jumbo-cli 3.13.0 → 3.14.0

package/dist/infrastructure/context/project/init/AgentFileProtocol.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"AgentFileProtocol.d.ts","sourceRoot":"","sources":["../../../../../src/infrastructure/context/project/init/AgentFileProtocol.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAKH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,MAAM,gEAAgE,CAAC;AACzG,OAAO,EAAE,kBAAkB,EAAE,MAAM,oEAAoE,CAAC;AACxG,OAAO,EAAE,iBAAiB,EAAE,MAAM,mEAAmE,CAAC;AAyBtG,qBAAa,iBAAkB,YAAW,kBAAkB;IAU9C,OAAO,CAAC,QAAQ,CAAC,kBAAkB;IAT/C,OAAO,CAAC,QAAQ,CAAC,WAAW,CAO1B;gBAE2B,kBAAkB,GAAE,MAAqC;IAEtF;;OAEG;IACG,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBvD;;OAEG;IACG,cAAc,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBxD;;OAEG;IACG,yBAAyB,CAC7B,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,IAAI,CAAC;IAQhB;;OAEG;IACG,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBvD;;OAEG;IACG,cAAc,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBxD;;OAEG;IACG,yBAAyB,CAC7B,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,IAAI,CAAC;IAYhB,kBAAkB,IAAI,SAAS,cAAc,EAAE;IAI/C;;OAEG;IACG,qBAAqB,CACzB,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,iBAAiB,EAAE,CAAC;YA+BjB,0BAA0B;YAiC1B,yBAAyB;YAkCzB,0BAA0B;YA8B1B,qBAAqB;IAanC,OAAO,CAAC,cAAc;IAStB,OAAO,CAAC,iBAAiB;CAW1B"}
+{"version":3,"file":"AgentFileProtocol.d.ts","sourceRoot":"","sources":["../../../../../src/infrastructure/context/project/init/AgentFileProtocol.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAKH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,MAAM,gEAAgE,CAAC;AACzG,OAAO,EAAE,kBAAkB,EAAE,MAAM,oEAAoE,CAAC;AACxG,OAAO,EAAE,iBAAiB,EAAE,MAAM,mEAAmE,CAAC;AAwBtG,qBAAa,iBAAkB,YAAW,kBAAkB;IAG9C,OAAO,CAAC,QAAQ,CAAC,kBAAkB;IAF/C,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAgB;gBAEf,kBAAkB,GAAE,MAAqC;IAWtF;;OAEG;IACG,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBvD;;OAEG;IACG,cAAc,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBxD;;OAEG;IACG,yBAAyB,CAC7B,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,IAAI,CAAC;IAQhB;;OAEG;IACG,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBvD;;OAEG;IACG,cAAc,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAyBxD;;OAEG;IACG,yBAAyB,CAC7B,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,IAAI,CAAC;IAYhB,kBAAkB,IAAI,SAAS,cAAc,EAAE;IAI/C;;OAEG;IACG,qBAAqB,CACzB,WAAW,EAAE,MAAM,EACnB,gBAAgB,CAAC,EAAE,SAAS,OAAO,EAAE,GACpC,OAAO,CAAC,iBAAiB,EAAE,CAAC;YA+BjB,0BAA0B;YAiC1B,yBAAyB;YAkCzB,0BAA0B;YA8B1B,qBAAqB;IAanC,OAAO,CAAC,cAAc;IAStB,OAAO,CAAC,iBAAiB;CAW1B"}

package/dist/infrastructure/context/project/init/AgentFileProtocol.js

@@ -34,7 +34,7 @@ export class AgentFileProtocol {
             new GeminiConfigurer(),
             new CopilotConfigurer(),
             new VibeConfigurer(),
-            new CodexConfigurer(),
+            new CodexConfigurer(templateSkillsRoot),
             new CursorConfigurer(),
         ];
     }

package/dist/infrastructure/context/project/init/AgentFileProtocol.js.map

@@ -1 +1 @@
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package/dist/infrastructure/context/project/init/CodexConfigurer.d.ts

@@ -3,9 +3,12 @@
  *
  * Encapsulates all knowledge about OpenAI Codex configuration:
  * - .codex/hooks.json with Codex lifecycle hooks
- * - Skills distributed to .codex/skills
+ * - Skills distributed to .agents/skills
+ * - Cleanup of obsolete Jumbo-managed skill copies under .codex/skills
  *
  * Codex reads AGENTS.md natively, so no instruction file is needed.
+ * Codex reads repo skills from .agents/skills and repo hooks from
+ * the trusted project .codex configuration layer.
  * Codex hooks parse JSON stdout as hook-control envelopes, so Jumbo
  * lifecycle commands use text output to avoid parser conflicts.
  *
@@ -14,11 +17,13 @@
 import { IConfigurer } from "./IConfigurer.js";
 import { PlannedFileChange } from "../../../../application/context/project/init/PlannedFileChange.js";
 export declare class CodexConfigurer implements IConfigurer {
+    private readonly templateSkillsRoot;
     readonly agent: {
         readonly id: "codex";
         readonly name: "Codex";
     };
-    readonly skillPlatforms: readonly [".codex/skills"];
+    readonly skillPlatforms: readonly [".agents/skills"];
+    constructor(templateSkillsRoot: string);
     /**
      * Configure all OpenAI Codex requirements for Jumbo.
      * Codex reads AGENTS.md natively; lifecycle hooks are configured
@@ -28,17 +33,39 @@ export declare class CodexConfigurer implements IConfigurer {
      */
     configure(projectRoot: string): Promise<void>;
     /**
-     * Repair Codex configuration by replacing stale Jumbo hook commands.
+     * Repair Codex configuration by replacing stale Jumbo hook commands
+     * and cleaning obsolete Jumbo-managed skill copies.
      */
     repair(projectRoot: string): Promise<void>;
     private ensureCodexHooks;
+    private mergeJumboHooks;
+    private ensureTrailingNewline;
     private getJumboHooks;
-    private mergeHooks;
-    private mergeMatcherGroups;
-    private mergeHookArray;
-    private removeStaleJumboHooks;
-    private removeStaleJumboHooksFromMatcher;
-    private isJumboLifecycleHook;
+    private isJsonObject;
+    private replaceStaleJumboCommandValues;
+    private addMissingJumboHooks;
+    private addMissingJumboMatcherGroupHook;
+    private hasSameHookCommand;
+    private parseCodexHooksDocument;
+    private applyJsoncEdit;
+    /**
+     * Remove Jumbo-managed skill copies from the obsolete .codex/skills
+     * location now that Codex reads repo skills from .agents/skills.
+     */
+    private removeObsoleteManagedSkillCopies;
+    private getTemplateSkillNames;
+    /**
+     * A .codex skill copy is only considered Jumbo-managed (and safe to delete)
+     * when its entire content is byte-identical to the current managed template:
+     * every file matches and no extra entries exist. Any deviation — customized
+     * bodies, extra user files, or unknown entry types — marks it user-owned.
+     */
+    private isObsoleteManagedSkillCopy;
+    private directoryContentMatchesManagedTemplate;
+    private fileContentMatchesManagedTemplate;
+    private isDirectory;
+    private isFile;
+    private removeDirectoryIfEmpty;
     /**
      * Return what changes this configurer will make without executing.
      */

package/dist/infrastructure/context/project/init/CodexConfigurer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"CodexConfigurer.d.ts","sourceRoot":"","sources":["../../../../../src/infrastructure/context/project/init/CodexConfigurer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAIH,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,mEAAmE,CAAC;AAsBtG,qBAAa,eAAgB,YAAW,WAAW;IACjD,QAAQ,CAAC,KAAK;;;MAGH;IAEX,QAAQ,CAAC,cAAc,6BAA8B;IAErD;;;;;;OAMG;IACG,SAAS,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAInD;;OAEG;IACG,MAAM,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;YAIlC,gBAAgB;IAiC9B,OAAO,CAAC,aAAa;IAIrB,OAAO,CAAC,UAAU;IAalB,OAAO,CAAC,kBAAkB;IAuB1B,OAAO,CAAC,cAAc;IAkBtB,OAAO,CAAC,qBAAqB;IA+B7B,OAAO,CAAC,gCAAgC;IAmBxC,OAAO,CAAC,oBAAoB;IAgB5B;;OAEG;IACG,qBAAqB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,EAAE,CAAC;CAW/E"}
+{"version":3,"file":"CodexConfigurer.d.ts","sourceRoot":"","sources":["../../../../../src/infrastructure/context/project/init/CodexConfigurer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAKH,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,mEAAmE,CAAC;AAkCtG,qBAAa,eAAgB,YAAW,WAAW;IAQrC,OAAO,CAAC,QAAQ,CAAC,kBAAkB;IAP/C,QAAQ,CAAC,KAAK;;;MAGH;IAEX,QAAQ,CAAC,cAAc,8BAA+B;gBAEzB,kBAAkB,EAAE,MAAM;IAEvD;;;;;;OAMG;IACG,SAAS,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAKnD;;;OAGG;IACG,MAAM,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;YAKlC,gBAAgB;IA+B9B,OAAO,CAAC,eAAe;IAUvB,OAAO,CAAC,qBAAqB;IAI7B,OAAO,CAAC,aAAa;IAIrB,OAAO,CAAC,YAAY;IAIpB,OAAO,CAAC,8BAA8B;IA6CtC,OAAO,CAAC,oBAAoB;IA2B5B,OAAO,CAAC,+BAA+B;IA6CvC,OAAO,CAAC,kBAAkB;IAI1B,OAAO,CAAC,uBAAuB;IAU/B,OAAO,CAAC,cAAc;IAOtB;;;OAGG;YACW,gCAAgC;YAyBhC,qBAAqB;IASnC;;;;;OAKG;YACW,0BAA0B;YAe1B,sCAAsC;YAgCtC,iCAAiC;YAejC,WAAW;YAQX,MAAM;YAQN,sBAAsB;IAWpC;;OAEG;IACG,qBAAqB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,EAAE,CAAC;CAW/E"}

package/dist/infrastructure/context/project/init/CodexConfigurer.js

@@ -3,9 +3,12 @@
  *
  * Encapsulates all knowledge about OpenAI Codex configuration:
  * - .codex/hooks.json with Codex lifecycle hooks
- * - Skills distributed to .codex/skills
+ * - Skills distributed to .agents/skills
+ * - Cleanup of obsolete Jumbo-managed skill copies under .codex/skills
  *
  * Codex reads AGENTS.md natively, so no instruction file is needed.
+ * Codex reads repo skills from .agents/skills and repo hooks from
+ * the trusted project .codex configuration layer.
  * Codex hooks parse JSON stdout as hook-control envelopes, so Jumbo
  * lifecycle commands use text output to avoid parser conflicts.
  *
@@ -13,14 +16,27 @@
  */
 import path from "path";
 import fs from "fs-extra";
+import { applyEdits, modify, parse } from "jsonc-parser";
 import { AgentFileAssetContent } from "../../../../domain/project/AgentFileAssetContent.js";
+const JSON_FORMATTING_OPTIONS = {
+    insertSpaces: true,
+    tabSize: 2,
+    eol: "\n",
+};
+const STALE_JUMBO_COMMAND_REPLACEMENTS = {
+    "jumbo session start": "jumbo session start --format text",
+    "jumbo work resume": "jumbo work resume --format text",
+    "jumbo work pause": "jumbo work pause --format text",
+};
+const OBSOLETE_CODEX_SKILLS_RELATIVE_PATH = ".codex/skills";
 export class CodexConfigurer {
-    constructor() {
+    constructor(templateSkillsRoot) {
+        this.templateSkillsRoot = templateSkillsRoot;
         this.agent = {
             id: "codex",
             name: "Codex",
         };
-        this.skillPlatforms = [".codex/skills"];
+        this.skillPlatforms = [".agents/skills"];
     }
     /**
      * Configure all OpenAI Codex requirements for Jumbo.
@@ -31,12 +47,15 @@ export class CodexConfigurer {
      */
     async configure(projectRoot) {
         await this.ensureCodexHooks(projectRoot);
+        await this.removeObsoleteManagedSkillCopies(projectRoot);
     }
     /**
-     * Repair Codex configuration by replacing stale Jumbo hook commands.
+     * Repair Codex configuration by replacing stale Jumbo hook commands
+     * and cleaning obsolete Jumbo-managed skill copies.
      */
     async repair(projectRoot) {
         await this.ensureCodexHooks(projectRoot);
+        await this.removeObsoleteManagedSkillCopies(projectRoot);
     }
     async ensureCodexHooks(projectRoot) {
         try {
@@ -48,117 +67,242 @@ export class CodexConfigurer {
                 return;
             }
             const existingContent = await fs.readFile(hooksPath, "utf-8");
-            let existingHooks = {};
-            if (existingContent.trim()) {
-                try {
-                    existingHooks = JSON.parse(existingContent);
-                }
-                catch {
-                    await fs.writeFile(hooksPath, JSON.stringify(this.getJumboHooks(), null, 2) + "\n", "utf-8");
-                    return;
-                }
+            const parseErrors = [];
+            const existingHooks = existingContent.trim()
+                ? parse(existingContent, parseErrors, { allowTrailingComma: true })
+                : {};
+            if (parseErrors.length > 0 || !this.isJsonObject(existingHooks)) {
+                await fs.writeFile(hooksPath, JSON.stringify(this.getJumboHooks(), null, 2) + "\n", "utf-8");
+                return;
             }
-            const normalizedExistingHooks = this.removeStaleJumboHooks(existingHooks);
-            const mergedHooks = this.mergeHooks(normalizedExistingHooks, this.getJumboHooks());
-            await fs.writeFile(hooksPath, JSON.stringify(mergedHooks, null, 2) + "\n", "utf-8");
+            const mergedContent = this.mergeJumboHooks(existingContent, existingHooks);
+            await fs.writeFile(hooksPath, this.ensureTrailingNewline(mergedContent), "utf-8");
         }
         catch (error) {
             console.warn(`Warning: Failed to configure Codex hooks: ${error instanceof Error ? error.message : String(error)}`);
         }
     }
+    mergeJumboHooks(existingContent, existingHooks) {
+        if (!existingContent.trim()) {
+            return JSON.stringify(this.getJumboHooks(), null, 2);
+        }
+        const updatedContent = this.replaceStaleJumboCommandValues(existingContent, existingHooks);
+        const updatedHooks = this.parseCodexHooksDocument(updatedContent);
+        return this.addMissingJumboHooks(updatedContent, updatedHooks ?? {});
+    }
+    ensureTrailingNewline(content) {
+        return content.endsWith("\n") ? content : `${content}\n`;
+    }
     getJumboHooks() {
         return AgentFileAssetContent.readJson("codex-hooks.fragment.json");
     }
-    mergeHooks(existing, jumbo) {
-        const result = { ...existing };
-        const mergedHooks = { ...(result.hooks ?? {}) };
-        for (const [eventName, matcherGroups] of Object.entries(jumbo.hooks ?? {})) {
-            const existingGroups = mergedHooks[eventName] ?? [];
-            mergedHooks[eventName] = this.mergeMatcherGroups(existingGroups, matcherGroups);
-        }
-        result.hooks = mergedHooks;
-        return result;
-    }
-    mergeMatcherGroups(existing, additions) {
-        const merged = [...existing];
-        for (const addition of additions) {
-            const existingIndex = merged.findIndex((entry) => entry?.matcher === addition.matcher);
-            if (existingIndex >= 0) {
-                const current = merged[existingIndex];
-                merged[existingIndex] = {
-                    ...current,
-                    hooks: this.mergeHookArray(current.hooks ?? [], addition.hooks ?? []),
-                };
-            }
-            else {
-                merged.push(addition);
+    isJsonObject(value) {
+        return Boolean(value) && typeof value === "object" && !Array.isArray(value);
+    }
+    replaceStaleJumboCommandValues(existingContent, existingHooks) {
+        const rawHooks = existingHooks.hooks;
+        if (!this.isJsonObject(rawHooks)) {
+            return existingContent;
+        }
+        let updatedContent = existingContent;
+        for (const [eventName, matcherGroups] of Object.entries(rawHooks)) {
+            if (!Array.isArray(matcherGroups)) {
+                continue;
             }
+            matcherGroups.forEach((matcherGroup, matcherGroupIndex) => {
+                if (!this.isJsonObject(matcherGroup) || !Array.isArray(matcherGroup.hooks)) {
+                    return;
+                }
+                matcherGroup.hooks.forEach((hook, hookIndex) => {
+                    if (!this.isJsonObject(hook) || typeof hook.command !== "string") {
+                        return;
+                    }
+                    const replacement = STALE_JUMBO_COMMAND_REPLACEMENTS[hook.command];
+                    if (!replacement) {
+                        return;
+                    }
+                    updatedContent = this.applyJsoncEdit(updatedContent, [
+                        "hooks",
+                        eventName,
+                        matcherGroupIndex,
+                        "hooks",
+                        hookIndex,
+                        "command",
+                    ], replacement);
+                });
+            });
         }
-        return merged;
+        return updatedContent;
     }
-    mergeHookArray(existing, additions) {
-        const merged = [...existing];
-        const existingKeys = new Set(existing.map((hook) => JSON.stringify(hook)));
-        for (const addition of additions) {
-            const additionKey = JSON.stringify(addition);
-            if (!existingKeys.has(additionKey)) {
-                merged.push(addition);
-                existingKeys.add(additionKey);
+    addMissingJumboHooks(existingContent, existingHooks) {
+        const jumboHooks = this.getJumboHooks();
+        if (!this.isJsonObject(existingHooks.hooks)) {
+            return this.applyJsoncEdit(existingContent, ["hooks"], jumboHooks.hooks ?? {});
+        }
+        let updatedContent = existingContent;
+        for (const [eventName, jumboMatcherGroups] of Object.entries(jumboHooks.hooks ?? {})) {
+            const currentHooks = this.parseCodexHooksDocument(updatedContent);
+            const currentMatcherGroups = currentHooks?.hooks?.[eventName];
+            if (!Array.isArray(currentMatcherGroups)) {
+                updatedContent = this.applyJsoncEdit(updatedContent, ["hooks", eventName], jumboMatcherGroups);
+                continue;
+            }
+            for (const jumboMatcherGroup of jumboMatcherGroups) {
+                updatedContent = this.addMissingJumboMatcherGroupHook(updatedContent, eventName, jumboMatcherGroup);
             }
         }
-        return merged;
+        return updatedContent;
     }
-    removeStaleJumboHooks(existing) {
-        if (!existing || typeof existing !== "object") {
-            return {};
+    addMissingJumboMatcherGroupHook(existingContent, eventName, jumboMatcherGroup) {
+        const currentHooks = this.parseCodexHooksDocument(existingContent);
+        const currentMatcherGroups = currentHooks?.hooks?.[eventName];
+        if (!Array.isArray(currentMatcherGroups)) {
+            return existingContent;
         }
-        const source = existing;
-        const result = { ...source };
-        const rawHooks = source.hooks;
-        if (!rawHooks || typeof rawHooks !== "object") {
-            return result;
+        const matcherGroupIndex = currentMatcherGroups.findIndex((matcherGroup) => matcherGroup.matcher === jumboMatcherGroup.matcher);
+        if (matcherGroupIndex === -1) {
+            return this.applyJsoncEdit(existingContent, ["hooks", eventName, -1], jumboMatcherGroup);
         }
-        const normalizedHooks = {};
-        for (const [eventName, matcherGroups] of Object.entries(rawHooks)) {
-            if (!Array.isArray(matcherGroups)) {
+        const currentMatcherGroup = currentMatcherGroups[matcherGroupIndex];
+        if (!Array.isArray(currentMatcherGroup.hooks)) {
+            return this.applyJsoncEdit(existingContent, ["hooks", eventName, matcherGroupIndex, "hooks"], jumboMatcherGroup.hooks ?? []);
+        }
+        let updatedContent = existingContent;
+        for (const jumboHook of jumboMatcherGroup.hooks ?? []) {
+            const refreshedHooks = this.parseCodexHooksDocument(updatedContent);
+            const refreshedHookArray = refreshedHooks?.hooks?.[eventName]?.[matcherGroupIndex]?.hooks;
+            if (refreshedHookArray?.some((hook) => this.hasSameHookCommand(hook, jumboHook))) {
                 continue;
             }
-            const normalizedGroups = matcherGroups
-                .map((matcherGroup) => this.removeStaleJumboHooksFromMatcher(matcherGroup))
-                .filter((matcherGroup) => matcherGroup !== null);
-            if (normalizedGroups.length > 0) {
-                normalizedHooks[eventName] = normalizedGroups;
-            }
+            updatedContent = this.applyJsoncEdit(updatedContent, ["hooks", eventName, matcherGroupIndex, "hooks", -1], jumboHook);
         }
-        result.hooks = normalizedHooks;
-        return result;
+        return updatedContent;
     }
-    removeStaleJumboHooksFromMatcher(matcherGroup) {
-        if (!matcherGroup || typeof matcherGroup !== "object") {
+    hasSameHookCommand(existingHook, jumboHook) {
+        return existingHook.type === jumboHook.type && existingHook.command === jumboHook.command;
+    }
+    parseCodexHooksDocument(content) {
+        const parseErrors = [];
+        const parsed = parse(content, parseErrors, { allowTrailingComma: true });
+        if (parseErrors.length > 0 || !this.isJsonObject(parsed)) {
             return null;
         }
-        const candidate = matcherGroup;
-        const hooks = Array.isArray(candidate.hooks) ? candidate.hooks : [];
-        const nonJumboHooks = hooks.filter((hook) => !this.isJumboLifecycleHook(hook));
-        if (nonJumboHooks.length === 0) {
-            return null;
+        return parsed;
+    }
+    applyJsoncEdit(content, pathSegments, value) {
+        const edits = modify(content, pathSegments, value, {
+            formattingOptions: JSON_FORMATTING_OPTIONS,
+        });
+        return applyEdits(content, edits);
+    }
+    /**
+     * Remove Jumbo-managed skill copies from the obsolete .codex/skills
+     * location now that Codex reads repo skills from .agents/skills.
+     */
+    async removeObsoleteManagedSkillCopies(projectRoot) {
+        const obsoleteCodexSkillsRoot = path.join(projectRoot, OBSOLETE_CODEX_SKILLS_RELATIVE_PATH);
+        if (!(await fs.pathExists(obsoleteCodexSkillsRoot))) {
+            return;
+        }
+        for (const skillName of await this.getTemplateSkillNames()) {
+            const templateSkillDirectory = path.join(this.templateSkillsRoot, skillName);
+            const obsoleteSkillDirectory = path.join(obsoleteCodexSkillsRoot, skillName);
+            if (await this.isObsoleteManagedSkillCopy(obsoleteSkillDirectory, templateSkillDirectory)) {
+                try {
+                    await fs.remove(obsoleteSkillDirectory);
+                }
+                catch (error) {
+                    console.warn(`Warning: Failed to remove obsolete Codex managed skill '${skillName}': ${error instanceof Error ? error.message : String(error)}`);
+                }
+            }
+        }
+        await this.removeDirectoryIfEmpty(obsoleteCodexSkillsRoot);
+    }
+    async getTemplateSkillNames() {
+        if (!(await fs.pathExists(this.templateSkillsRoot))) {
+            return [];
+        }
+        const entries = await fs.readdir(this.templateSkillsRoot, { withFileTypes: true });
+        return entries.filter((entry) => entry.isDirectory()).map((entry) => entry.name);
+    }
+    /**
+     * A .codex skill copy is only considered Jumbo-managed (and safe to delete)
+     * when its entire content is byte-identical to the current managed template:
+     * every file matches and no extra entries exist. Any deviation — customized
+     * bodies, extra user files, or unknown entry types — marks it user-owned.
+     */
+    async isObsoleteManagedSkillCopy(skillDirectory, templateSkillDirectory) {
+        try {
+            if (!(await this.isDirectory(skillDirectory)) || !(await this.isDirectory(templateSkillDirectory))) {
+                return false;
+            }
+            return await this.directoryContentMatchesManagedTemplate(skillDirectory, templateSkillDirectory);
+        }
+        catch {
+            return false;
+        }
+    }
+    async directoryContentMatchesManagedTemplate(directory, templateDirectory) {
+        const entries = await fs.readdir(directory, { withFileTypes: true });
+        if (entries.length === 0) {
+            return false;
+        }
+        for (const entry of entries) {
+            const entryPath = path.join(directory, entry.name);
+            const templateEntryPath = path.join(templateDirectory, entry.name);
+            if (entry.isDirectory()) {
+                if (!(await this.isDirectory(templateEntryPath)) ||
+                    !(await this.directoryContentMatchesManagedTemplate(entryPath, templateEntryPath))) {
+                    return false;
+                }
+            }
+            else if (entry.isFile()) {
+                if (!(await this.fileContentMatchesManagedTemplate(entryPath, templateEntryPath))) {
+                    return false;
+                }
+            }
+            else {
+                return false;
+            }
+        }
+        return true;
+    }
+    async fileContentMatchesManagedTemplate(filePath, templateFilePath) {
+        if (!(await this.isFile(templateFilePath))) {
+            return false;
+        }
+        const [fileContent, templateFileContent] = await Promise.all([
+            fs.readFile(filePath),
+            fs.readFile(templateFilePath),
+        ]);
+        return fileContent.equals(templateFileContent);
+    }
+    async isDirectory(directoryPath) {
+        try {
+            return (await fs.stat(directoryPath)).isDirectory();
+        }
+        catch {
+            return false;
         }
-        return {
-            ...candidate,
-            hooks: nonJumboHooks,
-        };
     }
-    isJumboLifecycleHook(hook) {
-        if (!hook || typeof hook !== "object") {
+    async isFile(filePath) {
+        try {
+            return (await fs.stat(filePath)).isFile();
+        }
+        catch {
             return false;
         }
-        const command = hook.command;
-        return (command === "jumbo session start" ||
-            command === "jumbo session start --format text" ||
-            command === "jumbo work resume" ||
-            command === "jumbo work resume --format text" ||
-            command === "jumbo work pause" ||
-            command === "jumbo work pause --format text");
+    }
+    async removeDirectoryIfEmpty(directoryPath) {
+        try {
+            const entries = await fs.readdir(directoryPath);
+            if (entries.length === 0) {
+                await fs.remove(directoryPath);
+            }
+        }
+        catch {
+            return;
+        }
     }
     /**
      * Return what changes this configurer will make without executing.

package/dist/infrastructure/context/project/init/CodexConfigurer.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "jumbo-cli",
-  "version": "3.13.0",
+  "version": "3.14.0",
   "description": "Memory and Context Orchestration for Coding Agents",
   "keywords": [
     "cli",