@code-yeongyu/senpi 2026.9.12-3 → 2026.9.13-2

package/dist/core/pi-manifest.d.ts

@@ -1,4 +1,6 @@
 export interface PiManifest {
+    /** The package is part of the harness; command-line packages with this flag resolve to the `system` scope. */
+    system?: boolean;
     extensions?: string[];
     skills?: string[];
     prompts?: string[];

package/dist/core/pi-manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pi-manifest.d.ts","sourceRoot":"","sources":["../../src/core/pi-manifest.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,UAAU;IAC1B,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CACjB;AAQD,wBAAgB,cAAc,CAAC,eAAe,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI,CAkBzE"}
+{"version":3,"file":"pi-manifest.d.ts","sourceRoot":"","sources":["../../src/core/pi-manifest.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,UAAU;IAC1B,8GAA8G;IAC9G,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CACjB;AAQD,wBAAgB,cAAc,CAAC,eAAe,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI,CAqBzE"}

package/dist/core/pi-manifest.js

@@ -11,6 +11,9 @@ export function readPiManifest(packageJsonPath) {
             return null;
         }
         const manifest = {};
+        if (typeof pkg.pi.system === "boolean") {
+            manifest.system = pkg.pi.system;
+        }
         for (const field of RESOURCE_FIELDS) {
             const entries = pkg.pi[field];
             if (Array.isArray(entries) && entries.every((entry) => typeof entry === "string")) {

package/dist/core/pi-manifest.js.map

@@ -1 +1 @@
-{"version":3,"file":"pi-manifest.js","sourceRoot":"","sources":["../../src/core/pi-manifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAU5C,MAAM,eAAe,GAAG,CAAC,YAAY,EAAE,QAAQ,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAC;AAExF,SAAS,QAAQ,CAAC,KAAc;IAC/B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;AAC7E,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,eAAuB;IACrD,IAAI,CAAC;QACJ,MAAM,GAAG,GAAY,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,YAAY,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC;QAClF,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;YACzC,OAAO,IAAI,CAAC;QACb,CAAC;QAED,MAAM,QAAQ,GAAe,EAAE,CAAC;QAChC,KAAK,MAAM,KAAK,IAAI,eAAe,EAAE,CAAC;YACrC,MAAM,OAAO,GAAG,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC;YAC9B,IAAI,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,OAAO,KAAK,KAAK,QAAQ,CAAC,EAAE,CAAC;gBACnF,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;YAC3B,CAAC;QACF,CAAC;QACD,OAAO,QAAQ,CAAC;IACjB,CAAC;IAAC,MAAM,CAAC;QACR,OAAO,IAAI,CAAC;IACb,CAAC;AACF,CAAC","sourcesContent":["import { readFileSync } from \"node:fs\";\nimport { stripBom } from \"../utils/text.ts\";\n\nexport interface PiManifest {\n\textensions?: string[];\n\tskills?: string[];\n\tprompts?: string[];\n\tthemes?: string[];\n\thooks?: string[];\n}\n\nconst RESOURCE_FIELDS = [\"extensions\", \"skills\", \"prompts\", \"themes\", \"hooks\"] as const;\n\nfunction isObject(value: unknown): value is Record<string, unknown> {\n\treturn typeof value === \"object\" && value !== null && !Array.isArray(value);\n}\n\nexport function readPiManifest(packageJsonPath: string): PiManifest | null {\n\ttry {\n\t\tconst pkg: unknown = JSON.parse(stripBom(readFileSync(packageJsonPath, \"utf-8\")));\n\t\tif (!isObject(pkg) || !isObject(pkg.pi)) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst manifest: PiManifest = {};\n\t\tfor (const field of RESOURCE_FIELDS) {\n\t\t\tconst entries = pkg.pi[field];\n\t\t\tif (Array.isArray(entries) && entries.every((entry) => typeof entry === \"string\")) {\n\t\t\t\tmanifest[field] = entries;\n\t\t\t}\n\t\t}\n\t\treturn manifest;\n\t} catch {\n\t\treturn null;\n\t}\n}\n"]}
+{"version":3,"file":"pi-manifest.js","sourceRoot":"","sources":["../../src/core/pi-manifest.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAY5C,MAAM,eAAe,GAAG,CAAC,YAAY,EAAE,QAAQ,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAC;AAExF,SAAS,QAAQ,CAAC,KAAc;IAC/B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;AAC7E,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,eAAuB;IACrD,IAAI,CAAC;QACJ,MAAM,GAAG,GAAY,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,YAAY,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC;QAClF,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;YACzC,OAAO,IAAI,CAAC;QACb,CAAC;QAED,MAAM,QAAQ,GAAe,EAAE,CAAC;QAChC,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;YACxC,QAAQ,CAAC,MAAM,GAAG,GAAG,CAAC,EAAE,CAAC,MAAM,CAAC;QACjC,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,eAAe,EAAE,CAAC;YACrC,MAAM,OAAO,GAAG,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC;YAC9B,IAAI,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,OAAO,KAAK,KAAK,QAAQ,CAAC,EAAE,CAAC;gBACnF,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;YAC3B,CAAC;QACF,CAAC;QACD,OAAO,QAAQ,CAAC;IACjB,CAAC;IAAC,MAAM,CAAC;QACR,OAAO,IAAI,CAAC;IACb,CAAC;AACF,CAAC","sourcesContent":["import { readFileSync } from \"node:fs\";\nimport { stripBom } from \"../utils/text.ts\";\n\nexport interface PiManifest {\n\t/** The package is part of the harness; command-line packages with this flag resolve to the `system` scope. */\n\tsystem?: boolean;\n\textensions?: string[];\n\tskills?: string[];\n\tprompts?: string[];\n\tthemes?: string[];\n\thooks?: string[];\n}\n\nconst RESOURCE_FIELDS = [\"extensions\", \"skills\", \"prompts\", \"themes\", \"hooks\"] as const;\n\nfunction isObject(value: unknown): value is Record<string, unknown> {\n\treturn typeof value === \"object\" && value !== null && !Array.isArray(value);\n}\n\nexport function readPiManifest(packageJsonPath: string): PiManifest | null {\n\ttry {\n\t\tconst pkg: unknown = JSON.parse(stripBom(readFileSync(packageJsonPath, \"utf-8\")));\n\t\tif (!isObject(pkg) || !isObject(pkg.pi)) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst manifest: PiManifest = {};\n\t\tif (typeof pkg.pi.system === \"boolean\") {\n\t\t\tmanifest.system = pkg.pi.system;\n\t\t}\n\t\tfor (const field of RESOURCE_FIELDS) {\n\t\t\tconst entries = pkg.pi[field];\n\t\t\tif (Array.isArray(entries) && entries.every((entry) => typeof entry === \"string\")) {\n\t\t\t\tmanifest[field] = entries;\n\t\t\t}\n\t\t}\n\t\treturn manifest;\n\t} catch {\n\t\treturn null;\n\t}\n}\n"]}

package/dist/core/resource-loader.d.ts

@@ -250,6 +250,15 @@ export declare class DefaultResourceLoader implements ResourceLoader {
     private loadThemeFromFile;
     private loadExtensionFactories;
     private getBundledExtensionEntryPaths;
+    /**
+     * Source info for an extension file the harness itself provides: a bundled extension entry, or a
+     * global-default shim this loader generated under the agent extensions directory. A file at a shim
+     * path that no longer carries the generated banner is user-authored and gets no system scope.
+     */
+    private getHarnessExtensionSourceInfo;
+    private isGeneratedGlobalDefaultExtensionShimPath;
+    /** Resolved entry path of every active bundled extension mapped to the root of the package that ships it. */
+    private getBundledExtensionPackageRoots;
     private resolvePackageExtensionEntries;
     private dedupePrompts;
     private dedupeThemes;

package/dist/core/resource-loader.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"resource-loader.d.ts","sourceRoot":"","sources":["../../src/core/resource-loader.ts"],"names":[],"mappings":"AAMA,OAAO,EAAqB,KAAK,KAAK,EAAE,MAAM,qCAAqC,CAAC;AACpF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAG3D,YAAY,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAI9E,OAAO,EAAkB,KAAK,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAc/D,OAAO,KAAK,EAIX,eAAe,EACf,oBAAoB,EACpB,iBAAiB,EACjB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAyB,KAAK,YAAY,EAAyB,MAAM,sBAAsB,CAAC;AACvG,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAE5D,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAKzC,MAAM,WAAW,sBAAsB;IACtC,UAAU,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;IAC7D,WAAW,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;IAC9D,UAAU,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;IAC7D,SAAS,CAAC,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,YAAY,CAAA;KAAE,CAAC,CAAC;CAC5D;AAED,MAAM,WAAW,2BAA2B;IAC3C,mBAAmB,CAAC,EAAE,CAAC,KAAK,EAAE;QAAE,gBAAgB,EAAE,oBAAoB,CAAA;KAAE,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC9F;;;;;;;OAOG;IACH,0BAA0B,CAAC,EAAE,eAAe,CAAC;CAC7C;AAED,MAAM,WAAW,cAAc;IAC9B,aAAa,IAAI,oBAAoB,CAAC;IACtC,kBAAkB,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,GAAG,IAAI,CAAC;IAC1D,gBAAgB,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC,IAAI,EAAE,OAAO,KAAK,IAAI,GAAG,MAAM,IAAI,CAAC;IACjF,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IACpE,UAAU,IAAI;QAAE,OAAO,EAAE,cAAc,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IAC/E,SAAS,IAAI;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,CAAC;IACpE,cAAc,IAAI;QAAE,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE,CAAC;IAC5E,eAAe,IAAI,MAAM,GAAG,SAAS,CAAC;IACtC,qBAAqB,IAAI;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,GAAG,SAAS,CAAC;IACtD,qBAAqB,IAAI,MAAM,EAAE,CAAC;IAClC,oBAAoB,CAAC,IAAI,iBAAiB,CAAC;IAC3C,4BAA4B,IAAI,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACxD,eAAe,CAAC,KAAK,EAAE,sBAAsB,GAAG,IAAI,CAAC;IACrD,MAAM,CAAC,OAAO,CAAC,EAAE,2BAA2B,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;CAC7D;AAgFD;;;;;;GAMG;AACH,wBAAgB,4CAA4C,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAMvF;AA4GD,wBAAgB,uBAAuB,CAAC,OAAO,EAAE;IAChD,GAAG,EAAE,MAAM,CAAC;IACZ,QAAQ,EAAE,MAAM,CAAC;CACjB,GAAG,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC,CAmC3C;AAED,MAAM,WAAW,4BAA4B;IAC5C,GAAG,EAAE,MAAM,CAAC;IACZ,QAAQ,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,eAAe,CAAC;IAClC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,wBAAwB,CAAC,EAAE,MAAM,EAAE,CAAC;IACpC,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,6BAA6B,CAAC,EAAE,MAAM,EAAE,CAAC;IACzC,oBAAoB,CAAC,EAAE,MAAM,EAAE,CAAC;IAChC,mBAAmB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC/B,kBAAkB,CAAC,EAAE,eAAe,EAAE,CAAC;IACvC,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,kBAAkB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC9B,kBAAkB,CAAC,EAAE,CAAC,IAAI,EAAE,oBAAoB,KAAK,oBAAoB,CAAC;IAC1E,cAAc,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAClF,MAAM,EAAE,KAAK,EAAE,CAAC;QAChB,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,eAAe,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,OAAO,EAAE,cAAc,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAC7F,OAAO,EAAE,cAAc,EAAE,CAAC;QAC1B,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,cAAc,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,MAAM,EAAE,KAAK,EAAE,CAAC;QAAC,WAAW,EAAE,kBAAkB,EAAE,CAAA;KAAE,KAAK;QAClF,MAAM,EAAE,KAAK,EAAE,CAAC;QAChB,WAAW,EAAE,kBAAkB,EAAE,CAAC;KAClC,CAAC;IACF,mBAAmB,CAAC,EAAE,CAAC,IAAI,EAAE;QAAE,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE,KAAK;QAC1F,WAAW,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KACtD,CAAC;CACF;AAED,qBAAa,qBAAsB,YAAW,cAAc;IAC3D,OAAO,CAAC,GAAG,CAAS;IACpB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,eAAe,CAAkB;IACzC,OAAO,CAAC,iBAAiB,CAAU;IACnC,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,cAAc,CAAwB;IAC9C,OAAO,CAAC,wBAAwB,CAAW;IAC3C,OAAO,CAAC,oBAAoB,CAAW;IACvC,OAAO,CAAC,6BAA6B,CAAW;IAChD,OAAO,CAAC,oBAAoB,CAAW;IACvC,OAAO,CAAC,mBAAmB,CAAW;IACtC,OAAO,CAAC,yBAAyB,CAA4B;IAC7D,OAAO,CAAC,kBAAkB,CAAoB;IAC9C,OAAO,CAAC,YAAY,CAAU;IAC9B,OAAO,CAAC,QAAQ,CAAU;IAC1B,OAAO,CAAC,iBAAiB,CAAU;IACnC,OAAO,CAAC,QAAQ,CAAU;IAC1B,OAAO,CAAC,cAAc,CAAU;IAChC,OAAO,CAAC,kBAAkB,CAAC,CAAS;IACpC,OAAO,CAAC,wBAAwB,CAAC,CAAW;IAC5C,OAAO,CAAC,kBAAkB,CAAC,CAAuD;IAClF,OAAO,CAAC,cAAc,CAAC,CAGrB;IACF,OAAO,CAAC,eAAe,CAAC,CAGtB;IACF,OAAO,CAAC,cAAc,CAAC,CAGrB;IACF,OAAO,CAAC,mBAAmB,CAAC,CAE1B;IAEF,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,MAAM,CAAU;IACxB,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,OAAO,CAAmB;IAClC,OAAO,CAAC,iBAAiB,CAAuB;IAChD,OAAO,CAAC,MAAM,CAAU;IACxB,OAAO,CAAC,gBAAgB,CAAuB;IAC/C,OAAO,CAAC,WAAW,CAA2C;IAC9D,OAAO,CAAC,YAAY,CAAC,CAAS;IAC9B,OAAO,CAAC,sBAAsB,CAAC,CAAS;IACxC,OAAO,CAAC,kBAAkB,CAAW;IACrC,OAAO,CAAC,6BAA6B,CAAW;IAChD,OAAO,CAAC,cAAc,CAAW;IACjC,OAAO,CAAC,yBA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package/dist/core/resource-loader.js

@@ -387,21 +387,21 @@ export class DefaultResourceLoader {
         const enabledHookResources = getEnabledResources(resolvedPaths.hooks);
         const enabledSkills = enabledSkillResources.map((resource) => this.mapSkillPath(resource, metadataByPath));
         // Add CLI paths metadata. Explicit -e/-s resources must keep CLI precedence
-        // even when they resolve through a package manifest.
-        for (const r of cliExtensionPaths.extensions) {
-            metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
-        }
-        for (const r of cliExtensionPaths.skills) {
-            metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
-        }
-        for (const r of cliExtensionPaths.prompts) {
-            metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
-        }
-        for (const r of cliExtensionPaths.themes) {
-            metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
-        }
-        for (const r of cliExtensionPaths.hooks) {
-            metadataByPath.set(r.path, { source: "cli", scope: "temporary", origin: "top-level" });
+        // even when they resolve through a package manifest. A package that declared
+        // itself part of the harness keeps the system scope and root it resolved to.
+        const cliMetadata = (resource) => resource.metadata.scope === "system"
+            ? { source: "cli", scope: "system", origin: "top-level", baseDir: resource.metadata.baseDir }
+            : { source: "cli", scope: "temporary", origin: "top-level" };
+        for (const resources of [
+            cliExtensionPaths.extensions,
+            cliExtensionPaths.skills,
+            cliExtensionPaths.prompts,
+            cliExtensionPaths.themes,
+            cliExtensionPaths.hooks,
+        ]) {
+            for (const r of resources) {
+                metadataByPath.set(r.path, cliMetadata(r));
+            }
         }
         const cliEnabledExtensions = getEnabledPaths(cliExtensionPaths.extensions);
         const cliEnabledSkills = getEnabledPaths(cliExtensionPaths.skills);
@@ -715,9 +715,11 @@ export class DefaultResourceLoader {
         this.themeDiagnostics = resolvedThemes.diagnostics;
     }
     applyExtensionSourceInfo(extensions, metadataByPath) {
+        const bundledPackageRoots = this.getBundledExtensionPackageRoots();
         for (const extension of extensions) {
             extension.sourceInfo =
-                this.findSourceInfoForPath(extension.path, undefined, metadataByPath) ??
+                this.getHarnessExtensionSourceInfo(extension, bundledPackageRoots) ??
+                    this.findSourceInfoForPath(extension.path, undefined, metadataByPath) ??
                     this.getDefaultSourceInfoForPath(extension.path);
             for (const command of extension.commands.values()) {
                 command.sourceInfo = extension.sourceInfo;
@@ -761,10 +763,11 @@ export class DefaultResourceLoader {
     }
     getDefaultSourceInfoForPath(filePath) {
         if (filePath.startsWith("<") && filePath.endsWith(">")) {
+            const source = filePath.slice(1, -1).split(":")[0] || "temporary";
             return {
                 path: filePath,
-                source: filePath.slice(1, -1).split(":")[0] || "temporary",
-                scope: "temporary",
+                source,
+                scope: source === "builtin" ? "system" : "temporary",
                 origin: "top-level",
             };
         }
@@ -1017,19 +1020,64 @@ export class DefaultResourceLoader {
         return { extensions, errors };
     }
     getBundledExtensionEntryPaths() {
-        const paths = new Set();
+        return new Set(this.getBundledExtensionPackageRoots().keys());
+    }
+    /**
+     * Source info for an extension file the harness itself provides: a bundled extension entry, or a
+     * global-default shim this loader generated under the agent extensions directory. A file at a shim
+     * path that no longer carries the generated banner is user-authored and gets no system scope.
+     */
+    getHarnessExtensionSourceInfo(extension, bundledPackageRoots) {
+        const bundledPackageRoot = bundledPackageRoots.get(extension.resolvedPath);
+        if (bundledPackageRoot !== undefined) {
+            return {
+                path: extension.path,
+                source: "builtin",
+                scope: "system",
+                origin: "top-level",
+                baseDir: bundledPackageRoot,
+            };
+        }
+        if (this.isGeneratedGlobalDefaultExtensionShimPath(extension.resolvedPath)) {
+            return {
+                path: extension.path,
+                source: "builtin",
+                scope: "system",
+                origin: "top-level",
+                baseDir: join(this.agentDir, "extensions"),
+            };
+        }
+        return undefined;
+    }
+    isGeneratedGlobalDefaultExtensionShimPath(resolvedPath) {
+        const shimPath = resolve(resolvedPath);
+        const isShimPath = globalDefaultExtensionIds.some((extensionId) => resolve(getGlobalDefaultExtensionShimPath(this.agentDir, extensionId)) === shimPath);
+        if (!isShimPath) {
+            return false;
+        }
+        try {
+            return isGeneratedGlobalDefaultExtensionShim(readFileSync(shimPath, "utf-8"));
+        }
+        catch {
+            return false;
+        }
+    }
+    /** Resolved entry path of every active bundled extension mapped to the root of the package that ships it. */
+    getBundledExtensionPackageRoots() {
+        const packageRoots = new Map();
         for (const bundledExtension of bundledBuiltinExtensions) {
             try {
                 const packageJsonPath = bundledExtension.resolvePackage();
+                const packageRoot = resolve(packageJsonPath, "..");
                 for (const extensionPath of this.resolvePackageExtensionEntries(packageJsonPath)) {
-                    paths.add(this.resolveExtensionLoadPath(extensionPath));
+                    packageRoots.set(this.resolveExtensionLoadPath(extensionPath), packageRoot);
                 }
             }
             catch {
                 // Bundled resolution errors are already reported by loadExtensionFactories().
             }
         }
-        return paths;
+        return packageRoots;
     }
     resolvePackageExtensionEntries(packageJsonPath) {
         const packageJson = JSON.parse(readFileSync(packageJsonPath, "utf-8"));