docs: restore parseNiceFlag docblock displaced by PRUNE_STATUSES; note --status/0d in top-level jobs help

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

src/cli.ts

@@ -2387,7 +2387,7 @@ JOBS (Minions)
   jobs get <id>                       Job details + history
   jobs cancel <id>                    Cancel job
   jobs retry <id>                     Re-queue failed/dead job
-  jobs prune [--older-than 30d]       Clean old jobs
+  jobs prune [--older-than 30d] [--status s,..]  Clean old terminal jobs (0d = no age floor)
   jobs stats                          Job health dashboard
   jobs work [--queue Q]               Start worker daemon (Postgres only)
 

src/commands/init.ts

@@ -161,7 +161,7 @@ interface ResolveAIOptionsArgs {
   nonInteractive: boolean;       // --non-interactive (forces D3 fail-loud, no picker)
 }
 
-export interface ResolvedAIOptions {
+interface ResolvedAIOptions {
   embedding_model?: string;
   embedding_dimensions?: number;
   expansion_model?: string;
@@ -170,41 +170,6 @@ export 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`.
  *
@@ -238,13 +203,18 @@ async function resolveAIOptions(opts: ResolveAIOptionsArgs): Promise<ResolvedAIO
   // user already opted into deferred mode.
   try {
     const { loadConfig } = await import('../core/config.ts');
-    // #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()));
+    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;
   } catch {
-    // loadConfig threw — treat as first-time install, fall through to env
-    // detection.
+    // loadConfig throws when no brain configured — first-time install, fall
+    // through to env detection.
   }
 
   // --- Tier 1+2: explicit flags ---------------------------------------------

src/commands/jobs.ts

@@ -106,6 +106,21 @@ export function parseMaxRssFlag(args: string[]): number | undefined {
   return parsed;
 }
 
+/** Terminal statuses `jobs prune --status` accepts (PR #2282). Matches what
+ *  queue.prune can safely delete; anything else (waiting/active/…) is live. */
+export const PRUNE_STATUSES = ['completed', 'failed', 'dead', 'cancelled'] as const satisfies readonly MinionJobStatus[];
+
+/** Parse a `--status a,b,c` value into prune statuses. Throws on any value
+ *  outside PRUNE_STATUSES (fail-fast, mirrors parseNiceValue). */
+export function parsePruneStatuses(raw: string): MinionJobStatus[] {
+  const requested = raw.split(',').map(s => s.trim()).filter(Boolean);
+  const invalid = requested.filter(s => !(PRUNE_STATUSES as readonly string[]).includes(s));
+  if (requested.length === 0 || invalid.length > 0) {
+    throw new Error(`--status accepts a comma-separated subset of [${PRUNE_STATUSES.join(', ')}]${invalid.length ? `. Invalid: ${invalid.join(', ')}` : ''}`);
+  }
+  return requested as MinionJobStatus[];
+}
+
 /** Parse `--nice N` (then `GBRAIN_NICE` env). Returns:
  *  - undefined if absent (no priority change — inherit)
  *  - the validated integer in [-20, 19] otherwise
@@ -208,7 +223,9 @@ USAGE
   gbrain jobs get <id>
   gbrain jobs cancel <id>
   gbrain jobs retry <id>
-  gbrain jobs prune [--older-than 30d]
+  gbrain jobs prune [--older-than 30d] [--status completed,failed,dead,cancelled]
+                            (--older-than 0d = no age floor: deletes ALL
+                             matching terminal jobs; pair with --status)
   gbrain jobs delete <id>
   gbrain jobs stats
   gbrain jobs smoke
@@ -600,16 +617,27 @@ HANDLER TYPES (built in)
     case 'prune': {
       const olderThanStr = parseFlag(args, '--older-than') ?? '30d';
       const days = parseInt(olderThanStr, 10);
-      if (isNaN(days) || days <= 0) {
-        console.error('Error: --older-than must be a positive number (days). Example: --older-than 30d');
+      if (isNaN(days) || days < 0) {
+        console.error('Error: --older-than must be a non-negative number (days). Example: --older-than 30d; --older-than 0d removes the age floor (deletes ALL matching terminal jobs).');
         process.exit(1);
       }
+      const statusFlag = parseFlag(args, '--status');
+      let statuses: MinionJobStatus[] | undefined;
+      if (statusFlag !== undefined) {
+        try { statuses = parsePruneStatuses(statusFlag); }
+        catch (e) { console.error(`Error: ${e instanceof Error ? e.message : String(e)}`); process.exit(1); }
+      }
 
       try { await queue.ensureSchema(); }
       catch (e) { console.error(e instanceof Error ? e.message : String(e)); process.exit(1); }
 
-      const count = await queue.prune({ olderThan: new Date(Date.now() - days * 86400000) });
-      console.log(`Pruned ${count} jobs older than ${days} days.`);
+      const count = await queue.prune({
+        olderThan: new Date(Date.now() - days * 86400000),
+        ...(statuses ? { status: statuses } : {}),
+      });
+      const statusLabel = statuses ? statuses.join('+') : 'completed+dead+cancelled';
+      const ageLabel = days === 0 ? 'regardless of age' : `older than ${days} days`;
+      console.log(`Pruned ${count} ${statusLabel} jobs ${ageLabel}.`);
       break;
     }
 

src/core/operations.ts

@@ -332,15 +332,6 @@ 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
@@ -3722,10 +3713,9 @@ 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: []}, 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.',
+    '{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.',
   params: {},
   scope: 'read',
   handler: async (ctx) => {
@@ -3737,12 +3727,6 @@ 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

@@ -32,12 +32,6 @@ 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`.
@@ -209,7 +203,6 @@ 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

@@ -42,10 +42,6 @@ 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/init-env-detection.test.ts

@@ -12,7 +12,7 @@
  */
 
 import { describe, test, expect } from 'bun:test';
-import { groupReadyByProvider, findEnvKeyTypos, seedAIOptionsFromConfig } from '../src/commands/init.ts';
+import { groupReadyByProvider, findEnvKeyTypos } from '../src/commands/init.ts';
 
 describe('groupReadyByProvider — embedding touchpoint', () => {
   test('OPENAI_API_KEY alone → openai is ready', async () => {
@@ -149,47 +149,3 @@ 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/jobs-prune-flags.test.ts

@@ -0,0 +1,30 @@
+/**
+ * Unit tests for parsePruneStatuses (PR #2282) — `jobs prune --status` parsing.
+ */
+
+import { describe, test, expect } from 'bun:test';
+import { parsePruneStatuses, PRUNE_STATUSES } from '../src/commands/jobs.ts';
+
+describe('parsePruneStatuses', () => {
+  test('parses a single status', () => {
+    expect(parsePruneStatuses('failed')).toEqual(['failed']);
+  });
+
+  test('parses a comma-separated list with whitespace', () => {
+    expect(parsePruneStatuses(' completed, dead ')).toEqual(['completed', 'dead']);
+  });
+
+  test('accepts every documented terminal status', () => {
+    expect(parsePruneStatuses(PRUNE_STATUSES.join(','))).toEqual([...PRUNE_STATUSES]);
+  });
+
+  test('throws on non-terminal statuses', () => {
+    expect(() => parsePruneStatuses('waiting')).toThrow(/Invalid: waiting/);
+    expect(() => parsePruneStatuses('completed,active')).toThrow(/Invalid: active/);
+  });
+
+  test('throws on empty value', () => {
+    expect(() => parsePruneStatuses('')).toThrow(/comma-separated subset/);
+    expect(() => parsePruneStatuses(',')).toThrow(/comma-separated subset/);
+  });
+});

test/minions.test.ts

@@ -702,6 +702,32 @@ describe('MinionQueue: Prune', () => {
     const count = await queue.prune({ olderThan: new Date(Date.now() + 86400000) }); // future date = prune everything old enough
     expect(count).toBe(1); // only the cancelled one
   });
+
+  // PR #2282: `jobs prune --status` passes an explicit status subset through.
+  test('status filter prunes only the requested terminal statuses', async () => {
+    const cancelled = await queue.add('sync', {});
+    await queue.cancelJob(cancelled.id);
+    const dead = await queue.add('embed', {}, { max_attempts: 1 });
+    await queue.claim('tok1', 30000, 'default', ['embed']);
+    await queue.failJob(dead.id, 'tok1', 'boom', 'dead');
+
+    const count = await queue.prune({ olderThan: new Date(Date.now() + 86400000), status: ['dead'] });
+    expect(count).toBe(1); // only the dead one
+
+    const remaining = await queue.getJobs({ status: 'cancelled' });
+    expect(remaining.length).toBe(1);
+  });
+
+  // PR #2282: `--older-than 0d` = no age floor — olderThan of "now" deletes
+  // terminal jobs that finished moments ago.
+  test('olderThan now (0d semantics) prunes just-terminated jobs', async () => {
+    const job = await queue.add('sync', {});
+    await queue.cancelJob(job.id);
+    await new Promise(r => setTimeout(r, 5)); // ensure updated_at < now
+
+    const count = await queue.prune({ olderThan: new Date() });
+    expect(count).toBe(1);
+  });
 });
 
 // --- Stats (1 test) ---

test/whoami.test.ts

@@ -94,35 +94,6 @@ 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.