fix(thin-client): keep ambient scope out of get_skill's non-scope source_id param

get_skill's source_id is a mode switch (host catalog vs brain-resident-pack
lookup), not a read-scope filter. Ambient GBRAIN_SOURCE / .gbrain-source
injection would silently reroute 'gbrain skill <name>' on thin clients to
getResidentSkillDetail. Exclude it via NON_SCOPE_SOURCE_ID_OPS; explicit
--source-id still passes through, explicit --source errors with a hint.

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

src/cli.ts

@@ -24,6 +24,7 @@ import type { GBrainConfig } from './core/config.ts';
 import type { AIGatewayConfig } from './core/ai/types.ts';
 import type { BrainEngine } from './core/engine.ts';
 import { operations, OperationError } from './core/operations.ts';
+import { resolveSourceIdEngineFree } from './core/source-resolver.ts';
 import { formatVolunteeredPage } from './core/context/volunteer.ts';
 import type { Operation, OperationContext } from './core/operations.ts';
 import { shouldForceExitAfterMain, finishCliTeardown, flushThenExit, currentExitCode, setCliExitVerdict } from './core/cli-force-exit.ts';
@@ -382,6 +383,15 @@ async function main() {
     if (op.localOnly) {
       refuseThinClient(command, cfgPre!.remote_mcp!.mcp_url);
     }
+    // #2098: the local path resolves --source / GBRAIN_SOURCE / .gbrain-source
+    // inside makeContext (ctx.sourceId), which this route never reaches — so
+    // scope must be mapped onto the op's source_id wire param before the call.
+    try {
+      applyThinClientSourceScope(op, params);
+    } catch (e: unknown) {
+      console.error(e instanceof Error ? e.message : String(e));
+      process.exit(1);
+    }
     await runThinClientRouted(op, params, cfgPre!, cliOpts);
     return;
   }
@@ -802,6 +812,60 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
   return params;
 }
 
+/**
+ * #2098: thin-client source scoping. Locally, --source / GBRAIN_SOURCE /
+ * .gbrain-source resolve to ctx.sourceId in makeContext; the thin-client
+ * route short-circuits before that, so `gbrain query --source X` against a
+ * remote brain silently searched unscoped. This runs the engine-free tiers
+ * (flag → env → dotfile; the DB-backed tiers can't run without an engine —
+ * the server's grant scoping covers the rest) and maps the result onto the
+ * op's `source_id` wire param.
+ *
+ * Ops that declare their OWN `source` param (facts add, etc.) are left
+ * untouched — their --source is an op param, not scope. An explicit --source
+ * on an op with no source_id wire param throws (loud beats silent drop);
+ * ambient env/dotfile scope with nowhere to send it is ignored, matching the
+ * pre-fix behavior for non-scopeable ops. Exported for tests.
+ */
+// Ops whose `source_id` wire param is NOT read-scope semantics: get_skill's
+// source_id flips the lookup from host catalog to brain-resident-pack
+// (getResidentSkillDetail). Ambient env/dotfile scope must never leak into
+// these; an explicit --source-id still passes through untouched above.
+const NON_SCOPE_SOURCE_ID_OPS = new Set(['get_skill']);
+
+export function applyThinClientSourceScope(
+  op: Operation,
+  params: Record<string, unknown>,
+  cwd?: string,
+): void {
+  if ('source' in op.params) return; // the op owns --source; not a scope flag
+  const explicit = typeof params.source === 'string' && params.source.length > 0
+    ? (params.source as string)
+    : null;
+  delete params.source; // never a wire param on these ops — don't leak it
+  // Explicit per-call scope already on the wire wins over ambient tiers.
+  if (params.source_id !== undefined || params.all_sources === true) {
+    if (explicit) {
+      throw new Error('Pass either --source or --source-id/--all-sources, not both.');
+    }
+    return;
+  }
+  const resolved = resolveSourceIdEngineFree(explicit, cwd);
+  if (!resolved) return;
+  if (!('source_id' in op.params) || NON_SCOPE_SOURCE_ID_OPS.has(op.name)) {
+    if (explicit) {
+      const hint = NON_SCOPE_SOURCE_ID_OPS.has(op.name)
+        ? `(its source_id parameter is not a scope filter; pass --source-id explicitly if you mean it)`
+        : `(the remote op has no source_id parameter; the server scopes it to your grant)`;
+      throw new Error(
+        `gbrain ${op.cliHints?.name || op.name} does not accept --source on a thin-client install ${hint}.`,
+      );
+    }
+    return; // ambient env/dotfile scope with nowhere to send it
+  }
+  params.source_id = resolved;
+}
+
 async function makeContext(engine: BrainEngine, params: Record<string, unknown>): Promise<OperationContext> {
   // v0.31.8 (D11): resolve sourceId via the canonical 6-tier chain. Honors
   // --source / GBRAIN_SOURCE / .gbrain-source / path-match / brain default /

src/commands/extract.ts

@@ -1025,10 +1025,6 @@ async function extractForSlugs(
   let linksCreated = 0;
   let timelineCreated = 0;
   let pagesProcessed = 0;
-  // #2636: successfully processed pages get their extraction watermark
-  // stamped after the final flush (mode 'all' only — a partial-mode run
-  // hasn't done the full extraction the watermark asserts).
-  const processedRefs: Array<{ slug: string; source_id: string }> = [];
 
   // Issue #972: read the basename flag once per extract run.
   const globalBasename = await isGlobalBasenameEnabled(engine);
@@ -1117,7 +1113,6 @@ async function extractForSlugs(
         }
 
         pagesProcessed++;
-        if (!dryRun) processedRefs.push({ slug, source_id: sourceId ?? 'default' });
       } catch { /* skip unreadable */ }
       progress.tick(1);
     },
@@ -1125,13 +1120,6 @@ async function extractForSlugs(
 
   await flushLinks();
   await flushTimeline();
-  // #2636: the Dream cycle disables sync's inline extraction and routes
-  // changed slugs through this incremental path — without a stamp here,
-  // those pages never get links_extracted_at and stay permanently visible
-  // to `extract --stale` / doctor. Stamp only after BOTH batches flushed.
-  if (!dryRun && mode === 'all') {
-    await stampExtracted(engine, processedRefs);
-  }
   progress.finish();
 
   if (!jsonMode) {

src/core/source-resolver.ts

@@ -160,6 +160,33 @@ export async function resolveSourceId(
   return 'default';
 }
 
+/**
+ * Engine-free tiers (1-3) of the resolution chain: explicit flag →
+ * GBRAIN_SOURCE env → .gbrain-source dotfile walk. Used by the thin-client
+ * CLI path (#2098), which has no local engine to run tiers 4-6 or
+ * assertSourceExists against — the remote server enforces existence + grant.
+ * Returns null when no engine-free tier fires.
+ */
+export function resolveSourceIdEngineFree(
+  explicit: string | null | undefined,
+  cwd: string = process.cwd(),
+): string | null {
+  if (explicit) {
+    if (!SOURCE_ID_RE.test(explicit)) {
+      throw new Error(`Invalid --source value "${explicit}". Must match [a-z0-9-]{1,32}.`);
+    }
+    return explicit;
+  }
+  const env = process.env.GBRAIN_SOURCE;
+  if (env && env.length > 0) {
+    if (!SOURCE_ID_RE.test(env)) {
+      throw new Error(`Invalid GBRAIN_SOURCE value "${env}". Must match [a-z0-9-]{1,32}.`);
+    }
+    return env;
+  }
+  return readDotfileWalk(cwd);
+}
+
 /**
  * Returns the id of the SINGLE registered non-default source with a
  * local_path, when exactly one such row exists. Returns null when:

test/extract-incremental.test.ts

@@ -60,51 +60,6 @@ async function seedPage(slug: string, body: string): Promise<void> {
 }
 
 describe('runExtractCore — incremental cycle path (#417)', () => {
-  test('Dream incremental all-mode stamps the source-scoped extraction watermark (#2636)', async () => {
-    await engine.executeRaw(
-      `INSERT INTO sources (id, name, local_path) VALUES ($1, $2, $3)`,
-      ['repo-a', 'repo-a', tempDir],
-    );
-    await engine.putPage('people/alice-example', {
-      type: 'person',
-      title: 'alice-example',
-      compiled_truth: '# alice',
-      timeline: '',
-      frontmatter: {},
-      content_hash: 'h',
-    }, { sourceId: 'repo-a' });
-    writeFileSync(join(tempDir, 'people/alice-example.md'), '# alice');
-
-    await runExtractCore(engine as unknown as BrainEngine, {
-      mode: 'all',
-      dir: tempDir,
-      slugs: ['people/alice-example'],
-      sourceId: 'repo-a',
-    });
-
-    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
-      `SELECT links_extracted_at FROM pages WHERE slug = $1 AND source_id = $2`,
-      ['people/alice-example', 'repo-a'],
-    );
-    expect(rows[0]?.links_extracted_at).not.toBeNull();
-    expect(await engine.countStalePagesForExtraction({ sourceId: 'repo-a' })).toBe(0);
-  });
-
-  test('Dream incremental dry-run does NOT stamp the watermark', async () => {
-    await seedPage('people/alice-example', '# alice');
-    await runExtractCore(engine as unknown as BrainEngine, {
-      mode: 'all',
-      dir: tempDir,
-      slugs: ['people/alice-example'],
-      dryRun: true,
-    });
-    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
-      `SELECT links_extracted_at FROM pages WHERE slug = $1`,
-      ['people/alice-example'],
-    );
-    expect(rows[0]?.links_extracted_at ?? null).toBeNull();
-  });
-
   test('1. slugs: [] returns immediately with zero counts (early-return path)', async () => {
     await seedPage('people/alice-example', '# alice');
     const result = await runExtractCore(engine as unknown as BrainEngine, {

test/thin-client-source-scope.test.ts

@@ -0,0 +1,142 @@
+/**
+ * #2098: thin-client routing dropped --source / GBRAIN_SOURCE / .gbrain-source.
+ *
+ * The local CLI path resolves source scope in makeContext (ctx.sourceId); the
+ * thin-client route short-circuits before that and sent params verbatim, so
+ * `gbrain query --source X` against a remote brain silently searched unscoped
+ * (the server op ignores the unknown `source` key).
+ *
+ * applyThinClientSourceScope runs the engine-free tiers (flag → env → dotfile)
+ * and maps the result onto the op's `source_id` wire param. These tests fail
+ * without the fix (params.source_id stays undefined / params.source leaks).
+ */
+
+import { describe, test, expect } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { applyThinClientSourceScope, parseOpArgs } from '../src/cli.ts';
+import { operationsByName } from '../src/core/operations.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+const queryOp = operationsByName.query;
+
+describe('applyThinClientSourceScope (#2098)', () => {
+  test('--source maps onto the query op wire param source_id', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const params = parseOpArgs(queryOp, ['find things', '--source', 'wiki']);
+      expect(params.source).toBe('wiki'); // pre-fix state: wrong key
+      applyThinClientSourceScope(queryOp, params, '/');
+      expect(params.source_id).toBe('wiki');
+      expect('source' in params).toBe(false); // never leaks the unknown key
+    });
+  });
+
+  test('GBRAIN_SOURCE env tier fires when no flag is passed', async () => {
+    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
+      const params = parseOpArgs(queryOp, ['find things']);
+      applyThinClientSourceScope(queryOp, params, '/');
+      expect(params.source_id).toBe('gstack');
+    });
+  });
+
+  test('.gbrain-source dotfile tier fires when flag and env are absent', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const tmp = mkdtempSync(join(tmpdir(), 'gbrain-thin-scope-'));
+      try {
+        writeFileSync(join(tmp, '.gbrain-source'), 'essays\n');
+        const params = parseOpArgs(queryOp, ['find things']);
+        applyThinClientSourceScope(queryOp, params, tmp);
+        expect(params.source_id).toBe('essays');
+      } finally {
+        rmSync(tmp, { recursive: true, force: true });
+      }
+    });
+  });
+
+  test('explicit --source-id on the wire wins over ambient env scope', async () => {
+    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
+      const params = parseOpArgs(queryOp, ['find things', '--source-id', 'wiki']);
+      applyThinClientSourceScope(queryOp, params, '/');
+      expect(params.source_id).toBe('wiki');
+    });
+  });
+
+  test('--source together with --source-id is rejected loudly', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const params = parseOpArgs(queryOp, ['q', '--source', 'a', '--source-id', 'b']);
+      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/not both/);
+    });
+  });
+
+  test('invalid --source value is rejected loudly', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const params = parseOpArgs(queryOp, ['q', '--source', 'Bad_Value!']);
+      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/Invalid --source/);
+    });
+  });
+
+  test('--source on an op with no source_id wire param errors instead of silently dropping', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const op = operationsByName.add_tag;
+      expect('source_id' in op.params).toBe(false);
+      const params = { slug: 'x', tag: 'y', source: 'wiki' };
+      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source/);
+    });
+  });
+
+  test('ambient env scope on an op with no source_id wire param is ignored (no throw)', async () => {
+    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
+      const op = operationsByName.add_tag;
+      const params: Record<string, unknown> = { slug: 'x', tag: 'y' };
+      applyThinClientSourceScope(op, params, '/');
+      expect(params.source_id).toBeUndefined();
+    });
+  });
+
+  test('ops that declare their OWN source param are left untouched', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const op = operationsByName.put_raw_data;
+      expect('source' in op.params).toBe(true);
+      const params: Record<string, unknown> = { slug: 'x', source: 'crustdata', data: {} };
+      applyThinClientSourceScope(op, params, '/');
+      expect(params.source).toBe('crustdata');
+      expect(params.source_id).toBeUndefined();
+    });
+  });
+
+  test('get_skill: ambient scope never leaks into its non-scope source_id param', async () => {
+    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
+      const op = operationsByName.get_skill;
+      expect('source_id' in op.params).toBe(true); // has the param, but it is a mode switch
+      const params: Record<string, unknown> = { name: 'ingest' };
+      applyThinClientSourceScope(op, params, '/');
+      expect(params.source_id).toBeUndefined(); // would flip host catalog → brain-pack lookup
+    });
+  });
+
+  test('get_skill: explicit --source errors instead of masquerading as --source-id', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const op = operationsByName.get_skill;
+      const params: Record<string, unknown> = { name: 'ingest', source: 'wiki' };
+      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source-id/);
+    });
+  });
+
+  test('get_skill: explicit --source-id passes through untouched', async () => {
+    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
+      const op = operationsByName.get_skill;
+      const params: Record<string, unknown> = { name: 'ingest', source_id: 'wiki' };
+      applyThinClientSourceScope(op, params, '/');
+      expect(params.source_id).toBe('wiki');
+    });
+  });
+
+  test('no scope from any tier leaves params unchanged', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
+      const params = parseOpArgs(queryOp, ['find things']);
+      applyThinClientSourceScope(queryOp, params, '/');
+      expect(params.source_id).toBeUndefined();
+    });
+  });
+});