agentopology 0.2.0 → 0.2.3

package/dist/scaffold/__tests__/settings-merge.test.js

@@ -0,0 +1,127 @@
+/**
+ * Tests for Change 3: Non-destructive scaffold of settings.json.
+ *
+ * Verifies that when settings.json already exists on disk, re-scaffolding
+ * without --force performs a MERGE:
+ *   - permissions.allow is union-merged (existing entries survive)
+ *   - permissions.deny is union-merged
+ *   - env is merged (generated wins on conflict)
+ *   - hooks are rewritten (topology owns hooks)
+ *   - user-only keys survive
+ *
+ * Also verifies that invalid existing JSON fails loudly.
+ */
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import * as fs from "node:fs";
+import * as path from "node:path";
+import * as os from "node:os";
+import { deepMergeSettingsJson } from "../merge.js";
+let tmpDir;
+beforeEach(() => {
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "settings-merge-test-"));
+});
+afterEach(() => {
+    fs.rmSync(tmpDir, { recursive: true, force: true });
+});
+// ---------------------------------------------------------------------------
+// deepMergeSettingsJson — the core merge function for settings.json
+// ---------------------------------------------------------------------------
+describe("Change 3 — deepMergeSettingsJson", () => {
+    it("union-merges permissions.allow arrays", () => {
+        const existing = JSON.stringify({
+            permissions: { allow: ["Read(/tmp/**)", "Write(/tmp/**)"] },
+            hooks: {},
+        });
+        const generated = JSON.stringify({
+            permissions: { allow: ["Read(**)", "Bash"] },
+            hooks: { PostToolUse: [] },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        // All entries from both must be present
+        expect(merged.permissions.allow).toContain("Read(/tmp/**)");
+        expect(merged.permissions.allow).toContain("Write(/tmp/**)");
+        expect(merged.permissions.allow).toContain("Read(**)");
+        expect(merged.permissions.allow).toContain("Bash");
+    });
+    it("union-merges permissions.deny arrays", () => {
+        const existing = JSON.stringify({
+            permissions: { deny: ["Bash", "Write"] },
+        });
+        const generated = JSON.stringify({
+            permissions: { deny: ["Edit"] },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        expect(merged.permissions.deny).toContain("Bash");
+        expect(merged.permissions.deny).toContain("Write");
+        expect(merged.permissions.deny).toContain("Edit");
+    });
+    it("deduplicates union-merged permission arrays", () => {
+        const existing = JSON.stringify({
+            permissions: { allow: ["Read(**)", "Bash"] },
+        });
+        const generated = JSON.stringify({
+            permissions: { allow: ["Read(**)", "Write"] },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        const count = merged.permissions.allow.filter((a) => a === "Read(**)").length;
+        expect(count).toBe(1);
+    });
+    it("generated wins on env key conflicts", () => {
+        const existing = JSON.stringify({
+            env: { FOO: "old-value", BAR: "preserved" },
+        });
+        const generated = JSON.stringify({
+            env: { FOO: "new-value", BAZ: "added" },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        // Generated wins on conflict
+        expect(merged.env.FOO).toBe("new-value");
+        // Existing-only key preserved
+        expect(merged.env.BAR).toBe("preserved");
+        // Generated-only key added
+        expect(merged.env.BAZ).toBe("added");
+    });
+    it("hooks are REWRITTEN by generated (topology owns hooks)", () => {
+        const existing = JSON.stringify({
+            hooks: {
+                PreToolUse: [{ matcher: "old", hooks: [{ type: "command", command: "old.sh" }] }],
+            },
+        });
+        const generated = JSON.stringify({
+            hooks: {
+                SubagentStop: [{ matcher: "new", hooks: [{ type: "command", command: "new.sh" }] }],
+            },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        // Old hooks gone — topology owns hooks
+        expect(merged.hooks.PreToolUse).toBeUndefined();
+        // New hooks present
+        expect(merged.hooks.SubagentStop).toBeDefined();
+    });
+    it("preserves user-only top-level keys", () => {
+        const existing = JSON.stringify({
+            model: "claude-opus-4-5",
+            theme: "dark",
+        });
+        const generated = JSON.stringify({
+            permissions: { allow: ["Read"] },
+        });
+        const merged = JSON.parse(deepMergeSettingsJson(existing, generated));
+        expect(merged.model).toBe("claude-opus-4-5");
+        expect(merged.theme).toBe("dark");
+        expect(merged.permissions.allow).toContain("Read");
+    });
+    it("throws a descriptive error when existing JSON is invalid", () => {
+        const existing = `{ "permissions": { "allow": ["Read"] `; // truncated
+        const generated = JSON.stringify({ permissions: { allow: ["Write"] } });
+        expect(() => deepMergeSettingsJson(existing, generated)).toThrow(/invalid JSON/i);
+    });
+    it("returns generated as-is when existing is empty string", () => {
+        const existing = "";
+        const generated = JSON.stringify({ permissions: { allow: ["Read"] } });
+        // Empty string means no prior settings — just use generated
+        const result = deepMergeSettingsJson(existing, generated);
+        expect(JSON.parse(result)).toEqual(JSON.parse(generated));
+    });
+});
+//# sourceMappingURL=settings-merge.test.js.map

package/dist/scaffold/__tests__/settings-merge.test.js.map

@@ -0,0 +1 @@
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package/dist/scaffold/incremental.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/scaffold/incremental.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAG/D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,cAAc,EAAE,aAAa,EAAE,EAC/B,QAAQ,EAAE,gBAAgB,GAAG,IAAI,GAChC,UAAU,EAAE,CA2Gd;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,UAAU,EAAE,EACrB,OAAO,EAAE;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,CAAA;CAAE,GAC1C;IACD,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB,CAuDA"}
+{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/scaffold/incremental.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAG/D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,cAAc,EAAE,aAAa,EAAE,EAC/B,QAAQ,EAAE,gBAAgB,GAAG,IAAI,GAChC,UAAU,EAAE,CAgHd;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,UAAU,EAAE,EACrB,OAAO,EAAE;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,CAAA;CAAE,GAC1C;IACD,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB,CAyDA"}

package/dist/scaffold/incremental.js

@@ -7,7 +7,7 @@
  *
  * @module
  */
-import { existsSync, mkdirSync, readFileSync, unlinkSync, writeFileSync } from "node:fs";
+import { chmodSync, existsSync, mkdirSync, readFileSync, unlinkSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
 import { mergeAgentFile, shouldOverwriteScript, deepMergeJson } from "./merge.js";
 /**
@@ -35,7 +35,12 @@ export function computeIncrementalPlan(basePath, target, generatedFiles, manifes
         const category = file.category ?? "machine";
         const onDisk = existsSync(absPath);
         if (!onDisk) {
-            actions.push({ type: "create", path: file.path, content: file.content });
+            actions.push({
+                type: "create",
+                path: file.path,
+                content: file.content,
+                ...(file.executable ? { executable: true } : {}),
+            });
             continue;
         }
         const existingContent = readFileSync(absPath, "utf-8");
@@ -144,6 +149,8 @@ export function executeActions(basePath, actions, options) {
                     mkdirSync(dir, { recursive: true });
                 }
                 writeFileSync(absPath, action.content, "utf-8");
+                if (action.executable)
+                    chmodSync(absPath, 0o755);
                 counts.created++;
                 break;
             }
@@ -153,6 +160,8 @@ export function executeActions(basePath, actions, options) {
                     mkdirSync(dir, { recursive: true });
                 }
                 writeFileSync(absPath, action.content, "utf-8");
+                if (action.executable)
+                    chmodSync(absPath, 0o755);
                 counts.updated++;
                 break;
             }

package/dist/scaffold/incremental.js.map

@@ -1 +1 @@
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package/dist/scaffold/merge.d.ts

@@ -49,4 +49,20 @@ export declare function shouldOverwriteScript(existingContent: string, manifestH
  * @returns Merged JSON string, or existingRaw if parse fails
  */
 export declare function deepMergeJson(existingRaw: string, generatedRaw: string): string;
+/**
+ * Merge settings.json files with domain-aware logic for Claude Code settings.
+ *
+ * Rules:
+ *   - permissions.allow: union-merge (deduplicated)
+ *   - permissions.deny: union-merge (deduplicated)
+ *   - env: shallow-merge (generated wins on key conflict)
+ *   - hooks: rewritten entirely from generated (topology owns hooks)
+ *   - All other top-level keys: existing wins (user-only keys preserved)
+ *
+ * @param existingRaw - Current settings.json content on disk (JSON string, or empty string)
+ * @param generatedRaw - Freshly generated settings.json content (JSON string)
+ * @returns Merged JSON string
+ * @throws {Error} if existingRaw is non-empty and is invalid JSON
+ */
+export declare function deepMergeSettingsJson(existingRaw: string, generatedRaw: string): string;
 //# sourceMappingURL=merge.d.ts.map

package/dist/scaffold/merge.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"merge.d.ts","sourceRoot":"","sources":["../../src/scaffold/merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAuBH;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,MAAM,CA4CR;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,qBAAqB,CACnC,eAAe,EAAE,MAAM,EACvB,YAAY,EAAE,MAAM,GACnB,OAAO,CAET;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,aAAa,CAAC,WAAW,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAc/E;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,qBAAqB,CAAC,WAAW,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,CAmEvF"}

package/dist/scaffold/merge.js

@@ -109,6 +109,83 @@ export function deepMergeJson(existingRaw, generatedRaw) {
     const merged = mergeObjects(existing, generated);
     return JSON.stringify(merged, null, 2) + "\n";
 }
+/**
+ * Merge settings.json files with domain-aware logic for Claude Code settings.
+ *
+ * Rules:
+ *   - permissions.allow: union-merge (deduplicated)
+ *   - permissions.deny: union-merge (deduplicated)
+ *   - env: shallow-merge (generated wins on key conflict)
+ *   - hooks: rewritten entirely from generated (topology owns hooks)
+ *   - All other top-level keys: existing wins (user-only keys preserved)
+ *
+ * @param existingRaw - Current settings.json content on disk (JSON string, or empty string)
+ * @param generatedRaw - Freshly generated settings.json content (JSON string)
+ * @returns Merged JSON string
+ * @throws {Error} if existingRaw is non-empty and is invalid JSON
+ */
+export function deepMergeSettingsJson(existingRaw, generatedRaw) {
+    // Empty existing means first scaffold — return generated unchanged
+    if (existingRaw.trim() === "") {
+        return generatedRaw;
+    }
+    let existing;
+    let generated;
+    try {
+        existing = JSON.parse(existingRaw);
+    }
+    catch (err) {
+        throw new Error(`invalid JSON in existing settings.json: ${err.message}`);
+    }
+    try {
+        generated = JSON.parse(generatedRaw);
+    }
+    catch (err) {
+        throw new Error(`invalid JSON in generated settings.json: ${err.message}`);
+    }
+    // Start with existing (preserves all user-only top-level keys)
+    const merged = { ...existing };
+    // --- permissions: union-merge allow and deny arrays ---
+    const existingPerms = (existing.permissions ?? {});
+    const generatedPerms = (generated.permissions ?? {});
+    if (generated.permissions !== undefined || existing.permissions !== undefined) {
+        const mergedPerms = {};
+        for (const key of ["allow", "deny"]) {
+            const ex = Array.isArray(existingPerms[key]) ? existingPerms[key] : [];
+            const gen = Array.isArray(generatedPerms[key]) ? generatedPerms[key] : [];
+            const union = Array.from(new Set([...ex, ...gen]));
+            if (union.length > 0) {
+                mergedPerms[key] = union;
+            }
+        }
+        if (Object.keys(mergedPerms).length > 0) {
+            merged.permissions = mergedPerms;
+        }
+    }
+    // --- env: shallow-merge, generated wins on conflict ---
+    if (generated.env !== undefined) {
+        const existingEnv = (existing.env ?? {});
+        const generatedEnv = generated.env;
+        merged.env = { ...existingEnv, ...generatedEnv };
+    }
+    // --- hooks: rewritten entirely from generated (topology owns hooks) ---
+    if (generated.hooks !== undefined) {
+        merged.hooks = generated.hooks;
+    }
+    else {
+        // No hooks in generated — remove the hooks key (topology no longer declares any)
+        delete merged.hooks;
+    }
+    // --- all other generated keys: add if missing, do NOT overwrite existing ---
+    for (const [key, value] of Object.entries(generated)) {
+        if (key === "permissions" || key === "env" || key === "hooks")
+            continue;
+        if (merged[key] === undefined) {
+            merged[key] = value;
+        }
+    }
+    return JSON.stringify(merged, null, 2) + "\n";
+}
 function mergeObjects(existing, generated) {
     // Start with a copy of existing (preserves user-only keys)
     const result = { ...existing };

package/dist/scaffold/merge.js.map

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package/dist/scaffold/types.d.ts

@@ -31,11 +31,13 @@ export type FileAction = {
     type: "create";
     path: string;
     content: string;
+    executable?: boolean;
 } | {
     type: "update";
     path: string;
     content: string;
     detail: string;
+    executable?: boolean;
 } | {
     type: "delete";
     path: string;

package/dist/scaffold/types.d.ts.map

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