corydora 0.3.2 → 1.0.3

package/CHANGELOG.md

@@ -2,6 +2,75 @@
 
 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
+
+- add initial release package and update README with new logo format ([dd696d1](https://github.com/glorioustephan/corydora/commit/dd696d14b8dd5ee2e29d585ac5b288398e7aaecb))
+- **adding caffeine support on macos:** preventing machine from sleeping when preferred ([7838627](https://github.com/glorioustephan/corydora/commit/7838627225526ecb22af6ec744a3fa8e7e405a3e))
+- **cli:** add --no-verify option to skip git commit hooks ([cd9efc3](https://github.com/glorioustephan/corydora/commit/cd9efc3cb7ce7c2168680c495e2638266cdb0a39))
+- **cli:** add --no-verify option to skip git commit hooks ([6fcb797](https://github.com/glorioustephan/corydora/commit/6fcb7977cd2ee2c35728d16ef4b93d7b269f46fc))
+- **cli:** add --no-verify option to skip git commit hooks ([8d27d31](https://github.com/glorioustephan/corydora/commit/8d27d31ec8f6e4639b4a5183912238741e34a51b))
+- **docs and ci:** updating docs infrastructure to work with github actions, adding release-please ([c71da43](https://github.com/glorioustephan/corydora/commit/c71da43b98dcac4f4585e6785492518699018e32))
+- enhance runtime configuration and documentation- Added configurable parameters for request ([7838627](https://github.com/glorioustephan/corydora/commit/7838627225526ecb22af6ec744a3fa8e7e405a3e))
+
+### Bug Fixes
+
+- **cli:** enhancing --version and --help flags ([2b65e59](https://github.com/glorioustephan/corydora/commit/2b65e59c97f656325e2e6cd5434d6556082161dd))
+- **cli:** enhancing --version and --help flags ([1832127](https://github.com/glorioustephan/corydora/commit/1832127f79a75c2f3efc7cb21f27f3c9148ab3c8))
+- **publish.yml:** updating publish.yml and release for CI to format changes ([#9](https://github.com/glorioustephan/corydora/issues/9)) ([332a605](https://github.com/glorioustephan/corydora/commit/332a6057dcfb6b27d3a8c9d887d9ca7282e22e2e))
+- **release-please:** updating process for release-please and use of token ([ba9c804](https://github.com/glorioustephan/corydora/commit/ba9c804ecab3be139a0a31ad79ae4adaf33514e9))
+- **release-please:** updating process for release-please and use of token ([#11](https://github.com/glorioustephan/corydora/issues/11)) ([f994a9a](https://github.com/glorioustephan/corydora/commit/f994a9a49ea5722270e859ffd265bbd8196ec55e))
+- **repository.ts:** adding pre-commit formatting ([1c91029](https://github.com/glorioustephan/corydora/commit/1c91029eadbb699786c7202bc8665b010e90ecc4))
+- **repository.ts:** adding pre-commit formatting ([031e1ce](https://github.com/glorioustephan/corydora/commit/031e1ceec47f7c026efa9857ffa2e62a420574bd))
+- **runtime:** avoid undefined optional flags in rebase conflict resolution ([97bf3e2](https://github.com/glorioustephan/corydora/commit/97bf3e26ff8e236d45cd8ef0a12a0dc4b8b967ba))
+- **utils:** making the todo.md file the catch-all for unknown catgories ([87c89db](https://github.com/glorioustephan/corydora/commit/87c89dbf8b8276f27a993edb173676f15ba14176))
+- **utils:** making the todo.md file the catch-all for unknown catgories ([c304926](https://github.com/glorioustephan/corydora/commit/c30492667217bbec9e460fb50e45f931005cc638))
+
+## [0.3.4](https://github.com/glorioustephan/corydora/compare/corydora-v0.3.3...corydora-v0.3.4) (2026-03-31)
+
+### Bug Fixes
+
+- **release-please:** updating process for release-please and use of token ([#11](https://github.com/glorioustephan/corydora/issues/11)) ([f994a9a](https://github.com/glorioustephan/corydora/commit/f994a9a49ea5722270e859ffd265bbd8196ec55e))
+
+## [0.3.3](https://github.com/glorioustephan/corydora/compare/corydora-v0.3.2...corydora-v0.3.3) (2026-03-31)
+
+### Bug Fixes
+
+- **publish.yml:** updating publish.yml and release for CI to format changes ([#9](https://github.com/glorioustephan/corydora/issues/9)) ([332a605](https://github.com/glorioustephan/corydora/commit/332a6057dcfb6b27d3a8c9d887d9ca7282e22e2e))
+
 ## [0.3.2](https://github.com/glorioustephan/corydora/compare/corydora-v0.3.1...corydora-v0.3.2) (2026-03-31)
 
 ### Bug Fixes

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>
@@ -106,6 +106,21 @@ pnpm check
 
 After feature/fix PRs merge into `main`, generate or refresh the release pull request:
 
+Set one of these tokens before running release planning:
+
+```bash
+export RELEASE_PLEASE_TOKEN=ghp_xxx
+# or:
+# export GITHUB_TOKEN=ghp_xxx
+# export GH_TOKEN=ghp_xxx
+```
+
+Optionally pin the repo explicitly:
+
+```bash
+export RELEASE_PLEASE_REPO_URL=https://github.com/glorioustephan/corydora
+```
+
 ```bash
 pnpm release:plan
 ```
@@ -116,6 +131,14 @@ This uses release-please to:
 - bump `package.json` version
 - update `CHANGELOG.md`
 
+`release:plan` also formats `CHANGELOG.md` after generation.
+
+If formatting or checks fail later, rerun:
+
+```bash
+pnpm release:check
+```
+
 Merge the release PR when ready.
 
 #### 3) Publish
@@ -190,8 +213,8 @@ Before the first public release, configure npm trusted publishing for this repos
    package page and settings exist.
 4. In npm package settings for `corydora`, add a trusted publisher for GitHub Actions with workflow
    filename `publish.yml`.
-5. Optionally add a `RELEASE_PLEASE_TOKEN` GitHub secret if you want bot-created release PRs to
-   trigger other workflows normally.
+5. Add `RELEASE_PLEASE_TOKEN` as a GitHub secret for `glorioustephan/corydora`; release planning and
+   local PR generation use this token and fall back to `GITHUB_TOKEN`/`GH_TOKEN`.
 6. Optionally protect the `npm` GitHub environment before enabling publish.
 7. After trusted publishing is configured, publish future releases by merging the release PR that
    release-please opens against `main`.
@@ -203,7 +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

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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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