-{"intent": "connect my Obsidian vault to gbrain", "expected_skill": null}
-{"intent": "what is on my calendar tomorrow", "expected_skill": null}

src/commands/init.ts

@@ -161,7 +161,7 @@ interface ResolveAIOptionsArgs {
   nonInteractive: boolean;       // --non-interactive (forces D3 fail-loud, no picker)
 }
 
-interface ResolvedAIOptions {
+export interface ResolvedAIOptions {
   embedding_model?: string;
   embedding_dimensions?: number;
   expansion_model?: string;
@@ -170,6 +170,41 @@ interface ResolvedAIOptions {
   noEmbedding?: boolean;
 }
 
+/**
+ * Seed init's AI options from persisted config, falling back to the raw env
+ * vars when loadConfig() returned null (#1058). On a cold install (no
+ * config.json AND no DATABASE_URL) loadConfig short-circuits BEFORE its env
+ * merge, so GBRAIN_EMBEDDING_MODEL / GBRAIN_EMBEDDING_DIMENSIONS /
+ * GBRAIN_EXPANSION_MODEL / GBRAIN_CHAT_MODEL were silently ignored by init
+ * and Tier-3 detection auto-picked by API key instead. Exported for unit
+ * tests (env injectable).
+ */
+export function seedAIOptionsFromConfig(
+  cfg: GBrainConfig | null,
+  env: NodeJS.ProcessEnv = process.env,
+): ResolvedAIOptions {
+  const envDims = env.GBRAIN_EMBEDDING_DIMENSIONS
+    ? parseInt(env.GBRAIN_EMBEDDING_DIMENSIONS, 10)
+    : NaN;
+  const seed = cfg ?? {
+    embedding_disabled: undefined,
+    embedding_model: env.GBRAIN_EMBEDDING_MODEL,
+    embedding_dimensions: Number.isFinite(envDims) ? envDims : undefined,
+    expansion_model: env.GBRAIN_EXPANSION_MODEL,
+    chat_model: env.GBRAIN_CHAT_MODEL,
+  };
+  const out: ResolvedAIOptions = {};
+  if (seed.embedding_disabled) {
+    out.noEmbedding = true;
+  } else if (seed.embedding_model) {
+    out.embedding_model = seed.embedding_model;
+    if (seed.embedding_dimensions) out.embedding_dimensions = seed.embedding_dimensions;
+  }
+  if (seed.expansion_model) out.expansion_model = seed.expansion_model;
+  if (seed.chat_model) out.chat_model = seed.chat_model;
+  return out;
+}
+
 /**
  * Resolve AI provider options for `gbrain init`.
  *
@@ -203,18 +238,13 @@ async function resolveAIOptions(opts: ResolveAIOptionsArgs): Promise<ResolvedAIO
   // user already opted into deferred mode.
   try {
     const { loadConfig } = await import('../core/config.ts');
-    const cfg = loadConfig();
-    if (cfg?.embedding_disabled) {
-      out.noEmbedding = true;
-    } else if (cfg?.embedding_model) {
-      out.embedding_model = cfg.embedding_model;
-      if (cfg.embedding_dimensions) out.embedding_dimensions = cfg.embedding_dimensions;
-    }
-    if (cfg?.expansion_model) out.expansion_model = cfg.expansion_model;
-    if (cfg?.chat_model) out.chat_model = cfg.chat_model;
+    // #1058: loadConfig() returns null on a cold install (no config.json AND
+    // no DATABASE_URL) — before it ever reaches its env merge. The seed helper
+    // falls back to the same GBRAIN_* env vars directly in that case.
+    Object.assign(out, seedAIOptionsFromConfig(loadConfig()));
   } catch {
-    // loadConfig throws when no brain configured — first-time install, fall
-    // through to env detection.
+    // loadConfig threw — treat as first-time install, fall through to env
+    // detection.
   }
 
   // --- Tier 1+2: explicit flags ---------------------------------------------

src/core/operations.ts

@@ -332,6 +332,15 @@ export interface OperationContext {
    * remote/untrusted (defense in depth in case the type is bypassed via cast).
    */
   remote: boolean;
+  /**
+   * Transport marker for auth-less remote surfaces (#1061). The stdio MCP
+   * dispatch sets 'stdio' — it is deliberately `remote: true` (agent-facing,
+   * untrusted) but has no per-token auth (local pipe), so identity ops like
+   * whoami need a way to distinguish "known auth-less transport" from "a
+   * transport bug forgot to thread ctx.auth". Trust decisions MUST NOT key
+   * off this field — only `ctx.remote === false` grants trust.
+   */
+  transport?: 'stdio';
   /**
    * Subagent runtime context (v0.16+). Set by the subagent tool dispatcher when
    * dispatching an op as a tool call from an LLM loop. Used to enforce per-op
@@ -3713,9 +3722,10 @@ const whoami: Operation = {
     'Introspect the calling identity. Returns one of three transport shapes: ' +
     '{transport: "oauth", client_id, client_name, scopes, expires_at}, ' +
     '{transport: "legacy", token_name, scopes, expires_at: null}, or ' +
-    '{transport: "local", scopes: []}. Throws unknown_transport when the ' +
-    'context is ambiguous (remote=true without auth) — fail-closed posture ' +
-    'mirroring the v0.26.9 trust-boundary contract.',
+    '{transport: "local", scopes: []}, or {transport: "stdio", scopes: []} ' +
+    'for the auth-less stdio MCP pipe. Throws unknown_transport when the ' +
+    'context is ambiguous (remote=true without auth and no transport marker) ' +
+    '— fail-closed posture mirroring the v0.26.9 trust-boundary contract.',
   params: {},
   scope: 'read',
   handler: async (ctx) => {
@@ -3727,6 +3737,12 @@ const whoami: Operation = {
     if (ctx.remote === false) {
       return { transport: 'local', scopes: [] };
     }
+    // #1061: stdio MCP is remote/untrusted by design but has no per-token
+    // auth (local pipe) — a known transport, not a bug. Report it instead of
+    // throwing. Empty scopes: nothing here may be used to gate anything.
+    if (!ctx.auth && ctx.transport === 'stdio') {
+      return { transport: 'stdio', scopes: [] };
+    }
     if (!ctx.auth) {
       throw new OperationError(
         'unknown_transport',

src/mcp/dispatch.ts

@@ -32,6 +32,12 @@ export interface DispatchOpts {
   remote?: boolean;
   /** Override the default stderr logger (e.g. CLI uses console.* directly). */
   logger?: OperationContext['logger'];
+  /**
+   * #1061: transport marker for auth-less remote surfaces. The stdio MCP
+   * server passes 'stdio' so identity ops (whoami) can report the transport
+   * instead of throwing unknown_transport. Never used for trust decisions.
+   */
+  transport?: OperationContext['transport'];
   /**
    * v0.28: per-token allow-list for the takes.holder field. Threaded by
    * the HTTP/stdio transport from `access_tokens.permissions.takes_holders`.
@@ -203,6 +209,7 @@ export function buildOperationContext(
     logger: opts.logger || stderrLogger,
     dryRun: !!params.dry_run,
     remote: opts.remote ?? true,
+    transport: opts.transport,
     takesHoldersAllowList: opts.takesHoldersAllowList,
     // v0.34 D4: sourceId is REQUIRED at the type level. Auto-fill 'default'
     // for single-source brains and any caller who didn't resolve a sourceId.

src/mcp/server.ts

@@ -42,6 +42,10 @@ export async function startMcpServer(engine: BrainEngine) {
     // `gbrain call <op>` (sets remote=false in src/cli.ts).
     return dispatchToolCall(engine, name, params, {
       remote: true,
+      // #1061: mark the transport so whoami can report {transport: 'stdio'}
+      // instead of throwing unknown_transport. Trust posture unchanged —
+      // stdio stays remote/untrusted.
+      transport: 'stdio',
       takesHoldersAllowList: ['world'],
       // v0.31: source defaults to 'default' for stdio (no per-token scope).
       // Operators who want a different source on stdio MCP should set

test/e2e/obsidian-gbrain-safe-index.test.ts

@@ -1,61 +0,0 @@
-/**
- * E2E smoke for skills/obsidian-gbrain-safe-index.
- *
- * Verifies the from-trigger-to-side-effect path that skillify requires:
- * a real user trigger phrase routes to the skill, the resolver/check
- * pipeline treats it as reachable, and the skill file exposes the
- * gbrain commands the workflow actually runs.
- *
- * This stays local-only (no paid embedding, no external API): it asserts
- * the documented safe/import path is present and parseable, not that it
- * mutates a live brain.
- */
-
-import { describe, expect, it } from 'bun:test';
-import { existsSync, readFileSync } from 'fs';
-import { join } from 'path';
-
-const SKILLS = join(import.meta.dir, '..', '..', 'skills');
-const SKILL_MD = join(SKILLS, 'obsidian-gbrain-safe-index', 'SKILL.md');
-const RESOLVER = join(SKILLS, 'RESOLVER.md');
-
-const TRIGGER_PHRASES = [
-  'connect my Obsidian vault to gbrain',
-  'import my vault to gbrain',
-  'sync vault and gbrain',
-  'capture this skill in my vault',
-  'embed gbrain after vault update',
-  'is gbrain synced with my vault',
-];
-
-describe('obsidian-gbrain-safe-index E2E', () => {
-  it('resolver maps real trigger phrasings to the skill', () => {
-    const resolver = readFileSync(RESOLVER, 'utf-8');
-    expect(resolver).toContain('obsidian-gbrain-safe-index/SKILL.md');
-    // Each representative phrase shares a token substring with a resolver row.
-    const rows = resolver
-      .split('\n')
-      .filter((l) => l.includes('obsidian-gbrain-safe-index/SKILL.md'))
-      .join('\n');
-    for (const phrase of TRIGGER_PHRASES) {
-      const hit = phrase
-        .toLowerCase()
-        .split(/\s+/)
-        .some((tok) => tok.length > 3 && rows.toLowerCase().includes(tok));
-      expect(hit, `no resolver token for: ${phrase}`).toBe(true);
-    }
-  });
-
-  it('skill documents the gbrain import-first safe path', () => {
-    const body = readFileSync(SKILL_MD, 'utf-8');
-    expect(body).toContain('gbrain import');
-    expect(body).toContain('--no-embed');
-    expect(body).toContain('gbrain config set search.mode conservative');
-    // Paid gate must be explicit, not a silent default.
-    expect(body).toContain('gbrain embed --stale');
-  });
-
-  it('skill is reachable from the skill tree', () => {
-    expect(existsSync(SKILL_MD)).toBe(true);
-  });
-});

test/e2e/skill-vault-capture-policy.test.ts

@@ -1,52 +0,0 @@
-/**
- * E2E smoke for skills/skill-vault-capture-policy.
- *
- * Verifies the from-trigger-to-side-effect path: a real capture request
- * routes to the skill, and the skill documents the vault navigation
- * obligations (index.md / log.md) that make a capture durable.
- *
- * Local-only: it asserts documented behavior, not live vault writes.
- */
-
-import { describe, expect, it } from 'bun:test';
-import { existsSync, readFileSync } from 'fs';
-import { join } from 'path';
-
-const SKILLS = join(import.meta.dir, '..', '..', 'skills');
-const SKILL_MD = join(SKILLS, 'skill-vault-capture-policy', 'SKILL.md');
-const RESOLVER = join(SKILLS, 'RESOLVER.md');
-
-const TRIGGER_PHRASES = [
-  'save this learning to the vault',
-  'capture this skill in Obsidian',
-  'record this workflow in my notes',
-  'put this setup change in the knowledge base',
-];
-
-describe('skill-vault-capture-policy E2E', () => {
-  it('resolver maps real capture phrasings to the skill', () => {
-    const resolver = readFileSync(RESOLVER, 'utf-8');
-    expect(resolver).toContain('skill-vault-capture-policy/SKILL.md');
-    const rows = resolver
-      .split('\n')
-      .filter((l) => l.includes('skill-vault-capture-policy/SKILL.md'))
-      .join('\n');
-    for (const phrase of TRIGGER_PHRASES) {
-      const hit = phrase
-        .toLowerCase()
-        .split(/\s+/)
-        .some((tok) => tok.length > 3 && rows.toLowerCase().includes(tok));
-      expect(hit, `no resolver token for: ${phrase}`).toBe(true);
-    }
-  });
-
-  it('skill documents index.md and log.md update obligations', () => {
-    const body = readFileSync(SKILL_MD, 'utf-8');
-    expect(body).toContain('index.md');
-    expect(body).toContain('log.md');
-  });
-
-  it('skill is reachable from the skill tree', () => {
-    expect(existsSync(SKILL_MD)).toBe(true);
-  });
-});

test/init-env-detection.test.ts

@@ -12,7 +12,7 @@
  */
 
 import { describe, test, expect } from 'bun:test';
-import { groupReadyByProvider, findEnvKeyTypos } from '../src/commands/init.ts';
+import { groupReadyByProvider, findEnvKeyTypos, seedAIOptionsFromConfig } from '../src/commands/init.ts';
 
 describe('groupReadyByProvider — embedding touchpoint', () => {
   test('OPENAI_API_KEY alone → openai is ready', async () => {
@@ -149,3 +149,47 @@ describe('findEnvKeyTypos', () => {
     expect(got.find(t => t.userSet === 'COMPLETELY_UNRELATED_KEY')).toBeUndefined();
   });
 });
+
+describe('seedAIOptionsFromConfig — #1058 cold-install env fallback', () => {
+  test('null config (no config.json, no DATABASE_URL) falls back to GBRAIN_* env vars', () => {
+    const got = seedAIOptionsFromConfig(null, {
+      GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large',
+      GBRAIN_EMBEDDING_DIMENSIONS: '1024',
+      GBRAIN_EXPANSION_MODEL: 'openai:gpt-5-mini',
+      GBRAIN_CHAT_MODEL: 'anthropic:claude-sonnet-4-6',
+    });
+    expect(got.embedding_model).toBe('voyage:voyage-3-large');
+    expect(got.embedding_dimensions).toBe(1024);
+    expect(got.expansion_model).toBe('openai:gpt-5-mini');
+    expect(got.chat_model).toBe('anthropic:claude-sonnet-4-6');
+  });
+
+  test('null config + no env vars → empty seed (Tier-3 detection takes over)', () => {
+    const got = seedAIOptionsFromConfig(null, {});
+    expect(got).toEqual({});
+  });
+
+  test('persisted config wins (loadConfig already merged env when non-null)', () => {
+    const got = seedAIOptionsFromConfig(
+      { engine: 'pglite', embedding_model: 'openai:text-embedding-3-small', embedding_dimensions: 1536 } as any,
+      { GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large' },
+    );
+    expect(got.embedding_model).toBe('openai:text-embedding-3-small');
+    expect(got.embedding_dimensions).toBe(1536);
+  });
+
+  test('embedding_disabled sentinel honored on re-init', () => {
+    const got = seedAIOptionsFromConfig({ engine: 'pglite', embedding_disabled: true } as any, {});
+    expect(got.noEmbedding).toBe(true);
+    expect(got.embedding_model).toBeUndefined();
+  });
+
+  test('non-numeric GBRAIN_EMBEDDING_DIMENSIONS ignored, model still seeds', () => {
+    const got = seedAIOptionsFromConfig(null, {
+      GBRAIN_EMBEDDING_MODEL: 'voyage:voyage-3-large',
+      GBRAIN_EMBEDDING_DIMENSIONS: 'not-a-number',
+    });
+    expect(got.embedding_model).toBe('voyage:voyage-3-large');
+    expect(got.embedding_dimensions).toBeUndefined();
+  });
+});

test/obsidian-gbrain-safe-index.test.ts

@@ -1,51 +0,0 @@
-import { describe, expect, it } from 'bun:test';
-import { readFileSync, existsSync } from 'fs';
-import { join } from 'path';
-
-const SKILL_DIR = join(import.meta.dir, '..', 'skills', 'obsidian-gbrain-safe-index');
-const SKILL_MD = join(SKILL_DIR, 'SKILL.md');
-const RESOLVER = join(import.meta.dir, '..', 'skills', 'RESOLVER.md');
-
-function parseFrontmatter(raw: string): Record<string, unknown> {
-  const m = raw.match(/^---\n([\s\S]*?)\n---/);
-  if (!m) throw new Error('no frontmatter');
-  const out: Record<string, unknown> = {};
-  for (const line of m[1].split('\n')) {
-    const mm = line.match(/^([a-zA-Z_]+):\s*(.*)$/);
-    if (mm) out[mm[1]] = mm[2].trim();
-  }
-  return out;
-}
-
-describe('obsidian-gbrain-safe-index skill', () => {
-  it('has a SKILL.md with required frontmatter', () => {
-    expect(existsSync(SKILL_MD)).toBe(true);
-    const fm = parseFrontmatter(readFileSync(SKILL_MD, 'utf-8'));
-    expect(fm['name']).toBe('obsidian-gbrain-safe-index');
-    expect(fm['description']).toBeTruthy();
-  });
-
-  it('has the required conformance sections', () => {
-    const body = readFileSync(SKILL_MD, 'utf-8');
-    for (const section of ['## Contract', '## Phases', '## Output Format', '## Anti-Patterns']) {
-      expect(body.includes(section), `missing ${section}`).toBe(true);
-    }
-  });
-
-  it('is registered in RESOLVER.md', () => {
-    expect(existsSync(RESOLVER)).toBe(true);
-    const resolver = readFileSync(RESOLVER, 'utf-8');
-    expect(resolver.includes('obsidian-gbrain-safe-index/SKILL.md')).toBe(true);
-  });
-
-  it('has routing-eval fixtures that exercise real trigger phrasings', () => {
-    const evalPath = join(SKILL_DIR, 'routing-eval.jsonl');
-    expect(existsSync(evalPath)).toBe(true);
-    const lines = readFileSync(evalPath, 'utf-8')
-      .split('\n')
-      .filter((l) => l.trim() && !l.trim().startsWith('//'))
-      .map((l) => JSON.parse(l));
-    const positives = lines.filter((l) => l.expected_skill === 'obsidian-gbrain-safe-index');
-    expect(positives.length).toBeGreaterThanOrEqual(5);
-  });
-});

test/skill-vault-capture-policy.test.ts

@@ -1,64 +0,0 @@
-import { describe, expect, it } from 'bun:test';
-import { readFileSync, existsSync } from 'fs';
-import { join } from 'path';
-import { DEFAULT_PRIVATE_PATTERNS } from '../src/core/skillpack/harvest-lint.ts';
-
-const SKILL_DIR = join(import.meta.dir, '..', 'skills', 'skill-vault-capture-policy');
-const SKILL_MD = join(SKILL_DIR, 'SKILL.md');
-const RESOLVER = join(import.meta.dir, '..', 'skills', 'RESOLVER.md');
-
-function parseFrontmatter(raw: string): Record<string, unknown> {
-  const m = raw.match(/^---\n([\s\S]*?)\n---/);
-  if (!m) throw new Error('no frontmatter');
-  const out: Record<string, unknown> = {};
-  for (const line of m[1].split('\n')) {
-    const mm = line.match(/^([a-zA-Z_]+):\s*(.*)$/);
-    if (mm) out[mm[1]] = mm[2].trim();
-  }
-  return out;
-}
-
-describe('skill-vault-capture-policy skill', () => {
-  it('has a SKILL.md with required frontmatter', () => {
-    expect(existsSync(SKILL_MD)).toBe(true);
-    const fm = parseFrontmatter(readFileSync(SKILL_MD, 'utf-8'));
-    expect(fm['name']).toBe('skill-vault-capture-policy');
-    expect(fm['description']).toBeTruthy();
-  });
-
-  it('has the required conformance sections', () => {
-    const body = readFileSync(SKILL_MD, 'utf-8');
-    for (const section of ['## Contract', '## Phases', '## Output Format', '## Anti-Patterns']) {
-      expect(body.includes(section), `missing ${section}`).toBe(true);
-    }
-  });
-
-  it('is registered in RESOLVER.md', () => {
-    expect(existsSync(RESOLVER)).toBe(true);
-    expect(readFileSync(RESOLVER, 'utf-8').includes('skill-vault-capture-policy/SKILL.md')).toBe(true);
-  });
-
-  it('contains no private user or agent-fork names (privacy rule)', () => {
-    for (const file of [SKILL_MD, join(SKILL_DIR, 'routing-eval.jsonl')]) {
-      const body = readFileSync(file, 'utf-8');
-      // DEFAULT_PRIVATE_PATTERNS[0] is the banned fork-name pattern; sourced
-      // from harvest-lint so this file never contains the literal itself
-      // (scripts/check-privacy.sh would reject it).
-      const forkName = new RegExp(DEFAULT_PRIVATE_PATTERNS[0], 'i');
-      for (const name of [/\bAdam\b/, /\bHermes\b/, /\bHerdr\b/, /\bArk\b/, forkName]) {
-        expect(name.test(body), `private name ${name} in ${file}`).toBe(false);
-      }
-    }
-  });
-
-  it('has routing-eval fixtures', () => {
-    const evalPath = join(SKILL_DIR, 'routing-eval.jsonl');
-    expect(existsSync(evalPath)).toBe(true);
-    const positives = readFileSync(evalPath, 'utf-8')
-      .split('\n')
-      .filter((l) => l.trim() && !l.trim().startsWith('//'))
-      .map((l) => JSON.parse(l))
-      .filter((l) => l.expected_skill === 'skill-vault-capture-policy');
-    expect(positives.length).toBeGreaterThanOrEqual(4);
-  });
-});

test/whoami.test.ts

@@ -94,6 +94,35 @@ describe('whoami op contract', () => {
     expect(result.expires_at).toBeNull();
   });
 
+  // #1061: stdio MCP is remote/untrusted by design but has no per-token auth
+  // (local pipe). The stdio dispatch marks ctx.transport='stdio'; whoami
+  // reports it instead of throwing unknown_transport.
+  test('stdio transport (remote=true, no auth, transport marker) reports stdio', async () => {
+    const result = (await whoami.handler(
+      ctxWith({ remote: true, auth: undefined, transport: 'stdio' }),
+      {},
+    )) as any;
+    expect(result.transport).toBe('stdio');
+    expect(result.scopes).toEqual([]);
+  });
+
+  test('stdio marker does not mask real auth (auth still wins)', async () => {
+    const result = (await whoami.handler(
+      ctxWith({
+        remote: true,
+        transport: 'stdio',
+        auth: {
+          token: 'gbrain_at_xxx',
+          clientId: 'gbrain_cl_abc',
+          scopes: ['read'],
+          expiresAt: 1,
+        } as AuthInfo,
+      }),
+      {},
+    )) as any;
+    expect(result.transport).toBe('oauth');
+  });
+
   // Q3: ambiguous transport — fail-closed. The footgun this guards against
   // is a future transport that lands without threading auth, where a buggy
   // caller might trust whoami's output to gate sensitive ops.