codex-orchestrator 0.1.28 → 0.1.29

package/CHANGELOG.md

@@ -6,6 +6,15 @@ The format is based on Keep a Changelog, and this project follows SemVer.
 
 ## [Unreleased]
 
+## [0.1.29] - 2026-05-18
+
+### Added
+- Setup now records a prompt manifest and supports `--sync-prompts` modes for
+  safe prompt refreshes, local-edit preservation, replacement, and appended
+  package updates.
+- Doctor now warns when package prompt updates are available and points users to
+  the setup command that applies safe prompt updates.
+
 ## [0.1.27] - 2026-05-18
 
 ### Changed

package/README.md

@@ -212,6 +212,10 @@ prompts into `.codex-orchestrator/prompts/workflows/`, and the runner reads the
 copied prompt files during `agent:auto` and `agent:plan-auto` runs. Workflow
 `skillName` values in config are descriptive metadata for the workflow role;
 they are not a runtime dependency on the user's local Codex skill directory.
+Setup also writes `.codex-orchestrator/prompts/manifest.json`, which lets later
+setup runs tell apart untouched package prompts from prompts edited by the
+project. By default, setup refreshes untouched prompts and reports conflicts for
+locally edited prompts.
 
 Configured checks run before publication. By default, missing
 `npm run <script>` checks are reported as skipped warnings, not failures. You can
@@ -344,9 +348,14 @@ codex-orchestrator daemon --target <path> [--once] \
 - `--target <path>` - override the target directory, which defaults to the current directory;
 - `--github-owner <owner>` - override the GitHub owner inferred from `origin`;
 - `--github-repo <repo>` - override the GitHub repo inferred from `origin`;
+- `--sync-prompts <auto|keep|replace|merge>` - choose how package-bundled
+  prompt updates are applied. `auto` refreshes untouched prompts and reports
+  local-edit conflicts, `keep` preserves existing prompts, `replace` overwrites
+  with bundled prompts, and `merge` appends bundled updates to locally edited
+  prompts;
 - `--replace-package-skills` - refresh package-bundled prompt files. The flag
-  name is kept for compatibility; it does not install or require local Codex
-  skills.
+  name is kept for compatibility and behaves like `--sync-prompts=replace`; it
+  does not install or require local Codex skills.
 
 Setup does not launch Codex, commit changes, or open pull requests.
 When the target repository already has a `package.json`, setup also adds

package/dist/src/cli.js

@@ -10,6 +10,7 @@ import { runPlanAutoCommand } from './runner/plan-auto-command.js';
 import { runScopedAutoCommand } from './runner/scoped-auto-command.js';
 import { runStatusCommand } from './runner/status-command.js';
 import { runSetupCommand } from './setup/setup-command.js';
+import { promptSyncModes } from './setup/prompt-sync.js';
 const helpText = `codex-orchestrator
 
 Usage:
@@ -17,7 +18,7 @@ Usage:
   codex-orchestrator --version
   codex-orchestrator health
   codex-orchestrator doctor --target <path> [--json]
-  codex-orchestrator setup [--target <path>] [--github-owner <owner>] [--github-repo <repo>] [--dry-run] [--prepare-labels]
+  codex-orchestrator setup [--target <path>] [--github-owner <owner>] [--github-repo <repo>] [--dry-run] [--prepare-labels] [--sync-prompts <mode>]
   codex-orchestrator status --target <path> [--dry-run] [--json]
   codex-orchestrator run --target <path> --issue <number>
   codex-orchestrator daemon --target <path> [--interval-seconds <number>] [--once] [--max-runs <number>]
@@ -33,6 +34,12 @@ Commands:
 Options:
   --help, -h      Show this help.
   --version, -v   Show package version.
+
+Prompt sync modes:
+  --sync-prompts auto      Update untouched prompts and report locally edited conflicts.
+  --sync-prompts keep      Keep existing prompts and install only missing prompts.
+  --sync-prompts replace   Replace prompts with bundled package versions.
+  --sync-prompts merge     Append bundled updates to locally edited prompts.
 `;
 async function main(args) {
     const [command] = args;
@@ -63,6 +70,7 @@ async function main(args) {
                 dryRun: parsed.value.dryRun,
                 prepareLabels: parsed.value.prepareLabels,
                 replacePackageSkills: parsed.value.replacePackageSkills,
+                promptSyncMode: parsed.value.promptSyncMode,
             });
             process.stdout.write(`${result.output}\n`);
             return 0;
@@ -345,6 +353,22 @@ function parseSetupArgs(args) {
             case '--prepare-labels':
                 parsed.prepareLabels = true;
                 break;
+            case '--sync-prompts':
+                if (!next || next.startsWith('--')) {
+                    return { ok: false, error: `${arg} requires a value` };
+                }
+                if (!isPromptSyncMode(next)) {
+                    return { ok: false, error: `${arg} must be one of ${promptSyncModes.join(', ')}` };
+                }
+                parsed.promptSyncMode = next;
+                index += 1;
+                break;
+            case '--sync-prompts=auto':
+            case '--sync-prompts=keep':
+            case '--sync-prompts=replace':
+            case '--sync-prompts=merge':
+                parsed.promptSyncMode = arg.replace('--sync-prompts=', '');
+                break;
             case '--replace-package-skills':
                 parsed.replacePackageSkills = true;
                 break;
@@ -354,6 +378,9 @@ function parseSetupArgs(args) {
     }
     return { ok: true, value: { ...parsed, target: parsed.target ?? process.cwd() } };
 }
+function isPromptSyncMode(value) {
+    return promptSyncModes.includes(value);
+}
 main(process.argv.slice(2))
     .then((exitCode) => {
     process.exitCode = exitCode;

package/dist/src/cli.js.map

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package/dist/src/runner/doctor-command.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor-command.d.ts","sourceRoot":"","sources":["../../../src/runner/doctor-command.ts"],"names":[],"mappings":"AAKA,OAAO,EAA4B,KAAK,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAC9G,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAE7D,OAAO,EAA+B,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAG/F,MAAM,MAAM,iBAAiB,GAAG,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;AAEzD,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,iBAAiB,CAAC;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,CAAC,CAAC;IACX,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACtC,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACtD,IAAI,EAAE,iBAAiB,EAAE,CAAC;IAC1B,IAAI,EAAE,iBAAiB,EAAE,CAAC;IAC1B,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,YAAY,CAAC,EAAE,kBAAkB,CAAC;IAClC,aAAa,CAAC,EAAE,oBAAoB,CAAC;IACrC,eAAe,CAAC,EAAE,yBAAyB,CAAC;CAC7C;AAED,MAAM,WAAW,mBAAmB;IAClC,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,mBAAmB,CAAC,CAwBlG"}
+{"version":3,"file":"doctor-command.d.ts","sourceRoot":"","sources":["../../../src/runner/doctor-command.ts"],"names":[],"mappings":"AAKA,OAAO,EAA4B,KAAK,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAC9G,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAG7D,OAAO,EAA+B,KAAK,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAG/F,MAAM,MAAM,iBAAiB,GAAG,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;AAEzD,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,iBAAiB,CAAC;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,CAAC,CAAC;IACX,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACtC,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IACtD,IAAI,EAAE,iBAAiB,EAAE,CAAC;IAC1B,IAAI,EAAE,iBAAiB,EAAE,CAAC;IAC1B,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,YAAY,CAAC,EAAE,kBAAkB,CAAC;IAClC,aAAa,CAAC,EAAE,oBAAoB,CAAC;IACrC,eAAe,CAAC,EAAE,yBAAyB,CAAC;CAC7C;AAED,MAAM,WAAW,mBAAmB;IAClC,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,mBAAmB,CAAC,CAwBlG"}

package/dist/src/runner/doctor-command.js

@@ -3,6 +3,7 @@ import { resolve } from 'node:path';
 import { codexPhaseKeys } from '../config/schema.js';
 import { resolveExecutableCommand } from '../setup/codex-command-resolver.js';
 import { GhCliLabelAdapter } from '../setup/github-label-adapter.js';
+import { checkPromptFiles } from '../setup/prompt-sync.js';
 import { defaultShellCommandExecutor } from '../process/command.js';
 import { readRunnerConfig } from './command-utils.js';
 export async function runDoctorCommand(options) {
@@ -37,6 +38,7 @@ async function collectReadinessChecks(targetRoot, config, labelAdapter, shellExe
     checks.push(await checkPath(targetRoot, 'target', 'Target directory'));
     checks.push(await checkPath(resolve(targetRoot, config.runner.stateDir), 'state-dir', 'Runner state directory', 'warn'));
     checks.push(await checkPath(resolve(targetRoot, config.runner.workspaceRoot), 'workspace-root', 'Runner workspace root', 'warn'));
+    checks.push(await checkPromptUpdates(targetRoot));
     checks.push(await checkCommand(commandResolver, config.codex.command, 'codex-command', 'Codex command'));
     checks.push(...await checkProfileCommands(config, commandResolver));
     checks.push(check('configured-checks', 'Configured checks', Object.keys(config.checks).length > 0 ? 'pass' : 'warn', Object.keys(config.checks).length > 0 ? `${Object.keys(config.checks).length} check(s) configured` : 'no configured checks'));
@@ -46,6 +48,17 @@ async function collectReadinessChecks(targetRoot, config, labelAdapter, shellExe
         : 'visual proof gate is disabled'));
     return checks;
 }
+async function checkPromptUpdates(targetRoot) {
+    const result = await checkPromptFiles(targetRoot);
+    const pending = result.installed.length + result.updated.length + result.conflicts.length;
+    if (pending === 0) {
+        return check('prompt-sync', 'Prompt sync', 'pass', 'project prompts match bundled package prompts');
+    }
+    return check('prompt-sync', 'Prompt sync', 'warn', `prompt updates available: ${result.installed.length} missing, ${result.updated.length} safe update(s), ${result.conflicts.length} conflict(s)`, [
+        'Run codex-orchestrator setup --sync-prompts=auto to apply safe prompt updates.',
+        'Use --sync-prompts=replace to overwrite local prompt edits with bundled prompts.',
+    ]);
+}
 async function checkProfileCommands(config, commandResolver) {
     const checks = [];
     for (const phase of codexPhaseKeys) {

package/dist/src/runner/doctor-command.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor-command.js","sourceRoot":"","sources":["../../../src/runner/doctor-command.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AACrD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,wBAAwB,EAAkC,MAAM,oCAAoC,CAAC;AAE9G,OAAO,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,2BAA2B,EAA6B,MAAM,uBAAuB,CAAC;AAC/F,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAoCtD,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,OAA6B;IAClE,MAAM,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;IAC/C,MAAM,MAAM,GAAwB,EAAE,CAAC;IACvC,IAAI,MAA2C,CAAC;IAEhD,IAAI,CAAC;QACH,MAAM,GAAG,MAAM,gBAAgB,CAAC,UAAU,CAAC,CAAC;QAC5C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,iBAAiB,CAAC,CAAC,CAAC;IACpE,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC;IAC/G,CAAC;IAED,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,aAAa,GAAG,OAAO,CAAC,aAAa,IAAI,2BAA2B,CAAC;QAC3E,MAAM,eAAe,GAAG,OAAO,CAAC,eAAe,IAAI,wBAAwB,CAAC;QAC5E,MAAM,YAAY,GAAG,OAAO,CAAC,YAAY,IAAI,IAAI,iBAAiB,CAAC,MAAM,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAC5G,MAAM,CAAC,IAAI,CAAC,GAAG,MAAM,sBAAsB,CAAC,UAAU,EAAE,MAAM,EAAE,YAAY,EAAE,aAAa,EAAE,eAAe,CAAC,CAAC,CAAC;IACjH,CAAC;IAED,MAAM,IAAI,GAAG,eAAe,CAAC,UAAU,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;IACzD,OAAO;QACL,MAAM,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,IAAI,CAAC;QAC7E,IAAI;KACL,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,sBAAsB,CACnC,UAAkB,EAClB,MAA+B,EAC/B,YAAgC,EAChC,aAAmC,EACnC,eAA0C;IAE1C,MAAM,MAAM,GAAwB,EAAE,CAAC;IACvC,MAAM,CAAC,IAAI,CAAC,MAAM,YAAY,CAAC,eAAe,EAAE,KAAK,EAAE,KAAK,EAAE,aAAa,CAAC,CAAC,CAAC;IAC9E,MAAM,CAAC,IAAI,CAAC,MAAM,UAAU,CAAC,aAAa,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,qCAAqC,EAAE,UAAU,CAAC,CAAC,CAAC;IACpI,MAAM,CAAC,IAAI,CAAC,MAAM,UAAU,CAC1B,aAAa,EACb,aAAa,EACb,aAAa,EACb,0BAA0B,UAAU,CAAC,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,EAC5D,UAAU,CACX,CAAC,CAAC;IACH,MAAM,CAAC,IAAI,CAAC,MAAM,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAC7G,MAAM,CAAC,IAAI,CAAC,MAAM,SAAS,CAAC,UAAU,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC,CAAC;IACvE,MAAM,CAAC,IAAI,CAAC,MAAM,SAAS,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,WAAW,EAAE,wBAAwB,EAAE,MAAM,CAAC,CAAC,CAAC;IACzH,MAAM,CAAC,IAAI,CAAC,MAAM,SAAS,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,aAAa,CAAC,EAAE,gBAAgB,EAAE,uBAAuB,EAAE,MAAM,CAAC,CAAC,CAAC;IAClI,MAAM,CAAC,IAAI,CAAC,MAAM,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC;IAClD,MAAM,CAAC,IAAI,CAAC,MAAM,YAAY,CAAC,eAAe,EAAE,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,eAAe,EAAE,eAAe,CAAC,CAAC,CAAC;IACzG,MAAM,CAAC,IAAI,CAAC,GAAG,MAAM,oBAAoB,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC,CAAC;IACpE,MAAM,CAAC,IAAI,CAAC,KAAK,CACf,mBAAmB,EACnB,mBAAmB,EACnB,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EACvD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,MAAM,sBAAsB,CAAC,CAAC,CAAC,sBAAsB,CAC5H,CAAC,CAAC;IACH,MAAM,CAAC,IAAI,CAAC,KAAK,CACf,gBAAgB,EAChB,gBAAgB,EAChB,MAAM,EACN,qFAAqF,CACtF,CAAC,CAAC;IACH,MAAM,CAAC,IAAI,CAAC,KAAK,CACf,cAAc,EACd,4BAA4B,EAC5B,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,uBAAuB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EACnH,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,OAAO;QACpC,CAAC,CAAC,8BAA8B;QAChC,CAAC,CAAC,+BAA+B,CACpC,CAAC,CAAC;IACH,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,KAAK,UAAU,kBAAkB,CAAC,UAAkB;IAClD,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,UAAU,CAAC,CAAC;IAClD,MAAM,OAAO,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IAC1F,IAAI,OAAO,KAAK,CAAC,EAAE,CAAC;QAClB,OAAO,KAAK,CAAC,aAAa,EAAE,aAAa,EAAE,MAAM,EAAE,+CAA+C,CAAC,CAAC;IACtG,CAAC;IAED,OAAO,KAAK,CACV,aAAa,EACb,aAAa,EACb,MAAM,EACN,6BAA6B,MAAM,CAAC,SAAS,CAAC,MAAM,aAAa,MAAM,CAAC,OAAO,CAAC,MAAM,oBAAoB,MAAM,CAAC,SAAS,CAAC,MAAM,cAAc,EAC/I;QACE,gFAAgF;QAChF,kFAAkF;KACnF,CACF,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,oBAAoB,CACjC,MAA+B,EAC/B,eAA0C;IAE1C,MAAM,MAAM,GAAwB,EAAE,CAAC;IACvC,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE,CAAC;QACnC,MAAM,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,EAAE,OAAO,CAAC;QACxD,IAAI,CAAC,OAAO,IAAI,OAAO,KAAK,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC;YACjD,SAAS;QACX,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,MAAM,YAAY,CAAC,eAAe,EAAE,OAAO,EAAE,iBAAiB,KAAK,EAAE,EAAE,iBAAiB,KAAK,EAAE,CAAC,CAAC,CAAC;IAChH,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,KAAK,UAAU,WAAW,CAAC,OAA2B,EAAE,cAAwB;IAC9E,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,UAAU,EAAE,CAAC;QAC1C,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5D,MAAM,OAAO,GAAG,cAAc,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;QACvE,OAAO,KAAK,CACV,eAAe,EACf,eAAe,EACf,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,C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package/dist/src/setup/prompt-sync.d.ts

@@ -0,0 +1,13 @@
+export declare const promptSyncModes: readonly ["auto", "keep", "replace", "merge"];
+export type PromptSyncMode = (typeof promptSyncModes)[number];
+export interface PromptSyncResult {
+    manifestPath: string;
+    installed: string[];
+    updated: string[];
+    preserved: string[];
+    conflicts: string[];
+}
+export declare function promptManifestPath(targetRoot: string): string;
+export declare function checkPromptFiles(targetRoot: string, mode?: PromptSyncMode): Promise<PromptSyncResult>;
+export declare function syncPromptFiles(targetRoot: string, mode: PromptSyncMode): Promise<PromptSyncResult>;
+//# sourceMappingURL=prompt-sync.d.ts.map

package/dist/src/setup/prompt-sync.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/setup/prompt-sync.js

@@ -0,0 +1,219 @@
+import { createHash } from 'node:crypto';
+import { cp, mkdir, readFile, writeFile } from 'node:fs/promises';
+import { dirname, join } from 'node:path';
+import { readPackageInfo } from '../package-info.js';
+import { workflowDefinitions } from './workflows.js';
+export const promptSyncModes = ['auto', 'keep', 'replace', 'merge'];
+export function promptManifestPath(targetRoot) {
+    return join(targetRoot, '.codex-orchestrator', 'prompts', 'manifest.json');
+}
+export async function checkPromptFiles(targetRoot, mode = 'auto') {
+    return visitPromptFiles(targetRoot, mode, false);
+}
+export async function syncPromptFiles(targetRoot, mode) {
+    return visitPromptFiles(targetRoot, mode, true);
+}
+async function visitPromptFiles(targetRoot, mode, write) {
+    const packageInfo = await readPackageInfo();
+    const manifestPath = promptManifestPath(targetRoot);
+    const manifest = await readPromptManifest(manifestPath, packageInfo.name, packageInfo.version);
+    const result = {
+        manifestPath,
+        installed: [],
+        updated: [],
+        preserved: [],
+        conflicts: [],
+    };
+    for (const definition of promptDefinitions()) {
+        const destination = join(targetRoot, definition.destinationRelativePath);
+        const source = new URL(`../../../prompts/${definition.sourceRelativePath}`, import.meta.url);
+        const packageContent = await readFile(source, 'utf8');
+        const packageHash = sha256(packageContent);
+        const existingContent = await readOptionalFile(destination);
+        const existingHash = existingContent === undefined ? undefined : sha256(existingContent);
+        const entry = manifest.prompts[definition.manifestKey];
+        if (mode === 'replace' || existingContent === undefined) {
+            if (write) {
+                await mkdir(dirname(destination), { recursive: true });
+                await cp(source, destination, { force: true });
+            }
+            manifest.prompts[definition.manifestKey] = manifestEntry(packageHash, packageInfo.version);
+            result[existingContent === undefined ? 'installed' : 'updated'].push(definition.manifestKey);
+            continue;
+        }
+        if (existingHash === packageHash) {
+            manifest.prompts[definition.manifestKey] = manifestEntry(packageHash, packageInfo.version);
+            result.preserved.push(definition.manifestKey);
+            continue;
+        }
+        if (!entry) {
+            if (mode === 'merge') {
+                manifest.prompts[definition.manifestKey] = await mergePromptUpdate({
+                    destination,
+                    existingContent,
+                    packageContent,
+                    packageHash,
+                    packageVersion: packageInfo.version,
+                    promptKey: definition.manifestKey,
+                    write,
+                });
+                result.updated.push(definition.manifestKey);
+            }
+            else if (mode === 'keep') {
+                result.preserved.push(definition.manifestKey);
+                manifest.prompts[definition.manifestKey] = manifestEntry(packageHash, packageInfo.version);
+            }
+            else {
+                result.conflicts.push(definition.manifestKey);
+                manifest.prompts[definition.manifestKey] = {
+                    ...manifestEntry(packageHash, packageInfo.version),
+                    conflict: true,
+                };
+            }
+            continue;
+        }
+        if (entry.conflict) {
+            if (mode === 'merge') {
+                manifest.prompts[definition.manifestKey] = await mergePromptUpdate({
+                    destination,
+                    existingContent,
+                    packageContent,
+                    packageHash,
+                    packageVersion: packageInfo.version,
+                    promptKey: definition.manifestKey,
+                    write,
+                });
+                result.updated.push(definition.manifestKey);
+            }
+            else if (mode === 'keep') {
+                result.preserved.push(definition.manifestKey);
+            }
+            else {
+                result.conflicts.push(definition.manifestKey);
+            }
+            continue;
+        }
+        const installedHash = entry?.installedHash ?? packageHash;
+        const previousPackageHash = entry?.packageHash ?? packageHash;
+        const localModified = existingHash !== installedHash;
+        const packageChanged = previousPackageHash !== packageHash;
+        const canAutoUpdate = !localModified && (mode === 'auto' || mode === 'merge');
+        if (canAutoUpdate) {
+            if (write) {
+                await writeFile(destination, packageContent, 'utf8');
+            }
+            manifest.prompts[definition.manifestKey] = manifestEntry(packageHash, packageInfo.version);
+            result.updated.push(definition.manifestKey);
+            continue;
+        }
+        if (localModified && packageChanged && mode === 'merge') {
+            manifest.prompts[definition.manifestKey] = await mergePromptUpdate({
+                destination,
+                existingContent,
+                packageContent,
+                packageHash,
+                packageVersion: packageInfo.version,
+                promptKey: definition.manifestKey,
+                write,
+            });
+            result.updated.push(definition.manifestKey);
+            continue;
+        }
+        if (localModified && packageChanged && mode === 'auto') {
+            result.conflicts.push(definition.manifestKey);
+        }
+        else {
+            result.preserved.push(definition.manifestKey);
+        }
+        manifest.prompts[definition.manifestKey] = {
+            installedHash,
+            packageHash,
+            packageVersion: packageInfo.version,
+        };
+    }
+    if (write) {
+        await mkdir(dirname(manifestPath), { recursive: true });
+        await writeFile(manifestPath, `${JSON.stringify(manifest, null, 2)}\n`, 'utf8');
+    }
+    return result;
+}
+async function readPromptManifest(path, packageName, packageVersion) {
+    try {
+        const content = await readFile(path, 'utf8');
+        const parsed = JSON.parse(content);
+        if (parsed.version === 1 && typeof parsed.prompts === 'object' && parsed.prompts !== null) {
+            return {
+                version: 1,
+                packageName,
+                packageVersion,
+                prompts: parsed.prompts,
+            };
+        }
+    }
+    catch (error) {
+        if (!(error instanceof Error && 'code' in error && error.code === 'ENOENT')) {
+            throw error;
+        }
+    }
+    return { version: 1, packageName, packageVersion, prompts: {} };
+}
+async function readOptionalFile(path) {
+    try {
+        return await readFile(path, 'utf8');
+    }
+    catch (error) {
+        if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {
+            return undefined;
+        }
+        throw error;
+    }
+}
+function promptDefinitions() {
+    return [
+        {
+            sourceRelativePath: 'setup-skill.md',
+            destinationRelativePath: '.codex-orchestrator/prompts/setup-skill.md',
+            manifestKey: 'setup-skill.md',
+        },
+        ...workflowDefinitions.map((definition) => {
+            const name = definition.promptPath.replace('.codex-orchestrator/prompts/', '');
+            return {
+                sourceRelativePath: name,
+                destinationRelativePath: definition.promptPath,
+                manifestKey: name,
+            };
+        }),
+    ];
+}
+function manifestEntry(packageHash, packageVersion) {
+    return {
+        installedHash: packageHash,
+        packageHash,
+        packageVersion,
+    };
+}
+async function mergePromptUpdate(input) {
+    const mergedContent = appendPackagePromptUpdate(input.existingContent, input.promptKey, input.packageVersion, input.packageContent);
+    if (input.write) {
+        await writeFile(input.destination, mergedContent, 'utf8');
+    }
+    return {
+        installedHash: sha256(mergedContent),
+        packageHash: input.packageHash,
+        packageVersion: input.packageVersion,
+    };
+}
+function appendPackagePromptUpdate(existingContent, promptKey, packageVersion, packageContent) {
+    return [
+        existingContent.trimEnd(),
+        '',
+        `<!-- codex-orchestrator package prompt update: ${promptKey} @ ${packageVersion} -->`,
+        packageContent.trimEnd(),
+        `<!-- end codex-orchestrator package prompt update: ${promptKey} @ ${packageVersion} -->`,
+        '',
+    ].join('\n');
+}
+function sha256(value) {
+    return createHash('sha256').update(value).digest('hex');
+}
+//# sourceMappingURL=prompt-sync.js.map

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package/dist/src/setup/setup-command.d.ts

@@ -1,6 +1,7 @@
 import type { CodexOrchestratorConfig } from '../config/schema.js';
 import { type CodexCommandResolver } from './codex-command-resolver.js';
 import type { GitHubLabelAdapter, LabelPlan } from './labels.js';
+import { type PromptSyncMode, type PromptSyncResult } from './prompt-sync.js';
 export interface SetupCommandOptions {
     targetRoot: string;
     githubOwner?: string;
@@ -8,6 +9,7 @@ export interface SetupCommandOptions {
     dryRun?: boolean;
     prepareLabels?: boolean;
     replacePackageSkills?: boolean;
+    promptSyncMode?: PromptSyncMode;
     labelAdapter?: GitHubLabelAdapter;
     codexCommandResolver?: CodexCommandResolver;
 }
@@ -17,6 +19,7 @@ export interface SetupCommandResult {
     dryRun: boolean;
     labelPlan: LabelPlan;
     promptFiles: string[];
+    promptSync?: PromptSyncResult;
     output: string;
 }
 export declare function runSetupCommand(options: SetupCommandOptions): Promise<SetupCommandResult>;

package/dist/src/setup/setup-command.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"setup-command.d.ts","sourceRoot":"","sources":["../../../src/setup/setup-command.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,qBAAqB,CAAC;AAEnE,OAAO,EAAuB,KAAK,oBAAoB,EAAE,MAAM,6BAA6B,CAAC;AAE7F,OAAO,KAAK,EAAE,kBAAkB,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAcjE,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,YAAY,CAAC,EAAE,kBAAkB,CAAC;IAClC,oBAAoB,CAAC,EAAE,oBAAoB,CAAC;CAC7C;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,uBAAuB,CAAC;IAChC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,OAAO,CAAC;IAChB,SAAS,EAAE,SAAS,CAAC;IACrB,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,wBAAsB,eAAe,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAqD/F"}
+{"version":3,"file":"setup-command.d.ts","sourceRoot":"","sources":["../../../src/setup/setup-command.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,qBAAqB,CAAC;AAEnE,OAAO,EAAuB,KAAK,oBAAoB,EAAE,MAAM,6BAA6B,CAAC;AAE7F,OAAO,KAAK,EAAE,kBAAkB,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAUjE,OAAO,EAAqC,KAAK,cAAc,EAAE,KAAK,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAKjH,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,cAAc,CAAC,EAAE,cAAc,CAAC;IAChC,YAAY,CAAC,EAAE,kBAAkB,CAAC;IAClC,oBAAoB,CAAC,EAAE,oBAAoB,CAAC;CAC7C;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,uBAAuB,CAAC;IAChC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,OAAO,CAAC;IAChB,SAAS,EAAE,SAAS,CAAC;IACrB,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,wBAAsB,eAAe,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,kBAAkB,CAAC,CA0D/F"}

package/dist/src/setup/setup-command.js

@@ -1,12 +1,13 @@
 import { execFile } from 'node:child_process';
-import { cp, mkdir, readFile, writeFile } from 'node:fs/promises';
-import { dirname, join } from 'node:path';
+import { readFile, writeFile } from 'node:fs/promises';
+import { join } from 'node:path';
 import { promisify } from 'node:util';
 import { validateConfig } from '../config/schema.js';
 import { resolveCodexCommand } from './codex-command-resolver.js';
 import { GhCliLabelAdapter } from './github-label-adapter.js';
 import { planLabels } from './labels.js';
 import { assertNoRuntimeState, buildProjectConfig, mergeExistingProjectConfig, projectConfigPath, readExistingConfig, writeProjectConfig, } from './project-config.js';
+import { checkPromptFiles, syncPromptFiles } from './prompt-sync.js';
 import { resolveWorkflowConfigs, workflowDefinitions } from './workflows.js';
 const execFileAsync = promisify(execFile);
 export async function runSetupCommand(options) {
@@ -38,19 +39,25 @@ export async function runSetupCommand(options) {
     const adapter = options.labelAdapter ?? new GhCliLabelAdapter(owner, repo);
     const labelPlan = await planLabels(adapter, config.github.labels, prepareLabels, dryRun);
     const promptFiles = workflowDefinitions.map((definition) => join(options.targetRoot, definition.promptPath));
-    if (!dryRun) {
+    const promptSyncMode = options.promptSyncMode ?? (options.replacePackageSkills ? 'replace' : 'auto');
+    let promptSync;
+    if (dryRun) {
+        promptSync = await checkPromptFiles(options.targetRoot, promptSyncMode);
+    }
+    else {
         await writeProjectConfig(options.targetRoot, config);
-        await copyPromptFiles(options.targetRoot, options.replacePackageSkills ?? false);
+        promptSync = await syncPromptFiles(options.targetRoot, promptSyncMode);
         await ensureRuntimeGitignoreEntries(options.targetRoot, config);
         await ensurePackageScripts(options.targetRoot);
     }
-    const output = formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun);
+    const output = formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun, promptSync);
     return {
         config,
         configPath,
         dryRun,
         labelPlan,
         promptFiles,
+        promptSync,
         output,
     };
 }
@@ -138,7 +145,7 @@ function normalizeExistingGitignoreLine(line) {
     }
     return gitignoreDirectory(trimmed);
 }
-function formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun) {
+function formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun, promptSync) {
     const workflowLines = Object.entries(config.workflows)
         .map(([id, workflow]) => `  - ${id}: ${workflow.source}`)
         .join('\n');
@@ -153,6 +160,7 @@ function formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun) {
         workflowLines,
         'prompts:',
         promptSummary,
+        formatPromptSync(promptSync),
         `checks: ${Object.keys(config.checks).join(', ')}`,
         `gitignore runtime entries: ${runtimeGitignoreEntries(config).join(', ')}`,
         `codex command: ${config.codex.command} ${config.codex.args.join(' ')}`,
@@ -162,31 +170,19 @@ function formatSetupOutput(configPath, labelPlan, config, promptFiles, dryRun) {
         'setup will not commit or open a pull request',
     ].join('\n');
 }
-async function copyPromptFiles(targetRoot, replacePackageSkills) {
-    await copyPrompt('setup-skill.md', join(targetRoot, '.codex-orchestrator', 'prompts', 'setup-skill.md'), replacePackageSkills);
-    for (const definition of workflowDefinitions) {
-        const sourceName = definition.promptPath.replace('.codex-orchestrator/prompts/workflows/', '');
-        await copyPrompt(join('workflows', sourceName), join(targetRoot, definition.promptPath), replacePackageSkills);
+function formatPromptSync(promptSync) {
+    if (!promptSync) {
+        return 'prompt sync: dry-run';
     }
-}
-async function copyPrompt(relativePromptPath, destination, replacePackageSkills) {
-    await mkdir(dirname(destination), { recursive: true });
-    const source = new URL(`../../../prompts/${relativePromptPath}`, import.meta.url);
-    if (replacePackageSkills) {
-        await cp(source, destination, { force: true });
-        return;
-    }
-    try {
-        await readFile(destination, 'utf8');
-    }
-    catch (error) {
-        if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {
-            const content = await readFile(source, 'utf8');
-            await writeFile(destination, content, 'utf8');
-            return;
-        }
-        throw error;
+    const line = `prompt sync: ${promptSync.installed.length} installed, ${promptSync.updated.length} updated, ${promptSync.preserved.length} preserved, ${promptSync.conflicts.length} conflict`;
+    if (promptSync.conflicts.length === 0) {
+        return line;
     }
+    return [
+        line,
+        `prompt conflicts: ${promptSync.conflicts.join(', ')}`,
+        'Run setup --sync-prompts=merge or --sync-prompts=replace to resolve package prompt updates.',
+    ].join('\n');
 }
 function readExistingString(config, section, key) {
     const sectionValue = config?.[section];

package/dist/src/setup/setup-command.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "codex-orchestrator",
-  "version": "0.1.28",
+  "version": "0.1.29",
   "description": "Reusable GitHub Issues runner for Codex.",
   "type": "module",
   "license": "MIT",