@detergent-software/atk 7.12.0-dev.1 → 7.12.0-dev.3

package/build/lib/config-file.js

@@ -0,0 +1,84 @@
+import { existsSync } from 'node:fs';
+import { readFile } from 'node:fs/promises';
+import { extname } from 'node:path';
+import { parse as parseToml } from 'smol-toml';
+import { writeJsonFile, writeTomlFile } from './write-file.js';
+/**
+ * Infer the config format from a file path. `.toml` (any case) → `toml`,
+ * everything else → `json`. Used where only a lockfile entry (file + key) is
+ * available and no placement is in scope.
+ */
+export function detectConfigFormat(filePath) {
+    return extname(filePath).toLowerCase() === '.toml' ? 'toml' : 'json';
+}
+/**
+ * Normalize a value so that what is checksummed equals what will be read back
+ * from disk after a write. TOML has no null: smol-toml silently drops
+ * null/undefined object members on serialize, so strip them up front. JSON is
+ * returned unchanged.
+ */
+export function normalizeForFormat(value, format) {
+    if (format !== 'toml') {
+        return value;
+    }
+    return stripNullish(value);
+}
+/**
+ * Parse config text in the given format. Throws on syntax errors
+ * (`SyntaxError` for JSON, `TomlError` for TOML).
+ */
+export function parseConfig(raw, format) {
+    return (format === 'toml' ? parseToml(raw) : JSON.parse(raw));
+}
+/**
+ * Read and parse a config file. Propagates filesystem errors (e.g. ENOENT)
+ * like `readFile` — callers keep their own existence guards.
+ */
+export async function readConfigFile(filePath, format) {
+    const raw = await readFile(filePath, 'utf-8');
+    return parseConfig(raw, format);
+}
+/**
+ * Resolve the format for a placement's config file: an explicit
+ * `configFormat` wins, otherwise the file extension decides.
+ */
+export function resolveConfigFormat(filePath, placement) {
+    return placement?.configFormat ?? detectConfigFormat(filePath);
+}
+/**
+ * Serialize and write a config file in the given format, idempotently.
+ *
+ * For TOML, re-serializing drops any comments the user had in the file; when
+ * that is about to happen, a one-line warning is emitted through `onProgress`
+ * so the loss is visible rather than silent.
+ */
+export async function writeConfigFile(filePath, data, format, onProgress) {
+    if (format === 'json') {
+        await writeJsonFile(filePath, data);
+        return;
+    }
+    if (onProgress && existsSync(filePath)) {
+        const existing = await readFile(filePath, 'utf-8');
+        if (/^\s*#/m.test(existing)) {
+            onProgress(`Warning: rewriting ${filePath} — TOML comments and custom formatting are not preserved`);
+        }
+    }
+    await writeTomlFile(filePath, data);
+}
+/** Recursively drop null/undefined members from plain objects (arrays are mapped, not filtered). */
+function stripNullish(value) {
+    if (Array.isArray(value)) {
+        return value.map(stripNullish);
+    }
+    if (value !== null && typeof value === 'object') {
+        const out = {};
+        for (const [key, member] of Object.entries(value)) {
+            if (member === null || member === undefined)
+                continue;
+            out[key] = stripNullish(member);
+        }
+        return out;
+    }
+    return value;
+}
+//# sourceMappingURL=config-file.js.map

package/build/lib/config-file.js.map

@@ -0,0 +1 @@
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package/build/lib/diff-command.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"diff-command.d.ts","sourceRoot":"","sources":["../../src/lib/diff-command.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAC5D,OAAO,KAAK,EAAE,cAAc,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAC3E,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAkB3D,MAAM,MAAM,WAAW,GACnB;IACE,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB,SAAS,EAAE,cAAc,CAAC;IAC1B,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,SAAS,CAAC;IACnB,aAAa,EAAE,aAAa,CAAC;IAC7B,WAAW,EAAE,OAAO,CAAC;CACtB,GACD;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,iBAAiB,CAAA;CAAE,GAC5C;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,eAAe,CAAA;CAAE,CAAC;AAE/C,0FAA0F;AAC1F,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,aAAa,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,MAAM,GAAG,SAAS,EAC/B,MAAM,EAAE,MAAM,GAAG,SAAS,EAC1B,SAAS,EAAE,MAAM,GAAG,SAAS,EAC7B,QAAQ,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,GAClC,OAAO,CAAC,WAAW,CAAC,CAyJtB"}

package/build/lib/diff-command.js

@@ -4,7 +4,7 @@ import { join } from 'node:path';
 import { resolveInstalledPaths } from './adapter.js';
 import { loadConfig } from './config.js';
 import { computeAddedFileDiff, computeRemovedFileDiff, computeUnifiedDiff } from './diff.js';
-import { findInstalledAsset, readLockfile } from './lockfile.js';
+import { findInstalledAssetWithFallback, readLockfile } from './lockfile.js';
 import { resolveActiveOrg } from './org.js';
 import { findProjectRoot } from './paths.js';
 import { fetchAssetFileBytes, fetchRegistry, findAsset, listAssetFiles, } from './registry.js';
@@ -30,14 +30,18 @@ export async function computeDiffOutcome(name, org, tool, context, refresh, proj
     const { adapter } = await resolveTool(tool);
     progress('Reading lockfile...');
     const lockfile = await readLockfile(projectDir);
+    // The active org is a preference: prefer that org's lockfile entry, fall back to
+    // the global entry (mirrors how `install` resolved the name).
     const resolvedOrg = resolveActiveOrg(inlineOrg ?? cliOrg, lockfile.org, config.org);
-    const installed = findInstalledAsset(lockfile, name, undefined, resolvedOrg);
+    const installed = findInstalledAssetWithFallback(lockfile, name, undefined, resolvedOrg);
     if (!installed) {
         return { name, outcome: 'not-installed' };
     }
     progress('Fetching registry...');
     const registry = await fetchRegistry({ force: refresh });
-    const foundAsset = findAsset(registry, name, installed.type, undefined, resolvedOrg);
+    // Look up the registry identity of the asset actually installed, so a global
+    // install is never diffed against a same-named org-scoped registry asset.
+    const foundAsset = findAsset(registry, name, installed.type, undefined, installed.org);
     if (!foundAsset) {
         return { name, outcome: 'not-in-registry' };
     }

package/build/lib/diff-command.js.map

@@ -1 +1 @@
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package/build/lib/init.d.ts.map

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package/build/lib/init.js

@@ -4,6 +4,7 @@ import { basename, extname, join, resolve } from 'node:path';
 import { promisify } from 'node:util';
 import { getPlacement, loadAdapter, loadAllAdapters, resolveInstalledPaths } from './adapter.js';
 import { collectFilesRecursive } from './checksum.js';
+import { parseConfig, resolveConfigFormat } from './config-file.js';
 import { parseOrgFromName } from './org.js';
 import { findProjectRoot } from './paths.js';
 import { writeJsonFile, writeTextFile } from './write-file.js';
@@ -172,7 +173,7 @@ export async function forkFromLocal(fromPath, assetType) {
             const projectRoot = findProjectRoot();
             const settingsPath = join(projectRoot, placement.configFile);
             const settingsRaw = await readFile(settingsPath, 'utf-8');
-            const settings = JSON.parse(settingsRaw);
+            const settings = parseConfig(settingsRaw, resolveConfigFormat(settingsPath, placement));
             const section = settings[placement.configKey];
             if (section && typeof section === 'object' && !Array.isArray(section)) {
                 const hookConfig = {};
@@ -444,15 +445,16 @@ export function validateAssetName(name) {
  */
 async function forkFromLocalMcpConfig(keyName, placement, manifest) {
     const projectRoot = findProjectRoot();
-    const mcpPath = join(projectRoot, placement.configFile ?? '.mcp.json');
+    const configFile = placement.configFile ?? '.mcp.json';
+    const mcpPath = join(projectRoot, configFile);
     let mcpRaw;
     try {
         mcpRaw = await readFile(mcpPath, 'utf-8');
     }
     catch {
-        throw new Error(`Cannot read "${mcpPath}". Ensure .mcp.json exists in the project root.`);
+        throw new Error(`Cannot read "${mcpPath}". Ensure ${configFile} exists in the project root.`);
     }
-    const mcpJson = JSON.parse(mcpRaw);
+    const mcpJson = parseConfig(mcpRaw, resolveConfigFormat(mcpPath, placement));
     const configKey = placement.configKey ?? 'mcpServers';
     const servers = mcpJson[configKey];
     if (!servers || !(keyName in servers)) {

package/build/lib/init.js.map

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package/build/lib/installer.d.ts

@@ -18,6 +18,13 @@ export interface InstallOptions {
     pin?: boolean;
     /** Project root directory. */
     projectDir: string;
+    /**
+     * When true, a plan containing only asset types this tool has no placement for resolves
+     * to an empty result instead of throwing. Multi-tool installs set this so a tool that
+     * lacks e.g. a `rule` placement steps aside while another tool installs the asset; see
+     * {@link assertInstalledByAnyTool} for the "nobody installed it" check.
+     */
+    skipUnsupported?: boolean;
 }
 export interface InstallResult {
     bundleOrigin?: {
@@ -45,6 +52,16 @@ export declare class InstallerError extends Error {
     hint?: string;
     constructor(message: string, options?: ErrorHintOptions);
 }
+/**
+ * Guard for multi-tool installs run with `skipUnsupported`. Each tool skips the asset
+ * types it cannot place, which is fine as long as some tool placed something. If every
+ * tool skipped every entry, nothing was installed — surface that as an error rather
+ * than reporting a successful no-op.
+ */
+export declare function assertInstalledByAnyTool(plan: InstallPlan, toolResults: Array<{
+    results: InstallResult[];
+    tool: string;
+}>): void;
 /**
  * Execute a full install plan — install all assets in order.
  * On partial failure, rolls back previously installed assets (deletes placed files,

package/build/lib/installer.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"installer.d.ts","sourceRoot":"","sources":["../../src/lib/installer.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,WAAW,EAAoB,MAAM,eAAe,CAAC;AACnE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AAepD,OAAO,EAAE,KAAK,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAQpD,MAAM,WAAW,cAAc;IAC7B,mCAAmC;IACnC,OAAO,EAAE,OAAO,CAAC;IACjB,kEAAkE;IAClE,YAAY,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,GAAG,CAAC,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/D,yEAAyE;IACzE,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,qCAAqC;IACrC,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,CAAC;IACvC,8CAA8C;IAC9C,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,8BAA8B;IAC9B,UAAU,EAAE,MAAM,CAAC;IACnB;;;;;OAKG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC;CAC3B;AAED,MAAM,WAAW,aAAa;IAC5B,YAAY,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,GAAG,CAAC,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/D,oBAAoB,EAAE,KAAK,CAAC;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,OAAO,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC/F,WAAW,EAAE,KAAK,CAAC;QAAE,WAAW,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC5D,aAAa,EAAE,YAAY,GAAG,QAAQ,CAAC;IACvC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAQD,qBAAa,cAAe,SAAQ,KAAK;IACvC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;gBAEF,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,gBAAqB;CAM5D;AAED;;;;;GAKG;AACH,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,WAAW,EACjB,WAAW,EAAE,KAAK,CAAC;IAAE,OAAO,EAAE,aAAa,EAAE,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,GAC7D,IAAI,CAUN;AAED;;;;;GAKG;AACH,wBAAsB,kBAAkB,CAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,EAAE,CAAC,CA2G7G"}

package/build/lib/installer.js

@@ -3,13 +3,14 @@ import { mkdir, readFile, unlink } from 'node:fs/promises';
 import { dirname, join } from 'node:path';
 import { getPlacement, isEntrypoint, resolveInstalledPaths } from './adapter.js';
 import { computeConfigEntryChecksum, computeHookGroupChecksum, hashBytes } from './checksum.js';
+import { detectConfigFormat, normalizeForFormat, readConfigFile, resolveConfigFormat, writeConfigFile, } from './config-file.js';
 import {} from './errors.js';
 import { ensureGitignoreEntries } from './gitignore.js';
 import { buildHookGroup, deriveHookCommand, hookGroupOwnsCommand, removeHookGroup } from './hook-config.js';
 import { addAssetToLockfile, readLockfile, removeAssetFromLockfile, writeLockfile } from './lockfile.js';
 import { toRelativePosix } from './paths.js';
 import { fetchAssetFileBytes, fetchAssetManifest, listAssetFiles } from './registry.js';
-import { writeBinaryFile, writeJsonFile, writeTextFile } from './write-file.js';
+import { writeBinaryFile, writeTextFile } from './write-file.js';
 export class InstallerError extends Error {
     command;
     hint;
@@ -20,6 +21,23 @@ export class InstallerError extends Error {
         this.command = options.command;
     }
 }
+/**
+ * Guard for multi-tool installs run with `skipUnsupported`. Each tool skips the asset
+ * types it cannot place, which is fine as long as some tool placed something. If every
+ * tool skipped every entry, nothing was installed — surface that as an error rather
+ * than reporting a successful no-op.
+ */
+export function assertInstalledByAnyTool(plan, toolResults) {
+    if (plan.entries.length === 0 || toolResults.some((r) => r.results.length > 0)) {
+        return;
+    }
+    const types = [...new Set(plan.entries.map((e) => e.asset.type))].join(', ');
+    const tools = toolResults.map((r) => r.tool).join(', ');
+    throw new InstallerError(`None of the configured tools (${tools}) support asset type "${types}"`, {
+        command: 'atk setup',
+        hint: 'Add a tool that supports this asset type, or install it in a project configured for one.',
+    });
+}
 /**
  * Execute a full install plan — install all assets in order.
  * On partial failure, rolls back previously installed assets (deletes placed files,
@@ -39,8 +57,25 @@ export async function executeInstallPlan(plan, options) {
     let lockfile = await readLockfile(options.projectDir);
     // Build set of ATK-managed file paths from the lockfile for conflict detection
     const managedPaths = buildManagedPathsSet(lockfile, options.projectDir, options.adapter);
+    // In multi-tool projects the same plan runs once per tool. A tool that has no
+    // placement for an asset type (e.g. Codex CLI has no `rule` placement) skips
+    // those entries instead of aborting the whole run for that tool. When the tool
+    // supports nothing in the plan, fail loudly so a single-tool install isn't a
+    // silent no-op.
+    const supportedEntries = [];
+    for (const entry of plan.entries) {
+        if (getPlacement(options.adapter, entry.asset.type)) {
+            supportedEntries.push(entry);
+        }
+        else {
+            options.onProgress?.(`Skipping ${entry.asset.name}: ${options.adapter.displayName} does not support ${entry.asset.type} assets`);
+        }
+    }
+    if (supportedEntries.length === 0 && plan.entries.length > 0 && !options.skipUnsupported) {
+        throw new InstallerError(`Tool "${options.adapter.tool}" does not support asset type "${plan.entries[0].asset.type}"`);
+    }
     try {
-        for (const entry of plan.entries) {
+        for (const entry of supportedEntries) {
             const { lockfile: updatedLockfile, result } = await installAsset(entry, options, managedPaths, lockfile);
             results.push(result);
             lockfile = updatedLockfile;
@@ -67,7 +102,9 @@ export async function executeInstallPlan(plan, options) {
                 // Revert config file entries (best-effort)
                 for (const entry of result.configEntriesCreated) {
                     try {
-                        await revertConfigEntry(join(options.projectDir, entry.file), entry.key, entry.command, options.onProgress);
+                        const configPath = join(options.projectDir, entry.file);
+                        const format = resolveConfigFormat(configPath, getPlacement(options.adapter, result.type));
+                        await revertConfigEntry(configPath, entry.key, entry.command, format, options.onProgress);
                     }
                     catch (error) {
                         options.onProgress?.(`Warning: Failed to revert config entry ${entry.key} during rollback — ${error instanceof Error ? error.message : String(error)}`);
@@ -88,7 +125,7 @@ export async function executeInstallPlan(plan, options) {
         // keeping any recovery hint/command (e.g. from an API auth failure).
         const originalMessage = error instanceof Error ? error.message : String(error);
         const original = error;
-        throw new InstallerError(`Install failed at asset "${plan.entries[results.length]?.asset.name ?? 'unknown'}" ` +
+        throw new InstallerError(`Install failed at asset "${supportedEntries[results.length]?.asset.name ?? 'unknown'}" ` +
             `and ${results.length} previously installed asset(s) were rolled back: ${originalMessage}`, {
             command: typeof original?.command === 'string' ? original.command : undefined,
             hint: typeof original?.hint === 'string' ? original.hint : undefined,
@@ -103,10 +140,10 @@ export async function executeInstallPlan(plan, options) {
  */
 async function addToEnabledList(enabledListFilePath, enabledListKey, names, onProgress) {
     try {
+        const format = detectConfigFormat(enabledListFilePath);
         let config = {};
         if (existsSync(enabledListFilePath)) {
-            const raw = await readFile(enabledListFilePath, 'utf-8');
-            config = JSON.parse(raw);
+            config = await readConfigFile(enabledListFilePath, format);
         }
         else {
             const dir = dirname(enabledListFilePath);
@@ -125,7 +162,7 @@ async function addToEnabledList(enabledListFilePath, enabledListKey, names, onPr
         }
         if (changed) {
             config[enabledListKey] = list;
-            await writeJsonFile(enabledListFilePath, config);
+            await writeConfigFile(enabledListFilePath, config, format, onProgress);
         }
     }
     catch (error) {
@@ -311,13 +348,18 @@ async function installAsset(entry, options, managedPaths, lockfile) {
             });
         }
     }
-    // Handle config file updates if needed
+    // Handle config file updates if needed. The target file's serialization format
+    // (JSON by default; TOML for tools like Codex CLI) is resolved once here and
+    // threaded into every merge helper.
+    const configFormat = placement.configFile
+        ? resolveConfigFormat(join(basePath, placement.configFile), placement)
+        : 'json';
     if (placement.configFile && placement.configKey && placement.configHookMerge) {
         // Hook placement: merge the asset's hookConfig event bindings into the tool
         // config file as valid event arrays (e.g. settings.json hooks.Stop[]), with the
         // command derived from the installed script path.
         const command = deriveHookCommand(placement.configCommandPrefix, placement.path.replace(/\{name\}/g, asset.name));
-        const hookEntries = await mergeHookConfig(join(basePath, placement.configFile), placement.configKey, entry.versionData.hookConfig, command, projectDir, onProgress);
+        const hookEntries = await mergeHookConfig(join(basePath, placement.configFile), placement.configKey, configFormat, entry.versionData.hookConfig, command, projectDir, onProgress);
         configEntries.push(...hookEntries);
     }
     else if (placement.configFile && placement.configKey) {
@@ -336,7 +378,7 @@ async function installAsset(entry, options, managedPaths, lockfile) {
             // (e.g. a whole .mcp.json). Merge the entries inside content[configKey] into
             // configFile[configKey] keyed by each entry's own name, instead of nesting the
             // whole content under the asset name.
-            const { entries, names } = await mergeFragmentConfig(join(basePath, placement.configFile), placement.configKey, projectDir, mergeContent, onProgress);
+            const { entries, names } = await mergeFragmentConfig(join(basePath, placement.configFile), placement.configKey, configFormat, projectDir, mergeContent, placement.configFragmentKey, onProgress);
             configEntries.push(...entries);
             // Auto-register the merged entry names into an enabled-list (e.g. enabledMcpjsonServers
             // in settings.local.json) so the tool auto-approves them.
@@ -345,7 +387,7 @@ async function installAsset(entry, options, managedPaths, lockfile) {
             }
         }
         else {
-            const configResult = await updateConfigFile(join(basePath, placement.configFile), placement.configKey, asset.name, asset.type, projectDir, mergeContent, onProgress);
+            const configResult = await updateConfigFile(join(basePath, placement.configFile), placement.configKey, configFormat, asset.name, asset.type, projectDir, mergeContent, onProgress);
             if (configResult) {
                 configEntries.push(configResult);
             }
@@ -394,26 +436,33 @@ async function installAsset(entry, options, managedPaths, lockfile) {
  * into `config[configKey]` keyed by their own names (not nested under the asset name), each tagged
  * with the `_managedBy: 'atk'` marker. Returns one config entry per merged name (for lockfile
  * tracking / checksum verification) plus the list of names that were merged.
+ *
+ * The inner map is looked up at `content[configKey]`, then `content[fragmentKey]` (for tools
+ * whose target key differs from the asset content's key, e.g. `mcp_servers` vs `mcpServers`),
+ * and finally the whole content is treated as the inner map.
  */
-async function mergeFragmentConfig(configFilePath, configKey, projectDir, mergeContent, onProgress) {
+async function mergeFragmentConfig(configFilePath, configKey, format, projectDir, mergeContent, fragmentKey, onProgress) {
     const empty = { entries: [], names: [] };
     if (!mergeContent) {
         return empty;
     }
     try {
-        // Tolerant extraction: prefer the inner map at content[configKey]; otherwise treat the
-        // whole content as the inner map.
-        const inner = mergeContent[configKey] && typeof mergeContent[configKey] === 'object'
-            ? mergeContent[configKey]
-            : mergeContent;
+        const pickMap = (key) => {
+            if (!key)
+                return undefined;
+            const candidate = mergeContent[key];
+            return candidate && typeof candidate === 'object' && !Array.isArray(candidate)
+                ? candidate
+                : undefined;
+        };
+        const inner = pickMap(configKey) ?? pickMap(fragmentKey) ?? mergeContent;
         const innerNames = Object.keys(inner).filter((name) => inner[name] && typeof inner[name] === 'object');
         if (innerNames.length === 0) {
             return empty;
         }
         let config = {};
         if (existsSync(configFilePath)) {
-            const raw = await readFile(configFilePath, 'utf-8');
-            config = JSON.parse(raw);
+            config = await readConfigFile(configFilePath, format);
         }
         else {
             const dir = dirname(configFilePath);
@@ -427,7 +476,7 @@ async function mergeFragmentConfig(configFilePath, configKey, projectDir, mergeC
         const section = config[configKey];
         const entries = [];
         for (const name of innerNames) {
-            const value = { ...inner[name], _managedBy: 'atk' };
+            const value = normalizeForFormat({ ...inner[name], _managedBy: 'atk' }, format);
             section[name] = value;
             entries.push({
                 checksum: computeConfigEntryChecksum(value),
@@ -435,7 +484,7 @@ async function mergeFragmentConfig(configFilePath, configKey, projectDir, mergeC
                 key: `${configKey}.${name}`,
             });
         }
-        await writeJsonFile(configFilePath, config);
+        await writeConfigFile(configFilePath, config, format, onProgress);
         return { entries, names: innerNames };
     }
     catch (error) {
@@ -454,7 +503,7 @@ async function mergeFragmentConfig(configFilePath, configKey, projectDir, mergeC
  * owned by this command is dropped before appending, so repeated install/sync doesn't duplicate.
  * Returns one lockfile config entry per event, checksummed over the ATK-owned group only.
  */
-async function mergeHookConfig(configFilePath, configKey, hookConfig, command, projectDir, onProgress) {
+async function mergeHookConfig(configFilePath, configKey, format, hookConfig, command, projectDir, onProgress) {
     const events = hookConfig ? Object.keys(hookConfig) : [];
     if (events.length === 0) {
         // No hookConfig (e.g. legacy asset or un-rebuilt registry index) — write nothing.
@@ -463,8 +512,7 @@ async function mergeHookConfig(configFilePath, configKey, hookConfig, command, p
     try {
         let config = {};
         if (existsSync(configFilePath)) {
-            const raw = await readFile(configFilePath, 'utf-8');
-            config = JSON.parse(raw);
+            config = await readConfigFile(configFilePath, format);
         }
         else {
             const dir = dirname(configFilePath);
@@ -491,7 +539,7 @@ async function mergeHookConfig(configFilePath, configKey, hookConfig, command, p
                 key: `${configKey}.${event}`,
             });
         }
-        await writeJsonFile(configFilePath, config);
+        await writeConfigFile(configFilePath, config, format, onProgress);
         return entries;
     }
     catch (error) {
@@ -528,13 +576,12 @@ function resolveFilePath(pathTemplate, assetName, basePath, relativePath, assetT
  * Reads the config file, removes the entry at the given key path (e.g., "mcpServers.my-mcp"),
  * and writes it back. If the parent section becomes empty, it is also removed.
  */
-async function revertConfigEntry(configFilePath, keyPath, command, onProgress) {
+async function revertConfigEntry(configFilePath, keyPath, command, format, onProgress) {
     if (!existsSync(configFilePath)) {
         return;
     }
     try {
-        const raw = await readFile(configFilePath, 'utf-8');
-        const config = JSON.parse(raw);
+        const config = await readConfigFile(configFilePath, format);
         // keyPath is "section.childKey" (e.g., "mcpServers.my-mcp" or "hooks.Stop")
         const dotIndex = keyPath.indexOf('.');
         if (dotIndex === -1) {
@@ -559,7 +606,7 @@ async function revertConfigEntry(configFilePath, keyPath, command, onProgress) {
                 delete config[sectionKey];
             }
         }
-        await writeJsonFile(configFilePath, config);
+        await writeConfigFile(configFilePath, config, format, onProgress);
     }
     catch (error) {
         onProgress?.(`Warning: Failed to revert config entry ${keyPath} in ${configFilePath} — ${error instanceof Error ? error.message : String(error)}`);
@@ -583,12 +630,11 @@ function stripAtkBlock(content, assetName) {
  * When mergeContent is provided, it is merged into the config section with _managedBy marker.
  * Otherwise, a simple marker is written.
  */
-async function updateConfigFile(configFilePath, configKey, assetName, assetType, projectDir, mergeContent, onProgress) {
+async function updateConfigFile(configFilePath, configKey, format, assetName, assetType, projectDir, mergeContent, onProgress) {
     try {
         let config = {};
         if (existsSync(configFilePath)) {
-            const raw = await readFile(configFilePath, 'utf-8');
-            config = JSON.parse(raw);
+            config = await readConfigFile(configFilePath, format);
         }
         else {
             const dir = dirname(configFilePath);
@@ -603,10 +649,10 @@ async function updateConfigFile(configFilePath, configKey, assetName, assetType,
         const section = config[configKey];
         if (mergeContent) {
             // Merge actual asset content with _managedBy marker
-            section[assetName] = {
+            section[assetName] = normalizeForFormat({
                 ...mergeContent,
                 _managedBy: 'atk',
-            };
+            }, format);
         }
         else {
             // Simple marker
@@ -615,7 +661,7 @@ async function updateConfigFile(configFilePath, configKey, assetName, assetType,
                 type: assetType,
             };
         }
-        await writeJsonFile(configFilePath, config);
+        await writeConfigFile(configFilePath, config, format, onProgress);
         const checksum = computeConfigEntryChecksum(section[assetName]);
         return { checksum, file: toRelativePosix(projectDir, configFilePath), key: `${configKey}.${assetName}` };
     }