corydora 0.4.0 → 1.0.3

package/CHANGELOG.md

@@ -2,6 +2,38 @@
 
 All notable changes to Corydora are documented in this file.
 
+## [1.0.3](https://github.com/glorioustephan/corydora/compare/corydora-v1.0.2...corydora-v1.0.3) (2026-04-14)
+
+
+### Bug Fixes
+
+* republish after npm trusted publishing setup ([853b8a2](https://github.com/glorioustephan/corydora/commit/853b8a250d5a02c5839861b27ca9ac781e27f356))
+
+## [1.0.2](https://github.com/glorioustephan/corydora/compare/corydora-v1.0.1...corydora-v1.0.2) (2026-04-14)
+
+
+### Bug Fixes
+
+* **publish.yml:** the workflow ran pnpm install --frozen-lockfile before any actions/checkout ([#19](https://github.com/glorioustephan/corydora/issues/19)) ([dd6b461](https://github.com/glorioustephan/corydora/commit/dd6b461c2d5609b291168cf41e0657bb6ff54898))
+
+## [1.0.1](https://github.com/glorioustephan/corydora/compare/corydora-v1.0.0...corydora-v1.0.1) (2026-04-14)
+
+
+### Bug Fixes
+
+* release PR [#17](https://github.com/glorioustephan/corydora/issues/17) changes ([2ded546](https://github.com/glorioustephan/corydora/commit/2ded546cb50365c49dff4e67ceb65396b6f7371d))
+
+## [1.0.0](https://github.com/glorioustephan/corydora/compare/corydora-v0.4.0...corydora-v1.0.0) (2026-04-13)
+
+
+### ⚠ BREAKING CHANGES
+
+* corydora status --json changed shape and status vocabulary.
+
+### Features
+
+* adding modes and introducing a background daemon with vNext ([#14](https://github.com/glorioustephan/corydora/issues/14)) ([66db5fc](https://github.com/glorioustephan/corydora/commit/66db5fc94805e68e6a364bbc4440d6d0d96aa540))
+
 ## [0.4.0](https://github.com/glorioustephan/corydora/compare/corydora-v0.3.4...corydora-v0.4.0) (2026-03-31)
 
 ### Features

package/README.md

@@ -6,7 +6,7 @@
 [![npm downloads](https://img.shields.io/npm/dm/corydora.svg)](https://www.npmjs.com/package/corydora)
 [![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](./LICENSE)
 [![Docs](https://img.shields.io/badge/docs-vitepress-7c3aed.svg)](https://glorioustephan.github.io/corydora/)
-
+[![Socket Badge](https://badge.socket.dev/npm/package/corydora/0.4.0)](https://badge.socket.dev/npm/package/corydora/0.4.0)
 <p align="center">
   <img src="./logo.webp" alt="Corydora" width="320px" />
 </p>
@@ -226,7 +226,7 @@ calls `npm publish`.
 ## Notes
 
 - Secrets never belong in `.corydora.json`.
-- `.corydora/.env.local` is ignored by default.
+- Add `.corydora/.env.local` to `.gitignore`, or let interactive `corydora init` append Corydora's recommended ignore block.
 - Markdown queue files are projections of machine state in `.corydora/state/`.
 - The root `CHANGELOG.md` is the canonical release history and is maintained by release-please.
 - The npm publish workflow assumes GitHub-hosted runners, which is also what npm trusted publishing

package/dist/commands/doctor.js

@@ -1,21 +1,51 @@
+import { existsSync } from 'node:fs';
+import { resolve } from 'node:path';
 import { detectProjectFingerprint } from '../filesystem/project.js';
 import { probeAvailableRuntimes, getRuntimeAdapters } from '../providers/index.js';
 import { supportsBackgroundKeepAwake, supportsTmux } from '../runtime/tmux.js';
+import { chooseValidationScript } from '../runtime/validation.js';
+import { preflightIsolationMode, resolveStageRoute } from '../runtime/routes.js';
+import { configExists, loadRequiredConfig } from './helpers.js';
 export async function runDoctorCommand(projectRoot, json, ui) {
-    const [fingerprint, probes] = await Promise.all([
+    const hasConfig = configExists(projectRoot);
+    const [fingerprint, probes, config] = await Promise.all([
         Promise.resolve(detectProjectFingerprint(projectRoot)),
         probeAvailableRuntimes(projectRoot),
+        hasConfig ? loadRequiredConfig(projectRoot) : Promise.resolve(null),
     ]);
     const runtimeChecks = await Promise.all(getRuntimeAdapters().map(async (adapter) => ({
         provider: adapter.id,
         checks: await adapter.doctor(projectRoot),
     })));
+    const fixRoute = config ? resolveStageRoute(config, 'fix') : null;
+    const validation = config
+        ? chooseValidationScript(projectRoot, config.modes.default, config.execution.validateAfterFix)
+        : null;
+    const isolationCheck = config && fixRoute
+        ? preflightIsolationMode({
+            projectRoot,
+            config,
+            fixRoute,
+            mode: config.modes.default,
+        })
+        : null;
     const payload = {
         fingerprint,
         tmuxAvailable: supportsTmux(),
         backgroundKeepAwakeAvailable: supportsBackgroundKeepAwake(),
         runtimes: probes,
         checks: runtimeChecks,
+        config: config
+            ? {
+                mode: config.modes.default,
+                fixProvider: fixRoute?.provider,
+                effectiveIsolationMode: isolationCheck?.effectiveIsolationMode,
+                validationCommand: validation ? [validation.command, ...validation.args].join(' ') : null,
+                lintPrerequisite: config.modes.default === 'linting'
+                    ? existsSync(resolve(projectRoot, 'package.json'))
+                    : null,
+            }
+            : null,
     };
     if (json) {
         ui.printJson(payload);
@@ -28,5 +58,11 @@ export async function runDoctorCommand(projectRoot, json, ui) {
     for (const probe of probes) {
         ui.info(`${probe.provider}: installed=${probe.installed} auth=${probe.auth.status} (${probe.auth.message})`);
     }
+    if (config && fixRoute && isolationCheck) {
+        ui.info(`Configured mode: ${config.modes.default}`);
+        ui.info(`Fix route: ${fixRoute.provider} (${fixRoute.model})`);
+        ui.info(`Isolation compatibility: ${config.git.isolationMode} -> ${isolationCheck.effectiveIsolationMode}`);
+        ui.info(`Validation command: ${validation ? [validation.command, ...validation.args].join(' ') : 'none available'}`);
+    }
 }
 //# sourceMappingURL=doctor.js.map

package/dist/commands/doctor.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.js","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AACpE,OAAO,EAAE,sBAAsB,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAC;AACnF,OAAO,EAAE,2BAA2B,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAC/E,OAAO,EAAE,sBAAsB,EAAE,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAE,sBAAsB,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AACjF,OAAO,EAAE,YAAY,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAC;AAGhE,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,WAAmB,EAAE,IAAa,EAAE,EAAM;IAC/E,MAAM,SAAS,GAAG,YAAY,CAAC,WAAW,CAAC,CAAC;IAC5C,MAAM,CAAC,WAAW,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QACtD,OAAO,CAAC,OAAO,CAAC,wBAAwB,CAAC,WAAW,CAAC,CAAC;QACtD,sBAAsB,CAAC,WAAW,CAAC;QACnC,SAAS,CAAC,CAAC,CAAC,kBAAkB,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC;KACpE,CAAC,CAAC;IAEH,MAAM,aAAa,GAAG,MAAM,OAAO,CAAC,GAAG,CACrC,kBAAkB,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC,CAAC;QAC3C,QAAQ,EAAE,OAAO,CAAC,EAAE;QACpB,MAAM,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,WAAW,CAAC;KAC1C,CAAC,CAAC,CACJ,CAAC;IAEF,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,iBAAiB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAClE,MAAM,UAAU,GAAG,MAAM;QACvB,CAAC,CAAC,sBAAsB,CAAC,WAAW,EAAE,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,gBAAgB,CAAC;QAC9F,CAAC,CAAC,IAAI,CAAC;IACT,MAAM,cAAc,GAClB,MAAM,IAAI,QAAQ;QAChB,CAAC,CAAC,sBAAsB,CAAC;YACrB,WAAW;YACX,MAAM;YACN,QAAQ;YACR,IAAI,EAAE,MAAM,CAAC,KAAK,CAAC,OAAO;SAC3B,CAAC;QACJ,CAAC,CAAC,IAAI,CAAC;IAEX,MAAM,OAAO,GAAG;QACd,WAAW;QACX,aAAa,EAAE,YAAY,EAAE;QAC7B,4BAA4B,EAAE,2BAA2B,EAAE;QAC3D,QAAQ,EAAE,MAAM;QAChB,MAAM,EAAE,aAAa;QACrB,MAAM,EAAE,MAAM;YACZ,CAAC,CAAC;gBACE,IAAI,EAAE,MAAM,CAAC,KAAK,CAAC,OAAO;gBAC1B,WAAW,EAAE,QAAQ,EAAE,QAAQ;gBAC/B,sBAAsB,EAAE,cAAc,EAAE,sBAAsB;gBAC9D,iBAAiB,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI;gBACzF,gBAAgB,EACd,MAAM,CAAC,KAAK,CAAC,OAAO,KAAK,SAAS;oBAChC,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,WAAW,EAAE,cAAc,CAAC,CAAC;oBAClD,CAAC,CAAC,IAAI;aACX;YACH,CAAC,CAAC,IAAI;KACT,CAAC;IAEF,IAAI,IAAI,EAAE,CAAC;QACT,EAAE,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;QACtB,OAAO;IACT,CAAC;IAED,EAAE,CAAC,IAAI,CAAC,oBAAoB,WAAW,CAAC,cAAc,EAAE,CAAC,CAAC;IAC1D,EAAE,CAAC,IAAI,CAAC,eAAe,WAAW,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,eAAe,EAAE,CAAC,CAAC;IAC/E,EAAE,CAAC,IAAI,CAAC,mBAAmB,YAAY,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;IAC5D,EAAE,CAAC,IAAI,CAAC,oCAAoC,2BAA2B,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;IAE5F,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,EAAE,CAAC,IAAI,CACL,GAAG,KAAK,CAAC,QAAQ,eAAe,KAAK,CAAC,SAAS,SAAS,KAAK,CAAC,IAAI,CAAC,MAAM,KAAK,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,CACpG,CAAC;IACJ,CAAC;IAED,IAAI,MAAM,IAAI,QAAQ,IAAI,cAAc,EAAE,CAAC;QACzC,EAAE,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;QACpD,EAAE,CAAC,IAAI,CAAC,cAAc,QAAQ,CAAC,QAAQ,KAAK,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAC;QAC/D,EAAE,CAAC,IAAI,CACL,4BAA4B,MAAM,CAAC,GAAG,CAAC,aAAa,OAAO,cAAc,CAAC,sBAAsB,EAAE,CACnG,CAAC;QACF,EAAE,CAAC,IAAI,CACL,uBAAuB,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,gBAAgB,EAAE,CAC5G,CAAC;IACJ,CAAC;AACH,CAAC"}

package/dist/commands/init.js

@@ -1,21 +1,78 @@
-import { confirm, intro, isCancel, outro, select, spinner, text } from '@clack/prompts';
+import { confirm, intro, isCancel, multiselect, outro, select, spinner, text, } from '@clack/prompts';
 import { BUILTIN_AGENTS } from '../agents/builtin-agents.js';
-import { saveConfig, ensureCorydoraStructure } from '../config/files.js';
+import { loadConfig, saveConfig, ensureCorydoraStructure } from '../config/files.js';
 import { getDefaultConfig } from '../config/schema.js';
-import { CONFIG_FILE_NAME } from '../constants.js';
-import { ensureGitignoreEntries } from '../filesystem/gitignore.js';
+import { BUILTIN_TASK_CATEGORIES, CONFIG_FILE_NAME } from '../constants.js';
+import { appendGitignoreEntries, findMissingGitignoreEntries } from '../filesystem/gitignore.js';
 import { detectProjectFingerprint } from '../filesystem/project.js';
 import { probeAvailableRuntimes } from '../providers/index.js';
+import { configExists } from './helpers.js';
 function selectBuiltinAgents(projectTechLenses) {
     const matching = BUILTIN_AGENTS.filter((agent) => agent.techLenses.some((lens) => projectTechLenses.includes(lens)));
     return (matching.length > 0 ? matching : BUILTIN_AGENTS).map((agent) => agent.id);
 }
+function categoriesForBuiltinAgents(selectedBuiltinAgents) {
+    const categories = new Set();
+    for (const agent of BUILTIN_AGENTS) {
+        if (!selectedBuiltinAgents.includes(agent.id)) {
+            continue;
+        }
+        for (const category of agent.categories) {
+            categories.add(category);
+        }
+    }
+    const ordered = BUILTIN_TASK_CATEGORIES.filter((category) => categories.has(category));
+    return ordered.length > 0 ? [...ordered] : ['bugs'];
+}
+function mergeInitConfig(options) {
+    const baseConfig = options.existingConfig ??
+        getDefaultConfig({
+            provider: options.provider,
+            model: options.model,
+            isolationMode: options.isolationMode,
+            selectedBuiltinAgents: options.selectedBuiltinAgents,
+            trackMarkdownQueues: options.trackMarkdownQueues,
+            backgroundByDefault: options.backgroundByDefault,
+        });
+    return {
+        ...baseConfig,
+        git: {
+            ...baseConfig.git,
+            isolationMode: options.isolationMode,
+            trackMarkdownQueues: options.trackMarkdownQueues,
+        },
+        runtime: {
+            ...baseConfig.runtime,
+            provider: options.provider,
+            model: options.model,
+        },
+        agents: {
+            ...baseConfig.agents,
+            selectedBuiltinAgents: options.selectedBuiltinAgents,
+            enabledCategories: options.enabledCategories,
+        },
+        execution: {
+            ...baseConfig.execution,
+            backgroundByDefault: options.backgroundByDefault,
+        },
+    };
+}
+function formatGitignoreGuidance(entries) {
+    return [
+        'Corydora did not modify `.gitignore`.',
+        'Add these entries yourself if you want generated files ignored:',
+        ...entries.map((entry) => `- ${entry}`),
+    ].join('\n');
+}
 export async function runInitCommand(options, ui) {
+    const hasExistingConfig = configExists(options.projectRoot);
+    const existingConfig = hasExistingConfig ? await loadConfig(options.projectRoot) : null;
     const fingerprint = detectProjectFingerprint(options.projectRoot);
     const runtimeProbes = (await probeAvailableRuntimes(options.projectRoot)).filter((probe) => probe.provider !== 'fake');
     const recommendedRuntime = runtimeProbes.find((probe) => probe.recommended)?.provider ??
         runtimeProbes.find((probe) => probe.installed)?.provider ??
         'claude-cli';
+    const detectedBuiltinAgents = selectBuiltinAgents(fingerprint.techLenses);
     const interactive = !options.yes && !options.json && process.stdout.isTTY;
     if (interactive) {
         intro('Corydora init');
@@ -25,15 +82,18 @@ export async function runInitCommand(options, ui) {
         loading.start('Detecting runtimes and project shape');
         loading.stop(`Detected ${runtimeProbes.length} runtimes and ${fingerprint.frameworks.length} framework(s).`);
     }
-    let provider = recommendedRuntime;
-    let model = runtimeProbes.find((probe) => probe.provider === provider)?.models[0] ??
+    let provider = existingConfig?.runtime.provider ?? recommendedRuntime;
+    let model = existingConfig?.runtime.model ??
+        runtimeProbes.find((probe) => probe.provider === provider)?.models[0] ??
         getDefaultConfig({
             provider,
             selectedBuiltinAgents: ['bug-investigator'],
         }).runtime.model;
-    let isolationMode = 'worktree';
-    let trackMarkdownQueues = false;
-    let backgroundByDefault = false;
+    let isolationMode = existingConfig?.git.isolationMode ?? 'worktree';
+    let trackMarkdownQueues = existingConfig?.git.trackMarkdownQueues ?? false;
+    let backgroundByDefault = existingConfig?.execution.backgroundByDefault ?? false;
+    const selectedBuiltinAgents = existingConfig?.agents.selectedBuiltinAgents ?? detectedBuiltinAgents;
+    let enabledCategories = existingConfig?.agents.enabledCategories ?? categoriesForBuiltinAgents(selectedBuiltinAgents);
     if (interactive) {
         const providerSelection = await select({
             message: 'Choose the default runtime',
@@ -70,9 +130,22 @@ export async function runInitCommand(options, ui) {
             throw new Error('Init cancelled.');
         }
         isolationMode = isolationSelection;
+        const categorySelection = await multiselect({
+            message: 'Choose which task categories Corydora may scan for',
+            options: BUILTIN_TASK_CATEGORIES.map((category) => ({
+                value: category,
+                label: category.charAt(0).toUpperCase() + category.slice(1),
+            })),
+            initialValues: enabledCategories,
+            required: true,
+        });
+        if (isCancel(categorySelection)) {
+            throw new Error('Init cancelled.');
+        }
+        enabledCategories = [...categorySelection];
         const trackQueuesAnswer = await confirm({
             message: 'Track markdown queue files in git?',
-            initialValue: false,
+            initialValue: trackMarkdownQueues,
         });
         if (isCancel(trackQueuesAnswer)) {
             throw new Error('Init cancelled.');
@@ -80,30 +153,50 @@ export async function runInitCommand(options, ui) {
         trackMarkdownQueues = Boolean(trackQueuesAnswer);
         const backgroundAnswer = await confirm({
             message: 'Launch long runs in the background by default?',
-            initialValue: false,
+            initialValue: backgroundByDefault,
         });
         if (isCancel(backgroundAnswer)) {
             throw new Error('Init cancelled.');
         }
         backgroundByDefault = Boolean(backgroundAnswer);
     }
-    const config = getDefaultConfig({
+    const config = mergeInitConfig({
+        existingConfig,
         provider,
         model,
         isolationMode,
-        selectedBuiltinAgents: selectBuiltinAgents(fingerprint.techLenses),
         trackMarkdownQueues,
         backgroundByDefault,
+        selectedBuiltinAgents,
+        enabledCategories,
     });
     await saveConfig(options.projectRoot, config);
     await ensureCorydoraStructure(options.projectRoot, config);
-    await ensureGitignoreEntries(options.projectRoot, config.git.trackMarkdownQueues);
+    const missingGitignoreEntries = await findMissingGitignoreEntries(options.projectRoot, config.git.trackMarkdownQueues);
+    let gitignoreUpdated = false;
+    if (interactive && missingGitignoreEntries.length > 0) {
+        const updateGitignoreAnswer = await confirm({
+            message: 'Append recommended Corydora entries to `.gitignore`?',
+            initialValue: false,
+        });
+        if (isCancel(updateGitignoreAnswer)) {
+            throw new Error('Init cancelled.');
+        }
+        if (updateGitignoreAnswer) {
+            gitignoreUpdated = await appendGitignoreEntries(options.projectRoot, missingGitignoreEntries);
+        }
+    }
     const payload = {
         projectRoot: options.projectRoot,
         provider,
         model,
         isolationMode,
+        enabledCategories,
         fingerprint,
+        gitignore: {
+            modified: gitignoreUpdated,
+            missingEntries: gitignoreUpdated ? [] : missingGitignoreEntries,
+        },
     };
     if (options.json) {
         ui.printJson(payload);
@@ -112,6 +205,13 @@ export async function runInitCommand(options, ui) {
     ui.success(`Created ${CONFIG_FILE_NAME} and .corydora/ in ${options.projectRoot}`);
     ui.info(`Default runtime: ${provider} (${model})`);
     ui.info(`Isolation mode: ${isolationMode}`);
+    ui.info(`Categories: ${enabledCategories.join(', ')}`);
+    if (gitignoreUpdated) {
+        ui.info('Appended a Corydora block to `.gitignore`.');
+    }
+    else if (missingGitignoreEntries.length > 0) {
+        ui.warn(formatGitignoreGuidance(missingGitignoreEntries));
+    }
     outro('Corydora init complete.');
 }
 //# sourceMappingURL=init.js.map

package/dist/commands/init.js.map

@@ -1 +1 @@
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package/dist/commands/run.d.ts

@@ -1,3 +1,4 @@
+import type { CorydoraMode } from '../types/domain.js';
 import type { Ui } from '../ui/output.js';
 export interface RunCommandOptions {
     projectRoot: string;
@@ -8,5 +9,7 @@ export interface RunCommandOptions {
     resume?: boolean;
     sessionName?: string;
     skipCommitHooks?: boolean;
+    mode?: CorydoraMode;
+    agentIds?: string[];
 }
 export declare function runRunCommand(options: RunCommandOptions, ui: Ui): Promise<void>;

package/dist/commands/run.js

@@ -1,39 +1,64 @@
 import { basename } from 'node:path';
 import { listAgents } from '../agents/catalog.js';
 import { loadRequiredConfig } from './helpers.js';
-import { discoverCandidateFiles } from '../filesystem/discovery.js';
-import { loadRunState, loadTaskStore } from '../queue/state.js';
+import { loadFileStore, loadTaskStore, reconcileFileStore } from '../queue/state.js';
 import { launchBackgroundRun, supportsTmux } from '../runtime/tmux.js';
 import { runCorydoraSession } from '../runtime/run-session.js';
-import { restoreSchedulerState, selectScanBatch } from '../runtime/scheduler.js';
+import { buildFileQueue, resolveSelectedAgents } from '../runtime/modes.js';
+import { detectProjectFingerprint } from '../filesystem/project.js';
+function nextRunnableTaskTitle(taskStore) {
+    const task = taskStore.tasks.find((candidate) => ['queued', 'deferred'].includes(candidate.status));
+    return task?.title ?? null;
+}
 export async function runRunCommand(options, ui) {
     const config = await loadRequiredConfig(options.projectRoot);
+    const mode = options.mode ?? config.modes.default;
+    const allAgents = await listAgents(options.projectRoot, config);
+    const fingerprint = detectProjectFingerprint(options.projectRoot);
+    const selectedAgents = resolveSelectedAgents({
+        allAgents,
+        config,
+        mode,
+        projectFingerprint: fingerprint,
+        ...(options.agentIds ? { overrideAgentIds: options.agentIds } : {}),
+    });
+    const selectedAgentIds = selectedAgents.map((agent) => agent.id);
     if (options.dryRun) {
-        const [store, runState] = await Promise.all([
+        const [taskStore, existingFileStore] = await Promise.all([
             loadTaskStore(options.projectRoot, config),
-            loadRunState(options.projectRoot, config),
+            loadFileStore(options.projectRoot, config),
         ]);
-        const files = discoverCandidateFiles(options.projectRoot, {
-            includeExtensions: config.scan.includeExtensions,
-            excludeDirectories: config.scan.excludeDirectories,
-        });
-        const scheduler = restoreSchedulerState(runState?.scheduler, files);
-        const nextScanBatch = selectScanBatch(scheduler, files, config.scan.batchSize);
-        const nextTask = store.tasks.find((task) => task.status === 'pending' && (config.scan.allowBroadRisk || task.risk !== 'broad')) ?? null;
+        const fileStore = reconcileFileStore(existingFileStore, buildFileQueue({
+            projectRoot: options.projectRoot,
+            workRoot: options.projectRoot,
+            config,
+            mode,
+            taskStore,
+        }));
+        const nextFiles = fileStore.files
+            .filter((file) => ['queued', 'deferred'].includes(file.status))
+            .sort((left, right) => right.score.total - left.score.total)
+            .slice(0, Math.max(1, config.execution.maxAnalyzeWorkers))
+            .map((file) => file.path);
         const preview = {
             dryRun: true,
             provider: config.runtime.provider,
             model: config.runtime.model,
-            nextScanBatch,
-            nextTask,
+            mode,
+            selectedAgents: selectedAgentIds,
+            nextScanBatch: nextFiles,
+            nextAnalysisBatch: nextFiles,
+            nextTask: nextRunnableTaskTitle(taskStore),
         };
         if (options.json) {
             ui.printJson(preview);
             return;
         }
         ui.info(`Dry run preview for ${config.runtime.provider} (${config.runtime.model})`);
-        ui.info(`Next scan batch: ${nextScanBatch.length > 0 ? nextScanBatch.join(', ') : 'none'}`);
-        ui.info(`Next task: ${nextTask ? nextTask.title : 'none queued'}`);
+        ui.info(`Mode: ${mode}`);
+        ui.info(`Agents: ${selectedAgentIds.join(', ') || 'none selected'}`);
+        ui.info(`Next analysis batch: ${nextFiles.length > 0 ? nextFiles.join(', ') : 'none'}`);
+        ui.info(`Next task: ${preview.nextTask ?? 'none queued'}`);
         return;
     }
     const shouldBackground = !options.foreground && (Boolean(options.background) || config.execution.backgroundByDefault);
@@ -50,8 +75,10 @@ export async function runRunCommand(options, ui) {
             '--foreground',
             '--session-name',
             sessionName,
+            '--mode',
+            mode,
+            ...(selectedAgentIds.length > 0 ? ['--agent', selectedAgentIds.join(',')] : []),
             ...(options.resume ? ['--resume'] : []),
-            ...(options.dryRun ? ['--dry-run'] : []),
             ...(options.skipCommitHooks ? ['--no-verify'] : []),
         ];
         const backgroundLaunch = launchBackgroundRun(sessionName, args, options.projectRoot, config.execution.preventIdleSleep);
@@ -65,13 +92,14 @@ export async function runRunCommand(options, ui) {
         }
         return;
     }
-    const agents = await listAgents(options.projectRoot, config);
     const state = await runCorydoraSession({
         projectRoot: options.projectRoot,
         config,
-        agents,
+        agents: selectedAgents,
         dryRun: Boolean(options.dryRun),
         resume: Boolean(options.resume),
+        mode,
+        selectedAgentIds,
         logToConsole: !options.json,
         skipCommitHooks: Boolean(options.skipCommitHooks),
         ...(options.sessionName ? { sessionName: options.sessionName } : {}),
@@ -82,7 +110,10 @@ export async function runRunCommand(options, ui) {
     }
     ui.success(`Run ${state.runId} finished with status "${state.status}".`);
     ui.info(`Provider: ${state.provider}`);
-    ui.info(`Isolation mode: ${state.isolationMode}`);
+    ui.info(`Configured isolation: ${state.isolationMode}`);
+    ui.info(`Effective isolation: ${state.effectiveIsolationMode}`);
+    ui.info(`Mode: ${state.mode}`);
+    ui.info(`Agents: ${state.selectedAgentIds.join(', ') || 'none selected'}`);
     if (state.branchName) {
         ui.info(`Branch: ${state.branchName}`);
     }

package/dist/commands/run.js.map

@@ -1 +1 @@
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+{"version":3,"file":"run.js","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,sBAAsB,CAAC;AAClD,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAC;AAClD,OAAO,EAAE,aAAa,EAAE,aAAa,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACrF,OAAO,EAAE,mBAAmB,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AACvE,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,qBAAqB,CAAC;AAC5E,OAAO,EAAE,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AAiBpE,SAAS,qBAAqB,CAC5B,SAAoD;IAEpD,MAAM,IAAI,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE,CAC9C,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC,QAAQ,CAAC,SAAS,CAAC,MAAM,CAAC,CAClD,CAAC;IACF,OAAO,IAAI,EAAE,KAAK,IAAI,IAAI,CAAC;AAC7B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,OAA0B,EAAE,EAAM;IACpE,MAAM,MAAM,GAAG,MAAM,kBAAkB,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,IAAI,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC;IAClD,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,OAAO,CAAC,WAAW,EAAE,MAAM,CAAC,CAAC;IAChE,MAAM,WAAW,GAAG,wBAAwB,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAClE,MAAM,cAAc,GAAG,qBAAqB,CAAC;QAC3C,SAAS;QACT,MAAM;QACN,IAAI;QACJ,kBAAkB,EAAE,WAAW;QAC/B,GAAG,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,gBAAgB,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KACpE,CAAC,CAAC;IACH,MAAM,gBAAgB,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IAEjE,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;QACnB,MAAM,CAAC,SAAS,EAAE,iBAAiB,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;YACvD,aAAa,CAAC,OAAO,CAAC,WAAW,EAAE,MAAM,CAAC;YAC1C,aAAa,CAAC,OAAO,CAAC,WAAW,EAAE,MAAM,CAAC;SAC3C,CAAC,CAAC;QACH,MAAM,SAAS,GAAG,kBAAkB,CAClC,iBAAiB,EACjB,cAAc,CAAC;YACb,WAAW,EAAE,OAAO,CAAC,WAAW;YAChC,QAAQ,EAAE,OAAO,CAAC,WAAW;YAC7B,MAAM;YACN,IAAI;YACJ,SAAS;SACV,CAAC,CACH,CAAC;QACF,MAAM,SAAS,GAAG,SAAS,CAAC,KAAK;aAC9B,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;aAC9D,IAAI,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC;aAC3D,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,MAAM,CAAC,SAAS,CAAC,iBAAiB,CAAC,CAAC;aACzD,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAE5B,MAAM,OAAO,GAAG;YACd,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,MAAM,CAAC,OAAO,CAAC,QAAQ;YACjC,KAAK,EAAE,MAAM,CAAC,OAAO,CAAC,KAAK;YAC3B,IAAI;YACJ,cAAc,EAAE,gBAAgB;YAChC,aAAa,EAAE,SAAS;YACxB,iBAAiB,EAAE,SAAS;YAC5B,QAAQ,EAAE,qBAAqB,CAAC,SAAS,CAAC;SAC3C,CAAC;QAEF,IAAI,OAAO,CAAC,IAAI,EAAE,CAAC;YACjB,EAAE,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;YACtB,OAAO;QACT,CAAC;QAED,EAAE,CAAC,IAAI,CAAC,uBAAuB,MAAM,CAAC,OAAO,CAAC,QAAQ,KAAK,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC;QACpF,EAAE,CAAC,IAAI,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC;QACzB,EAAE,CAAC,IAAI,CAAC,WAAW,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,eAAe,EAAE,CAAC,CAAC;QACrE,EAAE,CAAC,IAAI,CAAC,wBAAwB,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;QACxF,EAAE,CAAC,IAAI,CAAC,cAAc,OAAO,CAAC,QAAQ,IAAI,aAAa,EAAE,CAAC,CAAC;QAC3D,OAAO;IACT,CAAC;IAED,MAAM,gBAAgB,GACpB,CAAC,OAAO,CAAC,UAAU,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,MAAM,CAAC,SAAS,CAAC,mBAAmB,CAAC,CAAC;IAE/F,IAAI,gBAAgB,EAAE,CAAC;QACrB,IAAI,CAAC,YAAY,EAAE,EAAE,CAAC;YACpB,MAAM,IAAI,KAAK,CAAC,yDAAyD,CAAC,CAAC;QAC7E,CAAC;QAED,MAAM,WAAW,GACf,OAAO,CAAC,WAAW;YACnB,YAAY,QAAQ,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,kBAAkB,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,EAAE;iBACrF,QAAQ,EAAE;iBACV,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QACjB,MAAM,IAAI,GAAG;YACX,KAAK;YACL,cAAc;YACd,gBAAgB;YAChB,WAAW;YACX,QAAQ;YACR,IAAI;YACJ,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,EAAE,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACvC,GAAG,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;SACpD,CAAC;QACF,MAAM,gBAAgB,GAAG,mBAAmB,CAC1C,WAAW,EACX,IAAI,EACJ,OAAO,CAAC,WAAW,EACnB,MAAM,CAAC,SAAS,CAAC,gBAAgB,CAClC,CAAC;QAEF,IAAI,OAAO,CAAC,IAAI,EAAE,CAAC;YACjB,EAAE,CAAC,SAAS,CAAC,EAAE,UAAU,EAAE,IAAI,EAAE,WAAW,EAAE,SAAS,EAAE,gBAAgB,CAAC,SAAS,EAAE,CAAC,CAAC;YACvF,OAAO;QACT,CAAC;QAED,EAAE,CAAC,OAAO,CAAC,2CAA2C,WAAW,IAAI,CAAC,CAAC;QACvE,IAAI,gBAAgB,CAAC,SAAS,EAAE,CAAC;YAC/B,EAAE,CAAC,IAAI,CAAC,yDAAyD,CAAC,CAAC;QACrE,CAAC;QACD,OAAO;IACT,CAAC;IAED,MAAM,KAAK,GAAG,MAAM,kBAAkB,CAAC;QACrC,WAAW,EAAE,OAAO,CAAC,WAAW;QAChC,MAAM;QACN,MAAM,EAAE,cAAc;QACtB,MAAM,EAAE,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC;QAC/B,MAAM,EAAE,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC;QAC/B,IAAI;QACJ,gBAAgB;QAChB,YAAY,EAAE,CAAC,OAAO,CAAC,IAAI;QAC3B,eAAe,EAAE,OAAO,CAAC,OAAO,CAAC,eAAe,CAAC;QACjD,GAAG,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KACrE,CAAC,CAAC;IAEH,IAAI,OAAO,CAAC,IAAI,EAAE,CAAC;QACjB,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC;QACpB,OAAO;IACT,CAAC;IAED,EAAE,CAAC,OAAO,CAAC,OAAO,KAAK,CAAC,KAAK,0BAA0B,KAAK,CAAC,MAAM,IAAI,CAAC,CAAC;IACzE,EAAE,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC;IACvC,EAAE,CAAC,IAAI,CAAC,yBAAyB,KAAK,CAAC,aAAa,EAAE,CAAC,CAAC;IACxD,EAAE,CAAC,IAAI,CAAC,wBAAwB,KAAK,CAAC,sBAAsB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package/dist/commands/status.js

@@ -1,21 +1,40 @@
-import { countTasksByStatus, loadRunState, loadTaskStore } from '../queue/state.js';
+import { countTasksByStatus, loadFileStore, loadRunState, loadTaskStore } from '../queue/state.js';
 import { loadRequiredConfig } from './helpers.js';
 import { tmuxSessionExists } from '../runtime/tmux.js';
+function nextRetryTimes(taskStore) {
+    return taskStore.tasks
+        .filter((task) => task.nextEligibleAt)
+        .sort((left, right) => (left.nextEligibleAt ?? '').localeCompare(right.nextEligibleAt ?? ''))
+        .slice(0, 3)
+        .map((task) => `${task.id} @ ${task.nextEligibleAt}`);
+}
 export async function runStatusCommand(projectRoot, json, ui) {
     const config = await loadRequiredConfig(projectRoot);
-    const [runState, taskStore] = await Promise.all([
+    const [runState, taskStore, fileStore] = await Promise.all([
         loadRunState(projectRoot, config),
         loadTaskStore(projectRoot, config),
+        loadFileStore(projectRoot, config),
     ]);
     const payload = {
         runState,
         queue: {
-            pending: countTasksByStatus(taskStore, 'pending'),
-            claimed: countTasksByStatus(taskStore, 'claimed'),
+            queued: countTasksByStatus(taskStore, 'queued'),
+            leased: countTasksByStatus(taskStore, 'leased'),
+            applying: countTasksByStatus(taskStore, 'applying'),
+            validating: countTasksByStatus(taskStore, 'validating'),
             done: countTasksByStatus(taskStore, 'done'),
-            failed: countTasksByStatus(taskStore, 'failed'),
+            deferred: countTasksByStatus(taskStore, 'deferred'),
             blocked: countTasksByStatus(taskStore, 'blocked'),
+            manual: countTasksByStatus(taskStore, 'manual'),
+        },
+        files: {
+            queued: fileStore.files.filter((file) => file.status === 'queued').length,
+            leased: fileStore.files.filter((file) => file.status === 'leased').length,
+            analyzed: fileStore.files.filter((file) => file.status === 'analyzed').length,
+            deferred: fileStore.files.filter((file) => file.status === 'deferred').length,
+            manual: fileStore.files.filter((file) => file.status === 'manual').length,
         },
+        nextRetry: nextRetryTimes(taskStore),
         tmuxAttached: runState?.background?.sessionName
             ? tmuxSessionExists(runState.background.sessionName)
             : false,
@@ -30,8 +49,20 @@ export async function runStatusCommand(projectRoot, json, ui) {
     }
     ui.info(`Run: ${runState.runId} (${runState.status})`);
     ui.info(`Phase: ${runState.phase}`);
-    ui.info(`Pending tasks: ${payload.queue.pending}`);
+    ui.info(`Mode: ${runState.mode}`);
+    ui.info(`Queued tasks: ${payload.queue.queued}`);
+    ui.info(`Deferred tasks: ${payload.queue.deferred}`);
     ui.info(`Done tasks: ${payload.queue.done}`);
+    ui.info(`Queued files: ${payload.files.queued}`);
+    ui.info(`Effective isolation: ${runState.effectiveIsolationMode}`);
+    if (payload.nextRetry.length > 0) {
+        ui.info(`Next retries: ${payload.nextRetry.join(', ')}`);
+    }
+    if (runState.workers.length > 0) {
+        ui.info(`Workers: ${runState.workers
+            .map((worker) => `${worker.id}=${worker.status}${worker.details ? `(${worker.details})` : ''}`)
+            .join(', ')}`);
+    }
     if (runState.background?.sessionName) {
         ui.info(`tmux session: ${runState.background.sessionName}`);
         ui.info(`Keep awake: ${runState.background.keepAwake ? 'enabled' : 'disabled'}`);

package/dist/commands/status.js.map

@@ -1 +1 @@
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