fix(search): honor per-call source_id/all_sources in the search op — the #1484 hint's advised retry was silently ignored

The zero-hit CLI hint tells users to retry with --source-id __all__, which
works for `query` (routes through resolveRequestedScope) but the `search`
op had no source_id/all_sources params: the flag parsed into params, nothing
consumed it, and the retry re-ran the same single-source search — an
invisible false negative whose params.source_id also suppressed the hint on
the retry. search now resolves per-call scope through the same canonical
fail-closed resolver as query (local __all__ spans the brain; remote
collapses to the caller's grant; out-of-grant source_id is denied).

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/cli.ts

@@ -466,6 +466,11 @@ async function main() {
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
     const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
+    // #1484 — invisible-miss hint: a bare query/search that hit zero results
+    // on a multi-source brain tells the user (stderr) which source it
+    // actually searched and how to widen the scope.
+    const hint = await sourceScopeHint(op.name, params, ctx.sourceId, engine, result);
+    if (hint) console.error(hint);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
     // STILL runs (drains every background-work sink + disconnects). A bare
@@ -837,6 +842,44 @@ async function makeContext(engine: BrainEngine, params: Record<string, unknown>)
   };
 }
 
+/**
+ * #1484 — a bare `gbrain query`/`search` silently scopes to the resolved
+ * source (usually 'default'); on a multi-source brain a zero-hit run looks
+ * identical to "the brain doesn't know this" even when the answer lives in
+ * another source. Returns a stderr hint when (a) the op is query/search,
+ * (b) it returned zero results, (c) the caller did NOT scope explicitly
+ * (--source / --source-id / --all-sources), and (d) the brain has >1
+ * registered source. Best-effort: any lookup failure returns null.
+ *
+ * Exported for tests (same import-safety contract as formatResult).
+ */
+export async function sourceScopeHint(
+  opName: string,
+  params: Record<string, unknown>,
+  sourceId: string,
+  engine: BrainEngine,
+  result: unknown,
+): Promise<string | null> {
+  if (opName !== 'query' && opName !== 'search') return null;
+  if (!Array.isArray(result) || result.length > 0) return null;
+  // Explicit scoping (flag tier) = user intent; don't second-guess it.
+  if (params.source || params.source_id || params.all_sources) return null;
+  if (sourceId === '__all__') return null;
+  try {
+    const rows = await engine.executeRaw<{ n: number }>(
+      `SELECT count(*)::int AS n FROM sources`,
+    );
+    const n = Number(rows[0]?.n ?? 0);
+    if (n <= 1) return null;
+    return (
+      `Hint: this brain has ${n} sources; you searched only "${sourceId}". ` +
+      `Retry with --source-id __all__ (all sources) or --source-id <id>.`
+    );
+  } catch {
+    return null; // hint is best-effort; never fail the query over it
+  }
+}
+
 // Exported for tests (same import-safety contract as cliAliases/printOpHelp).
 export function formatResult(opName: string, result: unknown): string {
   switch (opName) {

src/core/ai/gateway.ts

@@ -1000,9 +1000,24 @@ const voyageCompatFetch = (async (input: RequestInfo | URL, init?: RequestInit)
   // Voyage diverges from OpenAI in two places that break the parser:
   //   - `embedding` is a base64 string (SDK schema expects `number[]`)
   //   - `usage` lacks `prompt_tokens` (SDK schema requires it when usage present)
+  //
+  // #1610: read the body ONCE via text() and JSON.parse it. The pre-fix
+  // `await resp.clone().json()` truncated large bodies on bun < 1.1.27
+  // (oven-sh/bun#6348) — the parse threw, the catch fell back to the raw
+  // response, and multi-chunk pages died with "Invalid JSON response".
+  // Every JSON return path below rebuilds the Response so a stale
+  // Content-Length/Content-Encoding header from the original can't lie
+  // about the rewritten body.
+  const bodyText = await resp.text();
+  const rebuild = (body: string) => {
+    const headers = new Headers(resp.headers);
+    headers.delete('content-length');
+    headers.delete('content-encoding');
+    return new Response(body, { status: resp.status, statusText: resp.statusText, headers });
+  };
   try {
-    const json: any = await resp.clone().json();
-    if (!json || typeof json !== 'object') return resp;
+    const json: any = JSON.parse(bodyText);
+    if (!json || typeof json !== 'object') return rebuild(bodyText);
     let modified = false;
     if (Array.isArray(json.data)) {
       for (const item of json.data) {
@@ -1037,22 +1052,19 @@ const voyageCompatFetch = (async (input: RequestInfo | URL, init?: RequestInit)
         : 0;
       modified = true;
     }
-    if (!modified) return resp;
-    return new Response(JSON.stringify(json), {
-      status: resp.status,
-      statusText: resp.statusText,
-      headers: resp.headers,
-    });
+    if (!modified) return rebuild(bodyText);
+    return rebuild(JSON.stringify(json));
   } catch (err) {
     // OOM-cap throws MUST propagate. The catch is here for "Voyage returned
     // JSON I can't reshape" (parse error, unexpected schema) — falling back
-    // to the original response is correct in that case. Letting the
+    // to the original body is correct in that case. Letting the
     // too-large response through here would defeat the entire purpose of
     // Layer 2 (the per-embedding cap that fires when Content-Length wasn't
     // available to Layer 1).
     if (err instanceof VoyageResponseTooLargeError) throw err;
-    // If parsing/transformation fails, fall back to the original response.
-    return resp;
+    // If parsing/transformation fails, pass the original body through
+    // (rebuilt — resp's body stream is already consumed by text()).
+    return rebuild(bodyText);
   }
 }) as unknown as typeof fetch;
 
@@ -1192,9 +1204,21 @@ const zeroEntropyCompatFetch = (async (input: RequestInfo | URL, init?: RequestI
   // validates. Also map usage.total_tokens → prompt_tokens (SDK requires
   // prompt_tokens when `usage` is present — same divergence Voyage hit at
   // gateway.ts:655).
+  //
+  // #1610: read the body ONCE via text() + JSON.parse — `resp.clone().json()`
+  // truncated large bodies on bun < 1.1.27 (oven-sh/bun#6348), so the parse
+  // threw and the catch fell back to the RAW ZE `{results: ...}` shape, which
+  // the AI SDK schema rejects → "Invalid JSON response" on multi-chunk pages.
+  const bodyText = await resp.text();
+  const rebuild = (body: string) => {
+    const headers = new Headers(resp.headers);
+    headers.delete('content-length');
+    headers.delete('content-encoding');
+    return new Response(body, { status: resp.status, statusText: resp.statusText, headers });
+  };
   try {
-    const json: any = await resp.clone().json();
-    if (!json || typeof json !== 'object') return resp;
+    const json: any = JSON.parse(bodyText);
+    if (!json || typeof json !== 'object') return rebuild(bodyText);
     let modified = false;
     if (Array.isArray(json.results) && !Array.isArray(json.data)) {
       // Layer 2 OOM cap — per-embedding size. ZE returns float[] arrays,
@@ -1228,20 +1252,25 @@ const zeroEntropyCompatFetch = (async (input: RequestInfo | URL, init?: RequestI
       // SDK also expects total_tokens; ZE provides it directly.
       modified = true;
     }
-    if (!modified) return resp;
-    return new Response(JSON.stringify(json), {
-      status: resp.status,
-      statusText: resp.statusText,
-      headers: resp.headers,
-    });
+    if (!modified) return rebuild(bodyText);
+    return rebuild(JSON.stringify(json));
   } catch (err) {
     // OOM-cap throws MUST propagate. Voyage's pattern: instanceof check on
     // its own tagged class. Same here — only rethrow our own cap class.
     if (err instanceof ZeroEntropyResponseTooLargeError) throw err;
-    return resp;
+    return rebuild(bodyText);
   }
 }) as unknown as typeof fetch;
 
+/**
+ * Test-only seams (#1610): the compat shims are module-private closures;
+ * exporting them lets tests drive the response-rewrite paths behaviorally
+ * (truncating clone(), stale Content-Length) without a live provider.
+ * Same pattern as __getShrinkStateForTests.
+ */
+export const __voyageCompatFetchForTests = voyageCompatFetch;
+export const __zeroEntropyCompatFetchForTests = zeroEntropyCompatFetch;
+
 /**
  * Generic asymmetric-embedding shim for openai-compatible recipes that
  * ship no compat fetch of their own (llama-server, litellm, ollama, ...).

src/core/operations.ts

@@ -499,7 +499,7 @@ export function linkReadScopeOpts(ctx: OperationContext): { sourceId?: string; s
  * FAIL-CLOSED: anything not strictly `ctx.remote === false` is untrusted.
  *
  * This is the SINGLE resolver for every read op that accepts a per-call
- * `source_id` / `all_sources` parameter (query, code_callers, code_callees,
+ * `source_id` / `all_sources` parameter (query, search, code_callers, code_callees,
  * get_page, search_by_image, code_blast, code_flow). Inlining the `__all__`
  * branch per handler is the bug class that leaked cross-source reads (#1924,
  * #1371): a remote client could pass `source_id: '__all__'` to opt out of its
@@ -1442,13 +1442,24 @@ const search: Operation = {
     limit: { type: 'number', description: 'Max results (default 20)' },
     offset: { type: 'number', description: 'Skip first N results (for pagination)' },
     mode: { type: 'string', description: 'Search mode (conservative|balanced|tokenmax). Local callers only.' },
+    source_id: {
+      type: 'string',
+      description:
+        "Scope search to a single source. Defaults to OperationContext.sourceId. Pass '__all__' to span every source for trusted local callers; for remote callers '__all__' spans only your granted sources.",
+    },
+    all_sources: { type: 'boolean', description: "Span sources (equivalent to source_id=__all__): every source locally, your grant remotely." },
   },
   handler: async (ctx, p) => {
     const startedAt = Date.now();
     const queryText = p.query as string;
     const limit = (p.limit as number) || 20;
     const offset = (p.offset as number) || 0;
-    const scope = sourceScopeOpts(ctx);
+    // #1484 follow-up: route through the canonical fail-closed resolver so
+    // `--source-id __all__` / `all_sources` behave the same as on `query`
+    // (the zero-hit CLI hint advises exactly that retry). Without a per-call
+    // param, `search` silently ignored --source-id — the retry looked like
+    // a genuine miss.
+    const scope = resolveRequestedScope(ctx, p.source_id as string | undefined, p.all_sources === true);
 
     // T4/D5 — per-call mode honored ONLY for trusted/local callers so a remote
     // OAuth client can't escalate to the costly tokenmax bundle. Local + unknown

src/core/search/hybrid.ts

@@ -1323,8 +1323,18 @@ export async function hybridSearch(
       if (effectiveModality === 'both' && imageVectorList !== null) {
         vectorLists = [...vectorLists, imageVectorList];
       }
-    } catch {
-      // Embedding failure is non-fatal, fall back to keyword-only
+    } catch (err) {
+      // Embedding/vector failure is non-fatal — fall back to keyword-only —
+      // but say WHY (#1626): this arm only runs when the embedding provider
+      // probed available, so a throw here is a real failure (embed timeout,
+      // transient pooler error on the searchVector fan-out). Pre-fix the bare
+      // catch made a cross-source `--source __all__` run silently collapse to
+      // keyword-only/"No results" with zero diagnostics.
+      warnOncePerProcess(
+        'hybrid-vector-arm-failed',
+        `[gbrain] vector arm failed (fail-open, keyword-only fallback): ` +
+          `${err instanceof Error ? err.message : String(err)}`,
+      );
     }
   }
 

test/ai/compat-fetch-body-read.serial.test.ts

@@ -0,0 +1,115 @@
+/**
+ * #1610 — Voyage/ZeroEntropy compat shims must read the response body ONCE
+ * via text() instead of `resp.clone().json()`.
+ *
+ * On bun < 1.1.27, Response.clone() truncates large bodies (oven-sh/bun#6348):
+ * the clone().json() parse threw, the shim's catch fell back to the ORIGINAL
+ * response — whose wire shape (ZE `{results: ...}`, Voyage base64 embeddings)
+ * the AI SDK's openai-compatible Zod schema rejects — and multi-chunk pages
+ * failed with "Invalid JSON response".
+ *
+ * These tests simulate the truncating clone() and assert the shims still
+ * return the fully rewritten body. They also pin that the rewritten Response
+ * does NOT carry the original (now stale) Content-Length header, which lied
+ * about the rewritten body's size (gateway.ts previously copied
+ * `headers: resp.headers` verbatim).
+ */
+
+import { afterEach, describe, expect, test } from 'bun:test';
+import {
+  __voyageCompatFetchForTests,
+  __zeroEntropyCompatFetchForTests,
+} from '../../src/core/ai/gateway.ts';
+
+const origFetch = globalThis.fetch;
+afterEach(() => {
+  globalThis.fetch = origFetch;
+});
+
+/** Build a Response whose clone() truncates the body (bun < 1.1.27 behavior). */
+function truncatingCloneResponse(body: string): Response {
+  const headers = {
+    'content-type': 'application/json',
+    // Deliberately stale after any rewrite: the original wire body's length.
+    'content-length': String(Buffer.byteLength(body)),
+  };
+  const resp = new Response(body, { status: 200, headers });
+  (resp as any).clone = () =>
+    new Response(body.slice(0, 32), { status: 200, headers });
+  return resp;
+}
+
+describe('voyageCompatFetch — single body read (#1610)', () => {
+  test('rewrites base64 embeddings even when clone() truncates the body', async () => {
+    const floats = new Float32Array([0.5, 0.25, -1]);
+    const b64 = Buffer.from(floats.buffer).toString('base64');
+    const wireBody = JSON.stringify({
+      object: 'list',
+      data: [{ object: 'embedding', embedding: b64, index: 0 }],
+      model: 'voyage-3',
+      usage: { total_tokens: 7 },
+    });
+    globalThis.fetch = (async () => truncatingCloneResponse(wireBody)) as unknown as typeof fetch;
+
+    const out = await __voyageCompatFetchForTests('https://api.voyageai.com/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'], model: 'voyage-3' }),
+      headers: { 'content-type': 'application/json' },
+    });
+
+    const json: any = await out.json();
+    expect(Array.from(json.data[0].embedding)).toEqual([0.5, 0.25, -1]);
+    expect(json.usage.prompt_tokens).toBe(7);
+    // Stale Content-Length from the wire body must not survive the rewrite.
+    expect(out.headers.get('content-length')).toBeNull();
+    expect(out.headers.get('content-encoding')).toBeNull();
+  });
+});
+
+describe('zeroEntropyCompatFetch — single body read (#1610)', () => {
+  test('rewrites {results} → {data} even when clone() truncates the body', async () => {
+    const wireBody = JSON.stringify({
+      results: [{ embedding: [0.1, 0.2] }, { embedding: [0.3, 0.4] }],
+      usage: { total_bytes: 42, total_tokens: 9 },
+    });
+    let fetchedUrl = '';
+    globalThis.fetch = (async (url: string | URL | Request) => {
+      fetchedUrl = String(url);
+      return truncatingCloneResponse(wireBody);
+    }) as unknown as typeof fetch;
+
+    const out = await __zeroEntropyCompatFetchForTests('https://api.zeroentropy.dev/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'], model: 'zembed-1' }),
+      headers: { 'content-type': 'application/json' },
+    });
+
+    expect(fetchedUrl.endsWith('/v1/models/embed')).toBe(true);
+    const json: any = await out.json();
+    // The AI SDK schema requires {data: [{embedding, index}]} — the raw ZE
+    // {results} fallback is exactly the pre-fix "Invalid JSON response".
+    expect(json.results).toBeUndefined();
+    expect(json.data).toHaveLength(2);
+    expect(json.data[0]).toEqual({ object: 'embedding', embedding: [0.1, 0.2], index: 0 });
+    expect(json.data[1].index).toBe(1);
+    expect(json.usage.prompt_tokens).toBe(9);
+    expect(out.headers.get('content-length')).toBeNull();
+  });
+
+  test('non-JSON body falls back to the original bytes (rebuilt, still readable)', async () => {
+    const wireBody = 'plain text, not json';
+    globalThis.fetch = (async () =>
+      new Response(wireBody, {
+        status: 200,
+        headers: { 'content-type': 'application/json' },
+      })) as unknown as typeof fetch;
+
+    const out = await __zeroEntropyCompatFetchForTests('https://api.zeroentropy.dev/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'] }),
+    });
+    // Body was consumed by the shim's single read; the fallback must
+    // rebuild a readable Response rather than return the drained original.
+    expect(await out.text()).toBe(wireBody);
+  });
+});

test/ai/zeroentropy-compat-fetch.test.ts

@@ -98,16 +98,18 @@ describe('zeroEntropyCompatFetch — OOM caps', () => {
     expect(src).toMatch(/MAX_ZEROENTROPY_RESPONSE_BYTES\s*=\s*256\s*\*\s*1024\s*\*\s*1024/);
   });
 
-  test('Layer 1: Content-Length pre-check before resp.clone().json()', async () => {
+  test('Layer 1: Content-Length pre-check before the body is read', async () => {
     const src = await Bun.file(GATEWAY_PATH).text();
     // Find the zeroEntropyCompatFetch block bounds, then assert ordering
-    // within it (mirroring the voyage cap test pattern).
+    // within it (mirroring the voyage cap test pattern). #1610 moved the
+    // body read from `resp.clone().json()` to a single `resp.text()` (bun
+    // < 1.1.27 truncates clone()d bodies, oven-sh/bun#6348).
     const zeFetchStart = src.indexOf('const zeroEntropyCompatFetch');
     expect(zeFetchStart).toBeGreaterThan(0);
-    const block = src.slice(zeFetchStart, zeFetchStart + 8000);
+    const block = src.slice(zeFetchStart, zeFetchStart + 9000);
 
     const preCheckIdx = block.indexOf("resp.headers.get('content-length')");
-    const jsonParseIdx = block.indexOf('await resp.clone().json()');
+    const jsonParseIdx = block.indexOf('const bodyText = await resp.text()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — Voyage's lesson

test/cli-source-scope-hint.test.ts

@@ -0,0 +1,61 @@
+/**
+ * #1484 — invisible-miss hint. A bare `gbrain query` resolves to a single
+ * source (usually 'default'); on a multi-source brain a zero-hit run gave no
+ * signal that the answer might live in another source. sourceScopeHint
+ * returns the stderr hint exactly when: query/search op + zero results +
+ * no explicit scoping param + >1 registered source.
+ */
+
+import { describe, expect, test } from 'bun:test';
+import { sourceScopeHint } from '../src/cli.ts';
+import type { BrainEngine } from '../src/core/engine.ts';
+
+function fakeEngine(sourceCount: number, fail = false): BrainEngine {
+  return {
+    executeRaw: async () => {
+      if (fail) throw new Error('sources table missing');
+      return [{ n: sourceCount }];
+    },
+  } as unknown as BrainEngine;
+}
+
+describe('sourceScopeHint (#1484)', () => {
+  test('fires on a bare zero-hit query against a multi-source brain', async () => {
+    const hint = await sourceScopeHint('query', {}, 'default', fakeEngine(3), []);
+    expect(hint).toContain('3 sources');
+    expect(hint).toContain('"default"');
+    expect(hint).toContain('--source-id __all__');
+  });
+
+  test('fires for search too', async () => {
+    const hint = await sourceScopeHint('search', {}, 'wiki', fakeEngine(2), []);
+    expect(hint).toContain('"wiki"');
+  });
+
+  test('silent when results were found', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3), [{ slug: 'a' }])).toBeNull();
+  });
+
+  test('silent when the caller scoped explicitly', async () => {
+    expect(await sourceScopeHint('query', { source_id: 'wiki' }, 'wiki', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', { source: 'wiki' }, 'wiki', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', { all_sources: true }, '__all__', fakeEngine(3), [])).toBeNull();
+  });
+
+  test('silent when the resolved scope is already __all__', async () => {
+    expect(await sourceScopeHint('query', {}, '__all__', fakeEngine(3), [])).toBeNull();
+  });
+
+  test('silent on a single-source brain', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(1), [])).toBeNull();
+  });
+
+  test('silent for non-search ops and non-array results', async () => {
+    expect(await sourceScopeHint('get_stats', {}, 'default', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3), { rows: [] })).toBeNull();
+  });
+
+  test('best-effort: sources lookup failure returns null, never throws', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3, true), [])).toBeNull();
+  });
+});

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/hybrid-vector-arm-warn.serial.test.ts

@@ -0,0 +1,77 @@
+/**
+ * #1626 — hybridSearch's text-vector arm must not fail DARK.
+ *
+ * The arm only runs when the embedding provider probed available, so a throw
+ * inside it (embed timeout, transient pooler error on searchVector) is a real
+ * failure. Pre-fix, a bare `catch {}` swallowed it and the run silently
+ * collapsed to keyword-only — under `--source __all__` on a strained pooler
+ * that read as a non-deterministic "No results". The fix logs the swallowed
+ * reason via warnOncePerProcess while keeping the keyword fallback.
+ */
+
+import { afterAll, beforeAll, describe, expect, test } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { hybridSearch } from '../src/core/search/hybrid.ts';
+import {
+  __setEmbedTransportForTests,
+  configureGateway,
+  resetGateway,
+} from '../src/core/ai/gateway.ts';
+import { _resetWarnOnceForTests } from '../src/core/utils.ts';
+
+let engine: PGLiteEngine;
+const origWarn = console.warn;
+
+beforeAll(async () => {
+  // Pin the gateway to OpenAI with a stub key (put-page-provenance pattern):
+  // embed() runs instantiateEmbedding — which requires OPENAI_API_KEY — BEFORE
+  // the stubbed transport is reached. Without this, a keyless CI environment
+  // throws the config error instead of the transport's, and the assertion on
+  // the swallowed reason fails. The key never leaves the process.
+  configureGateway({
+    embedding_model: 'openai:text-embedding-3-large',
+    embedding_dimensions: 1536,
+    env: { ...process.env, OPENAI_API_KEY: process.env.OPENAI_API_KEY || 'sk-test-stub' },
+  });
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+  await engine.putPage('people/alice-example', {
+    type: 'person',
+    title: 'Alice Example',
+    compiled_truth: 'Alice Example is a test person for the vector-arm warn test.',
+  });
+});
+
+afterAll(async () => {
+  console.warn = origWarn;
+  __setEmbedTransportForTests(null);
+  resetGateway();
+  await engine.disconnect();
+});
+
+describe('hybridSearch vector-arm failure telemetry (#1626)', () => {
+  test('embed failure logs the swallowed reason and falls back to keyword', async () => {
+    _resetWarnOnceForTests();
+    // Installing a transport makes isAvailable('embedding') true (test-seam
+    // fast path), so the vector arm RUNS — and then throws.
+    __setEmbedTransportForTests(() => {
+      throw new Error('pooler exploded mid-fanout');
+    });
+    const warnings: string[] = [];
+    console.warn = (...args: unknown[]) => {
+      warnings.push(args.map(String).join(' '));
+    };
+    try {
+      const results = await hybridSearch(engine, 'alice');
+      // Keyword fallback still returns results — fail-open preserved.
+      expect(results.some((r) => r.slug === 'people/alice-example')).toBe(true);
+    } finally {
+      console.warn = origWarn;
+      __setEmbedTransportForTests(null);
+    }
+    const armWarnings = warnings.filter((w) => w.includes('vector arm failed'));
+    expect(armWarnings).toHaveLength(1);
+    expect(armWarnings[0]).toContain('pooler exploded mid-fanout');
+  });
+});

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/search-op-source-scope.test.ts

@@ -0,0 +1,87 @@
+/**
+ * #1484 follow-up — the `search` op must honor per-call `source_id` /
+ * `all_sources` through the canonical fail-closed resolver
+ * (resolveRequestedScope), exactly like `query` does.
+ *
+ * Pre-fix, `search` had no source_id param at all: the zero-hit CLI hint
+ * advised "retry with --source-id __all__", the flag parsed into params,
+ * NOTHING consumed it, and the retry silently re-ran the same single-source
+ * search — an invisible false negative (and the retry's params.source_id
+ * suppressed the hint, so the user got no second warning).
+ */
+
+import { describe, expect, test } from 'bun:test';
+import { operationsByName } from '../src/core/operations.ts';
+import type { OperationContext } from '../src/core/operations.ts';
+import type { BrainEngine } from '../src/core/engine.ts';
+
+const searchOp = operationsByName['search'];
+
+/** Fake engine: keyword-only config so the handler's scope goes straight to
+ *  searchKeyword, where we capture the opts it was called with. */
+function makeCtx(remote: boolean, allowedSources?: string[]) {
+  const captured: { opts?: Record<string, unknown> } = {};
+  const engine = {
+    getConfig: async (key: string) => (key === 'search.mcp_keyword_only' ? 'true' : null),
+    searchKeyword: async (_q: string, opts: Record<string, unknown>) => {
+      captured.opts = opts;
+      return [];
+    },
+  } as unknown as BrainEngine;
+  const ctx = {
+    engine,
+    config: { engine: 'pglite' },
+    logger: { info: () => {}, warn: () => {}, error: () => {} },
+    dryRun: false,
+    remote,
+    sourceId: 'default',
+    ...(allowedSources ? { auth: { allowedSources } } : {}),
+  } as unknown as OperationContext;
+  return { ctx, captured };
+}
+
+describe('search op per-call source scope (#1484 follow-up)', () => {
+  test('op declares source_id + all_sources params (the CLI hint advises them)', () => {
+    expect(searchOp.params.source_id).toBeDefined();
+    expect(searchOp.params.all_sources).toBeDefined();
+  });
+
+  test('default: scopes to ctx.sourceId', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x' });
+    expect(captured.opts?.sourceId).toBe('default');
+  });
+
+  test("local + source_id '__all__' spans the whole brain (no source filter)", async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', source_id: '__all__' });
+    expect(captured.opts?.sourceId).toBeUndefined();
+    expect(captured.opts?.sourceIds).toBeUndefined();
+  });
+
+  test('local + all_sources=true spans the whole brain', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', all_sources: true });
+    expect(captured.opts?.sourceId).toBeUndefined();
+    expect(captured.opts?.sourceIds).toBeUndefined();
+  });
+
+  test('explicit source_id wins over ctx.sourceId', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', source_id: 'wiki' });
+    expect(captured.opts?.sourceId).toBe('wiki');
+  });
+
+  test("remote + '__all__' collapses to the caller's grant (fail-closed)", async () => {
+    const { ctx, captured } = makeCtx(true, ['wiki', 'essays']);
+    await searchOp.handler(ctx, { query: 'x', source_id: '__all__' });
+    expect(captured.opts?.sourceIds).toEqual(['wiki', 'essays']);
+  });
+
+  test('remote + out-of-grant source_id is denied', async () => {
+    const { ctx } = makeCtx(true, ['wiki']);
+    await expect(searchOp.handler(ctx, { query: 'x', source_id: 'secrets' })).rejects.toThrow(
+      /outside your granted sources/,
+    );
+  });
+});

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/voyage-response-cap.test.ts

@@ -34,7 +34,7 @@ describe('v0.31.8 — voyage Content-Length pre-check + per-item cap', () => {
     expect(source).toMatch(/MAX_VOYAGE_RESPONSE_BYTES\s*=\s*256\s*\*\s*1024\s*\*\s*1024/);
   });
 
-  test('Layer 1: Content-Length pre-check fires BEFORE resp.clone().json() (D10 OOM defense)', async () => {
+  test('Layer 1: Content-Length pre-check fires BEFORE the body is read (D10 OOM defense)', async () => {
     const source = await Bun.file(new URL('../src/core/ai/gateway.ts', import.meta.url)).text();
     // Anchor relative to the post-fetch handler block. The function declaration
     // contains an OUTBOUND request body section earlier; we want to verify
@@ -47,8 +47,10 @@ describe('v0.31.8 — voyage Content-Length pre-check + per-item cap', () => {
     // doesn't pin to comment text.
     const preCheckIdx = inboundBlock.indexOf("resp.headers.get('content-length')");
     // Use the full lvalue assignment so the match doesn't accidentally hit
-    // comment text that mentions `await resp.clone().json()` for context.
-    const jsonParseIdx = inboundBlock.indexOf('const json: any = await resp.clone().json()');
+    // comment text that mentions the body read for context. (#1610 moved the
+    // read from `resp.clone().json()` to a single `resp.text()` — bun <
+    // 1.1.27 truncates clone()d bodies, oven-sh/bun#6348.)
+    const jsonParseIdx = inboundBlock.indexOf('const bodyText = await resp.text()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — otherwise the OOM