@autodidacticon/orchestrator 0.1.0 → 0.3.0

package/dist/src/main.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
 /**
  * Daemon entrypoint.
- *   orchestrator --config orchestrator.yaml [--reap-on-exit]
+ *   orchestrator [--repo <path>] [--config orchestrator.yaml] [--reap-on-exit] [--mode m] [--default-mode m] [--set key=value]...
  * SIGTERM/SIGINT: graceful stop (agents keep running for adoption) unless --reap-on-exit.
  */
-import { readFileSync } from 'node:fs';
+import { readFileSync, writeFileSync } from 'node:fs';
 import { mkdir } from 'node:fs/promises';
 import { parse as parseYaml } from 'yaml';
 import path from 'node:path';
@@ -18,26 +18,36 @@ import { registerOperatorRoutes } from './operator/routes.js';
 import { ClaudeCodeRunner } from './runner/claude-code.js';
 import { SqliteStore } from './state/sqlite.js';
 import { GitVerifierBackend } from './verify/verifier.js';
-import { ensureRunDir, readRepoConfigRaw, resolveRepoPath, resolveRunConfig, runIdFor, writeDaemonJson, writeExitRecord } from './runs/runDir.js';
+import { DAEMON_PID, ensureRunDir, readRepoConfigRaw, resolveFileConfig, resolveRepoPath, resolveRunConfig, runIdFor, writeConfigJson, writeDaemonJson, writeExitRecord } from './runs/runDir.js';
+import { configSummary, mergeOverrides, parseSetFlags, readOverrides, reportOf } from './runs/resolve.js';
 import { digestOf } from './operator/routes.js';
 import { runIdOf, setRunId } from './state/store.js';
 import { randomUUID } from 'node:crypto';
 import { revParse } from './workspace/git.js';
 import { GitWorkspace } from './workspace/git-workspace.js';
 import { isEntrypoint } from './entry.js';
-export const stderrLogger = {
-    info: (msg, data) => process.stderr.write(`${new Date().toISOString()} INFO ${msg}${data ? ` ${JSON.stringify(data)}` : ''}\n`),
-    warn: (msg, data) => process.stderr.write(`${new Date().toISOString()} WARN ${msg}${data ? ` ${JSON.stringify(data)}` : ''}\n`),
-    error: (msg, data) => process.stderr.write(`${new Date().toISOString()} ERROR ${msg}${data ? ` ${JSON.stringify(data)}` : ''}\n`),
-};
+import { makeStderrLogger } from './log.js';
+/** Text by default; one JSON object per line with ORCH_LOG_FORMAT=json. */
+export const stderrLogger = makeStderrLogger();
+/** How long a signalled shutdown may wait for the in-flight tick and verifier job before exiting anyway. */
+const SHUTDOWN_GRACE_MS = 8_000;
 export const USAGE = `orchestrator: the daemon.
 
-  orchestrator [--repo <path>] [--config orchestrator.yaml] [--reap-on-exit] [--mode spawn|pull|mixed] [--default-mode spawn|pull|mixed]
+  orchestrator [--repo <path>] [--config orchestrator.yaml] [--reap-on-exit] [--mode spawn|pull|mixed] [--default-mode spawn|pull|mixed] [--set key=value]...
 
 With --repo (or inside a repository), run data lives under ORCH_HOME
 (~/.orchestrator) keyed by the repository path, and <repo>/orchestrator.yaml is
 read when present. With --config, the file's dataDir and graphPath are used.
 
+No file is needed: the check command, the integration branch, and the tools
+agents may run are detected from the repository root, and every value records
+where it came from (argument, file, pinned, detected, default) in
+<runDir>/config.json and in status. --set key=value stores a durable override
+for the run before resolving; keys: checkCommand, integrationBranch (start-only),
+capacity, allowedTools (a JSON array, or one rule per flag), runnerCommand. An
+unknown key or a bad value is a usage error (exit 2). While checkCommand is
+unresolved, submitted work is held until it is set (orchestrator-ctl config).
+
 Runs one orchestration for one repository: loads the graph file, launches
 agents up to capacity, verifies and publishes their work, and serves the agent
 and operator APIs on loopback. SIGTERM stops it gracefully; agents keep running
@@ -55,6 +65,7 @@ export async function main(argv = process.argv.slice(2)) {
             'reap-on-exit': { type: 'boolean', default: false },
             mode: { type: 'string' },
             'default-mode': { type: 'string' },
+            set: { type: 'string', multiple: true },
             help: { type: 'boolean', short: 'h', default: false },
         },
     });
@@ -62,22 +73,34 @@ export async function main(argv = process.argv.slice(2)) {
         process.stdout.write(USAGE);
         return;
     }
-    let config;
+    let flags;
+    try {
+        flags = parseSetFlags(values.set ?? []);
+    }
+    catch (err) {
+        process.stderr.write(`${err instanceof Error ? err.message : String(err)}\n\n${USAGE}`);
+        process.exit(2);
+    }
     let runId;
     let fileSetsMode = false;
+    let dataDir;
+    let resolveWith;
     if (values.config) {
-        config = await loadConfig(values.config);
-        fileSetsMode = rawRunnerMode(values.config) !== undefined;
+        const file = values.config;
+        dataDir = (await loadConfig(file)).dataDir;
+        fileSetsMode = rawRunnerMode(file) !== undefined;
+        resolveWith = (opts) => resolveFileConfig(file, opts);
     }
     else {
         const repo = await resolveRepoPath({ repo: values.repo });
         ensureRunDir(repo);
-        config = await resolveRunConfig(repo);
+        dataDir = (await resolveRunConfig(repo, process.env, { detect: false })).config.dataDir;
         runId = runIdFor(repo);
         fileSetsMode = readRepoConfigRaw(repo)?.['runner']?.mode !== undefined;
+        resolveWith = (opts) => resolveRunConfig(repo, process.env, opts);
     }
-    await mkdir(config.dataDir, { recursive: true });
-    const store = new SqliteStore(path.join(config.dataDir, 'store.sqlite'));
+    await mkdir(dataDir, { recursive: true });
+    const store = new SqliteStore(path.join(dataDir, 'store.sqlite'));
     // The run id names this run in tracker comments; by repository under a run directory, otherwise once per store.
     if (runId)
         setRunId(store, runId);
@@ -96,21 +119,58 @@ export async function main(argv = process.argv.slice(2)) {
         if (!store.getKv('runner.mode') && !fileSetsMode)
             store.setKv('runner.mode', mode);
     }
-    if (!store.getKv('baselineHead'))
+    // Arguments are durable overrides: merged over the store's document for resolution and persisted once the start is accepted, so a restart without flags keeps them and a refused start leaves nothing behind. See specs/toolchain-discovery "Resolution order and provenance".
+    const overrides = mergeOverrides(readOverrides(store), flags);
+    const pinned = store.getKv('integrationBranch') || undefined;
+    const resolved = await resolveWith({ overrides, pinned });
+    const config = resolved.config;
+    // The branch the run first used is pinned; only an explicit layer can name another one, and only on an untouched run. See specs/toolchain-discovery "Integration branch detection and pinning".
+    if (pinned && config.integrationBranch !== pinned) {
+        const launches = store.listLaunches().length;
+        const jobs = store.listJobs().length;
+        if (launches || jobs) {
+            const msg = `integration branch change refused: this run is pinned to ${pinned} and ${resolved.provenance.integrationBranch === 'file' ? 'orchestrator.yaml' : 'an argument'} names ${config.integrationBranch}; keep ${pinned} for this run (start without --set integrationBranch, or remove the key from orchestrator.yaml), or start from a fresh run directory to use ${config.integrationBranch}`;
+            stderrLogger.error(msg, { pinned, requested: config.integrationBranch, source: resolved.provenance.integrationBranch, launches, jobs });
+            store.close();
+            throw new Error(msg);
+        }
+        stderrLogger.info('integration branch re-pinned on an untouched run', { from: pinned, to: config.integrationBranch, source: resolved.provenance.integrationBranch });
+        store.setKv('integrationBranch', config.integrationBranch);
         store.setKv('baselineHead', await revParse(config.repoPath, config.integrationBranch));
-    const runner = new ClaudeCodeRunner({ command: config.runnerCommand, logDir: path.join(config.dataDir, 'logs'), retryWindowMs: config.retryWindowMs });
+    }
+    else {
+        if (!pinned)
+            store.setKv('integrationBranch', config.integrationBranch);
+        if (!store.getKv('baselineHead'))
+            store.setKv('baselineHead', await revParse(config.repoPath, config.integrationBranch));
+    }
+    if (Object.keys(flags).length)
+        store.setKv('config.overrides', JSON.stringify(overrides));
+    const report = reportOf(resolved, Date.now());
+    writeConfigJson(dataDir, report);
+    store.appendEvent({ kind: 'config.resolved', payload: configSummary(report) }, Date.now());
+    stderrLogger.info('configuration resolved', configSummary(report));
+    // The runner command, its allow list, and the check command are read from the effective configuration at every spawn and at every job start. See specs/toolchain-discovery "Runtime overrides and start-only keys".
+    let orch;
+    const runner = new ClaudeCodeRunner({
+        command: () => orch.effective().config.runnerCommand,
+        allowedTools: () => orch.effective().allowedTools.value,
+        logDir: path.join(config.dataDir, 'logs'),
+        retryWindowMs: config.retryWindowMs,
+    });
     const workspace = new GitWorkspace(config.repoPath, config.integrationBranch, path.join(config.dataDir, 'worktrees'));
     const verifier = new GitVerifierBackend({
         repo: config.repoPath,
         integrationBranch: config.integrationBranch,
         tempRoot: path.join(config.dataDir, 'verify'),
-        checkCommand: config.checkCommand,
+        checkCommand: () => orch.effective().config.checkCommand,
         checkTimeoutMs: config.checkTimeoutMs,
         baselineSha: store.getKv('baselineHead'),
     });
-    const orch = new Orchestrator({
+    orch = new Orchestrator({
         store,
         config,
+        resolved,
         graphSource: new FileGraphSource(config.graphPath),
         runner,
         workspace,
@@ -118,49 +178,71 @@ export async function main(argv = process.argv.slice(2)) {
         briefValidator: new SlotValidator(config.briefSlots),
         log: stderrLogger,
     });
+    orch.onConfigChanged = (r) => {
+        try {
+            writeConfigJson(dataDir, r);
+        }
+        catch (err) {
+            stderrLogger.warn('could not write config.json', { err: String(err) });
+        }
+    };
     const server = new ApiServer(orch);
     registerOperatorRoutes(server, orch);
     // Reuse the recorded port when the config does not pin one, so agents launched before a restart reconnect.
     const recorded = Number(store.getKv('apiPort') ?? 0);
+    // The advertised URL is apiBaseUrl when set (a cluster Service), else the bind address. See specs/cluster-runtime.
+    const listenOpts = { bind: config.apiBind, baseUrl: config.apiBaseUrl };
     let url;
     try {
-        url = await server.listen(config.apiPort || recorded);
+        url = await server.listen(config.apiPort || recorded, listenOpts);
     }
     catch (err) {
         if (config.apiPort)
             throw err;
         stderrLogger.warn('recorded port unavailable, picking a new one', { recorded, err: String(err) });
-        url = await server.listen(0);
+        url = await server.listen(0, listenOpts);
     }
     store.setKv('apiBaseUrl', url);
     store.setKv('apiPort', String(server.port));
+    // The daemon writes its own pid file as well, so a run directory nobody spawned from (a container) carries both files; in a container they are inert. See specs/operator-control "Container mode".
+    writeFileSync(path.join(config.dataDir, DAEMON_PID), `${process.pid}\n`, 'utf8');
     writeDaemonJson(config.dataDir, { pid: process.pid, url, port: server.port, startedAt: Date.now(), repo: config.repoPath });
     stderrLogger.info('listening', { url, pid: process.pid, dataDir: config.dataDir });
     let stopping = false;
-    const shutdown = async (cause) => {
+    const shutdown = async (cause, by) => {
         if (stopping)
             return;
         stopping = true;
         const reap = Boolean(values['reap-on-exit']);
-        stderrLogger.info('shutting down', { cause, reap });
-        await orch.stop({ reap });
-        await server.close();
         // The exit record says why the daemon is gone; a dead pid without one is a crash. See specs/operator-control "Exit record".
         const reason = cause === 'idle' ? 'idle' : cause === 'route' ? 'stop' : 'signal';
-        try {
-            writeExitRecord(config.dataDir, { at: Date.now(), reason, reap, digest: digestOf(orch) });
-        }
-        catch (err) {
-            stderrLogger.warn('could not write the exit record', { err: String(err) });
-        }
+        const recordExit = () => {
+            try {
+                writeExitRecord(config.dataDir, { at: Date.now(), reason, reap, digest: digestOf(orch), ...(by ? { by } : {}) });
+            }
+            catch (err) {
+                stderrLogger.warn('could not write the exit record', { err: String(err) });
+            }
+        };
+        stderrLogger.info('shutting down', { cause, reap, ...(by ? { by } : {}) });
+        // A container runtime kills the process after its grace period; a check still running past ours is abandoned and restarts from queued on the next start. See specs/crash-recovery.
+        setTimeout(() => {
+            stderrLogger.warn('shutdown grace elapsed; exiting with work in flight', { graceMs: SHUTDOWN_GRACE_MS });
+            recordExit();
+            process.exit(0);
+        }, SHUTDOWN_GRACE_MS).unref();
+        await orch.stop({ reap });
+        await server.close();
+        recordExit();
         store.close();
+        stderrLogger.info('stopped', { cause, reason });
         process.exit(0);
     };
     process.on('SIGTERM', () => void shutdown('SIGTERM'));
     process.on('SIGINT', () => void shutdown('SIGINT'));
-    orch.requestShutdown = (reason, reap) => {
+    orch.requestShutdown = (reason, reap, by) => {
         values['reap-on-exit'] = Boolean(reap) || Boolean(values['reap-on-exit']);
-        void shutdown(reason === 'idle' ? 'idle' : 'route');
+        void shutdown(reason === 'idle' ? 'idle' : 'route', by);
     };
     await orch.start();
 }

package/dist/src/main.js.map

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package/dist/src/operator/cli.js

@@ -2,6 +2,7 @@
 /**
  * Operator CLI over the daemon's HTTP API.
  *   orchestrator-ctl status
+ *   orchestrator-ctl config [--check-command <cmd>] [--capacity <n>] [--allow <rule>]... [--runner-command <cmd>] [--model <name>] [--effort <level>] [--clear <key>]...
  *   orchestrator-ctl answer <task> <text>
  *   orchestrator-ctl cancel <task> [--release] [--reason <text>]
  *   orchestrator-ctl reopen <task> [--cascade]
@@ -24,6 +25,7 @@
 import path from 'node:path';
 import { parseArgs } from 'node:util';
 import { daemonState, listRuns, reviveDaemon, startDaemon, stopDaemon } from '../runs/lifecycle.js';
+import { parseSetFlags } from '../runs/resolve.js';
 import { resolveRepoPath, runPaths } from '../runs/runDir.js';
 import { SqliteStore } from '../state/sqlite.js';
 import { isEntrypoint } from '../entry.js';
@@ -75,10 +77,14 @@ export async function call(base, method, route, body) {
 }
 export const USAGE = `orchestrator-ctl: operate a running orchestrator.
 
-  orchestrator-ctl start [--repo <path>]       start the daemon for a repository (idempotent)
+  orchestrator-ctl start [--repo <path>] [--set key=value]...   start the daemon for a repository (idempotent);
+                                               --set checkCommand=..., integrationBranch=..., capacity=..., allowedTools=..., runnerCommand=..., model=..., effort=...
   orchestrator-ctl stop [--reap] [--repo <path>]
   orchestrator-ctl runs                         list runs under ORCH_HOME
   orchestrator-ctl status
+  orchestrator-ctl config                       the resolved configuration: every key with its value and source, the toolchain, needsConfig
+  orchestrator-ctl config [--check-command <cmd>] [--capacity <n>] [--allow <rule>]... [--runner-command <cmd>] [--model <name>] [--effort <level>] [--clear <key>]...
+                                               model and effort are the worker defaults (claude-opus-5-5 at medium); effort is low, medium, high, xhigh, or max
   orchestrator-ctl answer <task> <text>
   orchestrator-ctl cancel <task> [--release] [--reason <text>]
   orchestrator-ctl reopen <task> [--cascade]       cascade resets started dependents and returns the plan
@@ -132,11 +138,19 @@ export async function runCli(argv) {
             payload: { type: 'string' },
             task: { type: 'string' },
             access: { type: 'string' },
+            set: { type: 'string', multiple: true },
+            'check-command': { type: 'string' },
+            capacity: { type: 'string' },
+            allow: { type: 'string', multiple: true },
+            'runner-command': { type: 'string' },
+            model: { type: 'string' },
+            effort: { type: 'string' },
+            clear: { type: 'string', multiple: true },
         },
     });
     const [cmd, a, ...rest] = positionals;
     if (cmd === 'start') {
-        const r = await startDaemon({ repo: values.repo });
+        const r = await startDaemon({ repo: values.repo, ...(values.set?.length ? { overrides: parseSetFlags(values.set) } : {}) });
         return { status: 200, body: r };
     }
     if (cmd === 'stop') {
@@ -150,6 +164,30 @@ export async function runCli(argv) {
     switch (cmd) {
         case 'status':
             return call(base, 'GET', '/v1/status');
+        case 'config': {
+            // One PUT for every flag given; `--allow` appends to the rules already set by argument. See specs/operator-control "Configuration route".
+            const patch = {};
+            for (const k of values.clear ?? [])
+                patch[k] = null;
+            if (values['check-command'] !== undefined)
+                patch['checkCommand'] = values['check-command'];
+            if (values.capacity !== undefined)
+                patch['capacity'] = Number(values.capacity);
+            if (values['runner-command'] !== undefined)
+                patch['runnerCommand'] = values['runner-command'];
+            if (values.model !== undefined)
+                patch['model'] = values.model;
+            if (values.effort !== undefined)
+                patch['effort'] = values.effort;
+            if (values.allow?.length) {
+                const cur = await call(base, 'GET', '/v1/config');
+                const existing = patch['allowedTools'] === null ? [] : (cur.body.overrides?.allowedTools ?? []);
+                patch['allowedTools'] = [...existing, ...values.allow.filter((r) => !existing.includes(r))];
+            }
+            if (!Object.keys(patch).length)
+                return call(base, 'GET', '/v1/config');
+            return call(base, 'PUT', '/v1/config', patch);
+        }
         case 'answer':
             return call(base, 'POST', `/v1/tasks/${a}/answer`, { text: rest.join(' ') });
         case 'cancel':

package/dist/src/operator/cli.js.map

@@ -1 +1 @@
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package/dist/src/operator/mcp-server.js

@@ -7,7 +7,8 @@ import { z } from 'zod';
 import { mapIssues, ImportError, importOptionsSchema, issueRecordSchema, trackerSchema } from '../import/mapping.js';
 import { randomUUID } from 'node:crypto';
 import { ancestorPids } from '../runs/ancestry.js';
-import { daemonState, listRuns, reviveDaemon, startDaemon, stopDaemon } from '../runs/lifecycle.js';
+import { daemonState, listRuns, remoteDaemonUrl, reviveDaemon, startDaemon, stopDaemon } from '../runs/lifecycle.js';
+import { EFFORT_LEVELS } from '../runner/selection.js';
 import { resolveRepoPath, runPaths } from '../runs/runDir.js';
 /** The cap keeps every tool call under Claude Code's two-minute foreground limit; ORCH_WAIT_CAP_MS shortens it for tests. */
 export const WAIT_CAP_MS = Number(process.env['ORCH_WAIT_CAP_MS'] ?? 90_000);
@@ -19,6 +20,7 @@ export const TOOL_NAMES = [
     'answer', 'cancel', 'reopen', 'unblock', 'accept', 'reject', 'pause', 'resume', 'logs',
     'outbox', 'ack', 'nudge', 'proposals', 'accept_proposal', 'reject_proposal',
     'claim', 'release', 'launch_heartbeat', 'launch_report', 'launch_block', 'launch_inbox', 'launch_log',
+    'configure',
 ];
 export function clampWait(ms) {
     if (ms === undefined || !Number.isFinite(ms))
@@ -54,6 +56,12 @@ export class OperatorClient {
     }
     /** The daemon's URL, reviving it after an idle exit or a crash; refused after an explicit stop or for a repository with no run directory. */
     async url() {
+        // A remote daemon (ORCH_URL on a non-loopback host) is used as is, without an attachment (its pids are not ours); reviveDaemon reports it unreachable rather than spawning one here.
+        const remote = remoteDaemonUrl(this.ctx.env);
+        if (remote) {
+            await reviveDaemon({ env: this.ctx.env });
+            return remote;
+        }
         const repo = await this.repo();
         const paths = runPaths(repo, this.ctx.env);
         const state = await daemonState(paths.runDir);
@@ -165,26 +173,50 @@ export async function startOperatorServer(argv, env = process.env) {
     const client = new OperatorClient({ repo: values.repo, env });
     const { McpServer } = await import('@modelcontextprotocol/sdk/server/mcp.js');
     const { StdioServerTransport } = await import('@modelcontextprotocol/sdk/server/stdio.js');
-    const server = new McpServer({ name: 'orchestrator-operator', version: '0.1.0' });
+    const server = new McpServer({ name: 'orchestrator-operator', version: '0.3.0' });
     const task = { task: z.string().describe('Task id as it appears in the graph, e.g. ENG-123') };
     const milestone = { milestone: z.string().describe('Milestone id') };
     server.registerTool('start', {
-        description: 'Start the daemon for this repository (idempotent). Returns url, pid, run directory, graph path, and the runner mode in force. mode: spawn (the daemon runs headless agents), pull (workers claim launches; this session works them through the run skill), or mixed; applied to a daemon already running too. Without mode, a run started from this plugin defaults to pull unless orchestrator.yaml sets runner.mode or the run chose a mode before; a running daemon keeps its mode. After an idle exit or a crash every other tool revives the daemon by itself.',
-        inputSchema: { mode: z.enum(['spawn', 'pull', 'mixed']).optional() },
-    }, async (a) => guarded(async () => ({ status: 200, body: await startDaemon({ repo: values.repo, env, mode: a.mode, ...(a.mode ? {} : { defaultMode: 'pull' }) }) })));
+        description: 'Start the daemon for this repository (idempotent). Returns url, pid, run directory, graph path, the runner mode in force, and the resolved configuration: config (every key as { value, source }: argument, file, pinned, detected, default, or unresolved), toolchain (what detection found in the repository root), needsConfig (keys no layer supplied; checkCommand there means submitted work is held until it is set), and applied / rejected for the configuration arguments. mode: spawn (the daemon runs headless agents), pull (workers claim launches; this session works them through the run skill), or mixed; applied to a daemon already running too. Without mode, a run started from this plugin defaults to pull unless orchestrator.yaml sets runner.mode or the run chose a mode before; a running daemon keeps its mode. Configuration arguments become durable overrides for the run: passed to a daemon this call spawns, applied through the configuration route to one already running; integrationBranch is start-only and lands under rejected on a running daemon. After an idle exit or a crash every other tool revives the daemon by itself.',
+        inputSchema: {
+            mode: z.enum(['spawn', 'pull', 'mixed']).optional(),
+            checkCommand: z.string().optional().describe('The command the verifier runs on every rebased submission, e.g. "npm test".'),
+            integrationBranch: z.string().optional().describe('Start-only: the branch work is published to; pinned for the run once chosen.'),
+            capacity: z.number().int().optional().describe('Agents in parallel.'),
+            allowedTools: z.array(z.string()).optional().describe('Rules appended to the derived allow list for spawned agents, e.g. "Bash(docker:*)".'),
+            runnerCommand: z.string().optional().describe('The runner command template; {allowedTools}, {model}, and {effort} are filled at spawn.'),
+            model: z.string().optional().describe('The worker model for launches prepared from now on (default claude-opus-5-5); a task payload or a model:<name> label overrides it per task.'),
+            effort: z.enum(EFFORT_LEVELS).optional().describe('The worker effort for launches prepared from now on (default medium); a task payload or an effort:<level> label overrides it per task.'),
+        },
+    }, async (a) => guarded(async () => {
+        const { mode, ...rest } = a;
+        const overrides = Object.fromEntries(Object.entries(rest).filter(([, v]) => v !== undefined));
+        return { status: 200, body: await startDaemon({ repo: values.repo, env, mode, ...(mode ? {} : { defaultMode: 'pull' }), ...(Object.keys(overrides).length ? { overrides } : {}) }) };
+    }));
+    server.registerTool('configure', {
+        description: 'Set or clear configuration overrides on the running daemon through the configuration route: checkCommand (applies to every verifier job that starts checking afterwards), capacity (the next admission pass), allowedTools and runnerCommand (every launch spawned afterwards), model and effort (every launch prepared afterwards; defaults claude-opus-5-5 at medium; effort is low, medium, high, xhigh, or max; a task payload or a model:/effort: label overrides them per task). A value sets the key; null clears it so the value falls back to the file, detection, or the default. Returns the new config block with applied; a 400 names an invalid key and value, a 409 names a start-only key (integrationBranch belongs to start).',
+        inputSchema: {
+            checkCommand: z.string().nullable().optional(),
+            capacity: z.number().int().nullable().optional(),
+            allowedTools: z.array(z.string()).nullable().optional(),
+            runnerCommand: z.string().nullable().optional(),
+            model: z.string().nullable().optional(),
+            effort: z.enum(EFFORT_LEVELS).nullable().optional(),
+        },
+    }, async (a) => guarded(() => client.call('PUT', '/v1/config', Object.fromEntries(Object.entries(a).filter(([, v]) => v !== undefined)))));
     server.registerTool('stop', { description: 'Stop the daemon. Agents keep running for adoption unless reap is true.', inputSchema: { reap: z.boolean().optional() } }, async (a) => guarded(async () => {
         const r = await stopDaemon({ repo: values.repo, env, reap: a.reap });
         return { status: r.stopped ? 200 : 409, body: r };
     }));
-    server.registerTool('status', { description: 'Current run status: sets by state, stall roots, open questions, milestones awaiting review, run facts, stuck tasks, pause reason, cost and budgets, per-launch health (with interruptions, the kept releases a task absorbed), deferred: ready tasks held back because their scope overlaps a running, waiting, submitted, or claimable task (each with the ids it overlaps), idle: whether the daemon is quiescent and how long it has been idle against its exit window, and attachments: the sessions attached and the launches each holds.', inputSchema: {} }, async () => guarded(() => client.call('GET', '/v1/status')));
+    server.registerTool('status', { description: 'Current run status: sets by state, stall roots, open questions, milestones awaiting review, run facts, stuck tasks, pause reason, cost and budgets, per-launch health (with interruptions, the kept releases a task absorbed), deferred: ready tasks held back because their scope overlaps a running, waiting, submitted, or claimable task (each with the ids it overlaps), idle: whether the daemon is quiescent and how long it has been idle against its exit window, attachments: the sessions attached and the launches each holds, config: every configuration key as { value, source } (allowedTools with its parts and whether the runner command applies it; model and effort likewise, each live launch also listing its own model and effort), toolchain: the detection record for the repository root, and needsConfig: keys no layer supplied (checkCommand there holds submitted work until configure sets it). Present even before a graph is loaded.', inputSchema: {} }, async () => guarded(() => client.call('GET', '/v1/status')));
     server.registerTool('runs', { description: 'List every run under ORCH_HOME with its repository, daemon liveness, and, for a daemon that is gone, its exit record (idle, stop, or signal with the last digest) or none after a crash.', inputSchema: {} }, async () => guarded(async () => ({ status: 200, body: { runs: await listRuns(env) } })));
     server.registerTool('import_issues', {
-        description: 'Map normalized tracker issues to the run graph and import it. Children of root become tasks; blockedBy becomes deps; blockers outside the set, done, cancelled and in-progress issues become external nodes; root becomes a gated milestone. Acceptance criteria are parsed from the description under the configured heading.',
+        description: 'Map normalized tracker issues to the run graph and import it. Children of root become tasks; blockedBy becomes deps; blockers outside the set, done, cancelled and in-progress issues become external nodes (done and cancelled ones already satisfied); root becomes a gated milestone. Acceptance criteria are parsed from the description under the configured heading. Records come from any tracker the session can read: Linear, Jira, or GitHub Issues (ids GH-<number>, urls on every record).',
         inputSchema: {
             root: z.string(),
             issues: z.array(issueRecordSchema),
             options: importOptionsSchema.partial().optional(),
-            tracker: trackerSchema.optional().describe('The tracker these issues came from; recorded by the daemon so the run skill can mirror states and comments back.'),
+            tracker: trackerSchema.optional().describe('The tracker these issues came from; recorded by the daemon so the run skill can mirror states and comments back. kind linear | atlassian | github; workspace is the Linear workspace, the Jira site, or the GitHub owner/repo; inProgressLabel (github only) names the label that stands for in progress.'),
         },
     }, async (a) => guarded(async () => {
         let mapped;
@@ -201,7 +233,7 @@ export async function startOperatorServer(argv, env = process.env) {
     }));
     server.registerTool('import_graph', { description: 'Import a graph file verbatim (YAML or JSON content) or as a node list.', inputSchema: { content: z.string().optional(), nodes: z.array(z.record(z.unknown())).optional() } }, async (a) => guarded(() => client.call('PUT', '/v1/graph', a)));
     server.registerTool('wait', {
-        description: `Block until something happens. Returns events after afterSeq (default: now), the latest seq, and a digest (openQuestions, awaitingReview, finished, stalled, stuck, pausedReason, deferred: the count of ready tasks held back by scope overlap, outboxPending, trackerErrors). until: question | review | finished | stalled | any; any also returns on launch.stuck, launch.unstuck, and budget.exceeded. timeoutMs default ${WAIT_DEFAULT_MS}, cap ${WAIT_CAP_MS}. Loop on this instead of polling status.`,
+        description: `Block until something happens. Returns events after afterSeq (default: now), the latest seq, and a digest (openQuestions, awaitingReview, finished, stalled, stuck, pausedReason, deferred: the count of ready tasks held back by scope overlap, needsConfig: configuration keys still unresolved, with checkCommand meaning submitted work is held until configure sets it, outboxPending, trackerErrors). until: question | review | finished | stalled | any; any also returns on launch.stuck, launch.unstuck, and budget.exceeded. timeoutMs default ${WAIT_DEFAULT_MS}, cap ${WAIT_CAP_MS}. Loop on this instead of polling status.`,
         inputSchema: { afterSeq: z.number().int().nonnegative().optional(), timeoutMs: z.number().int().nonnegative().optional(), until: z.enum(['question', 'review', 'finished', 'stalled', 'any']).optional() },
     }, async (a) => guarded(() => client.wait(a)));
     server.registerTool('review', { description: 'Review bundle for a submitted gated milestone: pinned sha, version, tag, diff stat, closure task summaries, acceptance criteria.', inputSchema: milestone }, async (a) => guarded(() => client.call('GET', `/v1/milestones/${encodeURIComponent(a.milestone)}/review`)));