agentopology 0.5.1 → 0.6.0

package/dist/scaffold/incremental.js

@@ -1,20 +1,58 @@
 /**
  * Incremental scaffold orchestrator.
  *
- * Computes a plan of file actions (create, update, delete, unchanged, conflict)
- * by comparing freshly generated files against what is on disk and what was
- * previously tracked in the scaffold manifest.
+ * Computes a plan of file actions (create, update, delete, unchanged, conflict,
+ * blocked) by comparing freshly generated files against what is on disk and
+ * what was previously tracked in the scaffold manifest.
+ *
+ * The rule the plan enforces: scaffold only changes what it owns. A file is
+ * owned when the manifest records it. Anything else on disk — a hand-written
+ * skill, a settings file, a symlink into another repo — is a conflict (kept
+ * unless --force) or blocked (never touched). The first scaffold used to skip
+ * this plan and write everything; it overwrote real files and, following a
+ * symlink, files in a second repository.
  *
  * @module
  */
-import { chmodSync, existsSync, mkdirSync, readFileSync, unlinkSync, writeFileSync } from "node:fs";
+import { chmodSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, rmdirSync, unlinkSync, writeFileSync, } from "node:fs";
 import { dirname, join } from "node:path";
+import { hashContent } from "./manifest.js";
 import { mergeAgentFile, shouldOverwriteScript, deepMergeJson, deepMergeSettingsJson, } from "./merge.js";
+export { unsafePathReason } from "../parser/paths.js";
+import { unsafePathReason } from "../parser/paths.js";
+/**
+ * The first symlink between `basePath` and the file, or null. Scaffold never
+ * writes through one: a linked skill folder belongs to somewhere else.
+ */
+function symlinkOnPath(basePath, relPath) {
+    let cur = basePath;
+    for (const seg of relPath.split("/")) {
+        cur = join(cur, seg);
+        try {
+            if (lstatSync(cur).isSymbolicLink())
+                return cur.slice(basePath.length + 1);
+        }
+        catch {
+            return null; // does not exist yet — nothing further down can be a link
+        }
+    }
+    return null;
+}
+function isDirectory(absPath) {
+    try {
+        return lstatSync(absPath).isDirectory();
+    }
+    catch {
+        return false;
+    }
+}
 /**
  * Compute an incremental scaffold plan.
  *
  * Compares generated files against what exists on disk and the previous
- * manifest to determine the minimal set of file operations needed.
+ * manifest to determine the minimal set of file operations needed. Used for
+ * the first scaffold too (manifest null): every existing file is then
+ * unmanaged and therefore a conflict, never an overwrite.
  *
  * @param basePath - Absolute path to the project root
  * @param target - Binding target name (e.g. "claude-code")
@@ -29,9 +67,26 @@ export function computeIncrementalPlan(basePath, target, generatedFiles, manifes
     for (const file of generatedFiles) {
         generatedMap.set(file.path, file);
     }
+    // Everything this topology writes or wrote: hooks whose command names one of
+    // these paths belong to it; every other hook in settings.json is the user's.
+    const ownedPaths = [...generatedMap.keys(), ...Object.keys(manifest?.files ?? {})];
     // Process each generated file
     for (const file of generatedFiles) {
+        const unsafe = unsafePathReason(file.path);
+        if (unsafe) {
+            actions.push({ type: "blocked", path: file.path, detail: unsafe, unsafe: true });
+            continue;
+        }
+        const link = symlinkOnPath(basePath, file.path);
+        if (link) {
+            actions.push({ type: "blocked", path: file.path, detail: `symlink at ${link} — never written through` });
+            continue;
+        }
         const absPath = join(basePath, file.path);
+        if (isDirectory(absPath)) {
+            actions.push({ type: "blocked", path: file.path, detail: "a directory exists at this path" });
+            continue;
+        }
         const category = file.category ?? "machine";
         const onDisk = existsSync(absPath);
         if (!onDisk) {
@@ -43,8 +98,46 @@ export function computeIncrementalPlan(basePath, target, generatedFiles, manifes
             });
             continue;
         }
+        if (file.createOnly) {
+            actions.push({ type: "kept", path: file.path, detail: "the user's own file; created only when missing" });
+            continue;
+        }
         const existingContent = readFileSync(absPath, "utf-8");
         const manifestEntry = manifest?.files[file.path] ?? null;
+        if (existingContent === file.content) {
+            actions.push({ type: "unchanged", path: file.path });
+            continue;
+        }
+        // Config files merge whether or not scaffold made them: the merge keeps
+        // every key, hook and rule the user wrote.
+        if (category === "shared-config") {
+            const isSettings = /(^|\/)settings\.json$/.test(file.path);
+            const merged = isSettings
+                ? deepMergeSettingsJson(existingContent, file.content, ownedPaths)
+                : deepMergeJson(existingContent, file.content);
+            if (merged === existingContent) {
+                actions.push({ type: "unchanged", path: file.path });
+            }
+            else {
+                actions.push({
+                    type: "update",
+                    path: file.path,
+                    content: merged,
+                    detail: "config merged",
+                });
+            }
+            continue;
+        }
+        // Not in the manifest: a file scaffold did not create. Never overwrite it.
+        if (!manifestEntry) {
+            actions.push({
+                type: "conflict",
+                path: file.path,
+                content: file.content,
+                detail: "exists, not created by scaffold",
+            });
+            continue;
+        }
         switch (category) {
             case "agent": {
                 const merged = mergeAgentFile(existingContent, file.content, target);
@@ -61,145 +154,192 @@ export function computeIncrementalPlan(basePath, target, generatedFiles, manifes
                 }
                 break;
             }
-            case "script": {
-                const manifestHash = manifestEntry?.hash ?? "";
-                if (shouldOverwriteScript(existingContent, manifestHash)) {
-                    // User hasn't edited — safe to overwrite
-                    if (file.content === existingContent) {
-                        actions.push({ type: "unchanged", path: file.path });
-                    }
-                    else {
-                        actions.push({
-                            type: "update",
-                            path: file.path,
-                            content: file.content,
-                            detail: "script regenerated",
-                        });
-                    }
-                }
-                else {
-                    // User has edited — conflict
-                    actions.push({
-                        type: "conflict",
-                        path: file.path,
-                        content: file.content,
-                        detail: "user edited",
-                    });
-                }
-                break;
-            }
-            case "shared-config": {
-                // settings.json needs the DOMAIN-AWARE merge, not the generic one.
-                // The generic `deepMergeJson` keeps the existing value whenever a key
-                // exists on both sides and either side is not a plain object — and
-                // `hooks[event]` is an ARRAY. So adding a hook to an event the file
-                // already declares silently dropped it, and removing a hook was
-                // impossible. `deepMergeSettingsJson` unions permissions, merges env,
-                // and lets the topology own `hooks` outright (including deleting it).
-                // It was written and fully tested but never reachable until now.
-                const isSettings = /(^|\/)settings\.json$/.test(file.path);
-                const merged = isSettings
-                    ? deepMergeSettingsJson(existingContent, file.content)
-                    : deepMergeJson(existingContent, file.content);
-                if (merged === existingContent) {
-                    actions.push({ type: "unchanged", path: file.path });
-                }
-                else {
+            case "script":
+            case "machine":
+            default: {
+                // Overwrite only what is still exactly as scaffold left it. CLAUDE.md,
+                // commands and crontab.fragment used to be overwritten on every run,
+                // edits and all.
+                if (shouldOverwriteScript(existingContent, manifestEntry.hash)) {
                     actions.push({
                         type: "update",
                         path: file.path,
-                        content: merged,
-                        detail: "config merged",
+                        content: file.content,
+                        detail: category === "script" ? "script regenerated" : "config updated",
+                        ...(file.executable ? { executable: true } : {}),
                     });
                 }
-                break;
-            }
-            case "machine":
-            default: {
-                if (file.content === existingContent) {
-                    actions.push({ type: "unchanged", path: file.path });
-                }
                 else {
                     actions.push({
-                        type: "update",
+                        type: "conflict",
                         path: file.path,
                         content: file.content,
-                        detail: "config updated",
+                        detail: "user edited",
                     });
                 }
                 break;
             }
         }
     }
-    // Check for files in manifest that are no longer generated (deletions)
+    // Files in the manifest that are no longer generated
     if (manifest) {
-        for (const manifestPath of Object.keys(manifest.files)) {
-            if (!generatedMap.has(manifestPath)) {
-                actions.push({ type: "delete", path: manifestPath });
+        for (const [manifestPath, entry] of Object.entries(manifest.files)) {
+            if (generatedMap.has(manifestPath))
+                continue;
+            if (unsafePathReason(manifestPath))
+                continue;
+            const absPath = join(basePath, manifestPath);
+            if (!existsSync(absPath))
+                continue;
+            if (symlinkOnPath(basePath, manifestPath)) {
+                actions.push({ type: "blocked", path: manifestPath, detail: "symlink — never deleted through" });
+                continue;
+            }
+            if (hashContent(readFileSync(absPath, "utf-8")) !== entry.hash) {
+                actions.push({ type: "blocked", path: manifestPath, detail: "no longer generated, but edited — kept" });
+                continue;
             }
+            actions.push({ type: "delete", path: manifestPath });
         }
     }
     return actions;
 }
+/** Remove now-empty directories from `absDir` up to (not including) `basePath`. */
+function removeEmptyDirs(basePath, absDir) {
+    let cur = absDir;
+    while (cur.startsWith(basePath + "/") && cur !== basePath) {
+        try {
+            if (readdirSync(cur).length > 0)
+                return;
+            rmdirSync(cur);
+        }
+        catch {
+            return;
+        }
+        cur = dirname(cur);
+    }
+}
 /**
  * Execute a set of file actions against the filesystem.
  *
+ * Refuses outright when the plan holds an unsafe path, so a bad plan writes
+ * nothing at all. A single failed write is recorded and the rest proceed, so
+ * the caller can still write a manifest that matches the disk.
+ *
  * @param basePath - Absolute path to the project root
  * @param actions - File actions computed by {@link computeIncrementalPlan}
  * @param options - Execution options
- * @returns Counts of each action type performed
+ * @returns Counts of each action type performed, plus what was written
  */
 export function executeActions(basePath, actions, options) {
-    const counts = { created: 0, updated: 0, deleted: 0, unchanged: 0, conflicts: 0 };
+    const unsafe = actions.filter((a) => a.type === "blocked" && a.unsafe);
+    if (unsafe.length > 0) {
+        throw new Error(`refusing to write: ${unsafe.length} unsafe path(s): ` +
+            unsafe.map((a) => `${a.path}`).join(", "));
+    }
+    const result = {
+        created: 0,
+        updated: 0,
+        deleted: 0,
+        unchanged: 0,
+        conflicts: 0,
+        blocked: 0,
+        written: new Map(),
+        removed: [],
+        failures: [],
+    };
+    const write = (path, content, executable) => {
+        const absPath = join(basePath, path);
+        try {
+            mkdirSync(dirname(absPath), { recursive: true });
+            writeFileSync(absPath, content, "utf-8");
+            if (executable)
+                chmodSync(absPath, 0o755);
+            result.written.set(path, content);
+            return true;
+        }
+        catch (err) {
+            result.failures.push({ path, error: err.message });
+            return false;
+        }
+    };
     for (const action of actions) {
-        const absPath = join(basePath, action.path);
         switch (action.type) {
             case "create": {
-                const dir = dirname(absPath);
-                if (!existsSync(dir)) {
-                    mkdirSync(dir, { recursive: true });
-                }
-                writeFileSync(absPath, action.content, "utf-8");
-                if (action.executable)
-                    chmodSync(absPath, 0o755);
-                counts.created++;
+                if (write(action.path, action.content, action.executable))
+                    result.created++;
                 break;
             }
             case "update": {
-                const dir = dirname(absPath);
-                if (!existsSync(dir)) {
-                    mkdirSync(dir, { recursive: true });
-                }
-                writeFileSync(absPath, action.content, "utf-8");
-                if (action.executable)
-                    chmodSync(absPath, 0o755);
-                counts.updated++;
+                if (write(action.path, action.content, action.executable))
+                    result.updated++;
                 break;
             }
             case "delete": {
+                const absPath = join(basePath, action.path);
                 if (options.prune && existsSync(absPath)) {
-                    unlinkSync(absPath);
+                    try {
+                        unlinkSync(absPath);
+                        result.removed.push(action.path);
+                        removeEmptyDirs(basePath, dirname(absPath));
+                    }
+                    catch (err) {
+                        result.failures.push({ path: action.path, error: err.message });
+                    }
                 }
-                counts.deleted++;
+                result.deleted++;
                 break;
             }
             case "conflict": {
-                if (options.force) {
-                    const dir = dirname(absPath);
-                    if (!existsSync(dir)) {
-                        mkdirSync(dir, { recursive: true });
-                    }
-                    writeFileSync(absPath, action.content, "utf-8");
-                }
-                counts.conflicts++;
+                if (options.force)
+                    write(action.path, action.content);
+                result.conflicts++;
+                break;
+            }
+            case "blocked": {
+                result.blocked++;
+                break;
+            }
+            case "kept": {
+                result.unchanged++;
                 break;
             }
             case "unchanged": {
-                counts.unchanged++;
+                result.unchanged++;
                 break;
             }
         }
     }
-    return counts;
+    return result;
+}
+/**
+ * The manifest after a run: exactly the files scaffold now owns, hashed as
+ * they are on disk.
+ *
+ * Owned = written or unchanged this run, plus earlier entries for files the
+ * run left alone (an edited file keeps its old hash, so it stays a conflict;
+ * an unpruned leftover stays tracked, so a later --prune can still remove it).
+ * A pre-existing file scaffold did not write is never claimed.
+ */
+export function nextManifestFiles(basePath, actions, generatedFiles, previous, result) {
+    const categoryOf = new Map(generatedFiles.map((f) => [f.path, f.category ?? "machine"]));
+    const files = {};
+    const removed = new Set(result.removed);
+    for (const action of actions) {
+        const prev = previous?.files[action.path];
+        const category = categoryOf.get(action.path) ?? prev?.category ?? "machine";
+        const written = result.written.get(action.path);
+        if (written !== undefined) {
+            files[action.path] = { hash: hashContent(written), category };
+        }
+        else if (action.type === "unchanged") {
+            const onDisk = readFileSync(join(basePath, action.path), "utf-8");
+            files[action.path] = { hash: hashContent(onDisk), category };
+        }
+        else if (prev && !removed.has(action.path)) {
+            files[action.path] = prev;
+        }
+    }
+    return files;
 }
 //# sourceMappingURL=incremental.js.map

package/dist/scaffold/incremental.js.map

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

@@ -17,10 +17,17 @@ export declare function getManifestPath(target: string): string;
 /**
  * Read an existing scaffold manifest from disk.
  * Returns `null` if the manifest does not exist or cannot be parsed.
+ *
+ * With `source` (the .at file name), returns only that topology's manifest:
+ * two topologies scaffolded into one project used to share one manifest, so
+ * the second treated the first one's files as its own — overwriting its
+ * crontab and, with --prune, deleting its scripts.
  */
-export declare function readManifest(basePath: string, target: string): ScaffoldManifest | null;
+export declare function readManifest(basePath: string, target: string, source?: string): ScaffoldManifest | null;
 /**
  * Write a scaffold manifest to disk, creating parent directories as needed.
+ * Never replaces another topology's manifest: when the shared file belongs to
+ * a different source, this one goes beside it.
  */
 export declare function writeManifest(basePath: string, target: string, manifest: ScaffoldManifest): void;
 /**

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

@@ -1 +1 @@
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+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/scaffold/manifest.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC;AAInD;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAkBtD;AAmBD;;;;;;;;GAQG;AACH,wBAAgB,YAAY,CAC1B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,MAAM,CAAC,EAAE,MAAM,GACd,gBAAgB,GAAG,IAAI,CAMzB;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,gBAAgB,GACzB,IAAI,CAWN;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEnD"}

package/dist/scaffold/manifest.js

@@ -36,26 +36,50 @@ export function getManifestPath(target) {
     }
 }
 /**
- * Read an existing scaffold manifest from disk.
- * Returns `null` if the manifest does not exist or cannot be parsed.
+ * Where one topology's manifest lives when the shared one belongs to another
+ * topology: `.scaffold-manifest.<source>.json` beside it.
  */
-export function readManifest(basePath, target) {
-    const manifestPath = join(basePath, getManifestPath(target));
-    if (!existsSync(manifestPath))
+function perSourcePath(target, source) {
+    return getManifestPath(target).replace(/\.json$/, `.${source.replace(/[^A-Za-z0-9_.-]/g, "_")}.json`);
+}
+function readJson(path) {
+    if (!existsSync(path))
         return null;
     try {
-        const raw = readFileSync(manifestPath, "utf-8");
-        return JSON.parse(raw);
+        return JSON.parse(readFileSync(path, "utf-8"));
     }
     catch {
         return null;
     }
 }
+/**
+ * Read an existing scaffold manifest from disk.
+ * Returns `null` if the manifest does not exist or cannot be parsed.
+ *
+ * With `source` (the .at file name), returns only that topology's manifest:
+ * two topologies scaffolded into one project used to share one manifest, so
+ * the second treated the first one's files as its own — overwriting its
+ * crontab and, with --prune, deleting its scripts.
+ */
+export function readManifest(basePath, target, source) {
+    const shared = readJson(join(basePath, getManifestPath(target)));
+    if (!source)
+        return shared;
+    const own = readJson(join(basePath, perSourcePath(target, source)));
+    if (own)
+        return own;
+    return shared && shared.source === source ? shared : null;
+}
 /**
  * Write a scaffold manifest to disk, creating parent directories as needed.
+ * Never replaces another topology's manifest: when the shared file belongs to
+ * a different source, this one goes beside it.
  */
 export function writeManifest(basePath, target, manifest) {
-    const manifestPath = join(basePath, getManifestPath(target));
+    const sharedPath = join(basePath, getManifestPath(target));
+    const shared = readJson(sharedPath);
+    const ownPath = join(basePath, perSourcePath(target, manifest.source));
+    const manifestPath = existsSync(ownPath) || (shared && shared.source !== manifest.source) ? ownPath : sharedPath;
     const dir = dirname(manifestPath);
     if (!existsSync(dir)) {
         mkdirSync(dir, { recursive: true });

package/dist/scaffold/manifest.js.map

@@ -1 +1 @@
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+{"version":3,"file":"manifest.js","sourceRoot":"","sources":["../../src/scaffold/manifest.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,SAAS,CAAC;AAC7E,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAI1C,MAAM,iBAAiB,GAAG,yBAAyB,CAAC;AAEpD;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAAC,MAAc;IAC5C,QAAQ,MAAM,EAAE,CAAC;QACf,KAAK,aAAa;YAChB,OAAO,IAAI,CAAC,SAAS,EAAE,iBAAiB,CAAC,CAAC;QAC5C,KAAK,OAAO;YACV,OAAO,IAAI,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;QAC3C,KAAK,YAAY;YACf,OAAO,IAAI,CAAC,SAAS,EAAE,iBAAiB,CAAC,CAAC;QAC5C,KAAK,aAAa;YAChB,OAAO,IAAI,CAAC,SAAS,EAAE,iBAAiB,CAAC,CAAC;QAC5C,KAAK,UAAU;YACb,OAAO,IAAI,CAAC,WAAW,EAAE,iBAAiB,CAAC,CAAC;QAC9C,KAAK,MAAM;YACT,OAAO,IAAI,CAAC,OAAO,EAAE,iBAAiB,CAAC,CAAC;QAC1C;YACE,4CAA4C;YAC5C,OAAO,iBAAiB,CAAC;IAC7B,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,SAAS,aAAa,CAAC,MAAc,EAAE,MAAc;IACnD,OAAO,eAAe,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE,IAAI,MAAM,CAAC,OAAO,CAAC,kBAAkB,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;AACxG,CAAC;AAED,SAAS,QAAQ,CAAC,IAAY;IAC5B,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IACnC,IAAI,CAAC;QACH,OAAO,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,OAAO,CAAC,CAAqB,CAAC;IACrE,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,YAAY,CAC1B,QAAgB,EAChB,MAAc,EACd,MAAe;IAEf,MAAM,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAC,QAAQ,EAAE,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IACjE,IAAI,CAAC,MAAM;QAAE,OAAO,MAAM,CAAC;IAC3B,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,QAAQ,EAAE,aAAa,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC;IACpE,IAAI,GAAG;QAAE,OAAO,GAAG,CAAC;IACpB,OAAO,MAAM,IAAI,MAAM,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC;AAC5D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAC3B,QAAgB,EAChB,MAAc,EACd,QAA0B;IAE1B,MAAM,UAAU,GAAG,IAAI,CAAC,QAAQ,EAAE,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC;IAC3D,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC;IACpC,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,EAAE,aAAa,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC;IACvE,MAAM,YAAY,GAChB,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,MAAM,KAAK,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC;IAC9F,MAAM,GAAG,GAAG,OAAO,CAAC,YAAY,CAAC,CAAC;IAClC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACrB,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IACtC,CAAC;IACD,aAAa,CAAC,YAAY,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,EAAE,OAAO,CAAC,CAAC;AACjF,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,OAAe;IACzC,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;AACrE,CAAC"}

package/dist/scaffold/merge.d.ts

@@ -52,17 +52,28 @@ export declare function deepMergeJson(existingRaw: string, generatedRaw: string)
 /**
  * Merge settings.json files with domain-aware logic for Claude Code settings.
  *
+ * The user's file is the base; scaffold only adds or replaces what it owns.
+ *
  * Rules:
- *   - permissions.allow: union-merge (deduplicated)
- *   - permissions.deny: union-merge (deduplicated)
+ *   - permissions: every existing key is kept (ask, defaultMode,
+ *     additionalDirectories, ...); allow, deny and ask arrays are
+ *     union-merged; a generated scalar is added only where none exists
  *   - env: shallow-merge (generated wins on key conflict)
- *   - hooks: rewritten entirely from generated (topology owns hooks)
+ *   - hooks: a hook group is the topology's when one of its commands names a
+ *     path in `ownedPaths`; those are replaced by the generated hooks, and
+ *     every other group — the user's — is kept. Without `ownedPaths`, nothing
+ *     existing is treated as owned, so nothing is removed
  *   - All other top-level keys: existing wins (user-only keys preserved)
  *
+ * This used to rebuild permissions from allow/deny alone and replace hooks
+ * wholesale, so a re-scaffold deleted the user's own hooks, ask rules and
+ * defaultMode, and two topologies in one repo deleted each other's hooks.
+ *
  * @param existingRaw - Current settings.json content on disk (JSON string, or empty string)
  * @param generatedRaw - Freshly generated settings.json content (JSON string)
+ * @param ownedPaths - Paths this topology writes or wrote (generated + manifest)
  * @returns Merged JSON string
  * @throws {Error} if existingRaw is non-empty and is invalid JSON
  */
-export declare function deepMergeSettingsJson(existingRaw: string, generatedRaw: string): string;
+export declare function deepMergeSettingsJson(existingRaw: string, generatedRaw: string, ownedPaths?: 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,CAgB/E;AAED;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,wBAAgB,qBAAqB,CACnC,WAAW,EAAE,MAAM,EACnB,YAAY,EAAE,MAAM,EACpB,UAAU,GAAE,MAAM,EAAO,GACxB,MAAM,CA+ER"}