@detergent-software/atk 8.7.0-dev.1 → 8.7.0-dev.10

package/build/lib/adapter.d.ts

@@ -1,4 +1,5 @@
 import type { AssetType } from './schemas/index.js';
+import type { InstalledAsset } from './schemas/lockfile.js';
 import type { Scope } from './scope.js';
 import { GuidedError } from './errors.js';
 import { type Adapter, type PlacementConfig } from './schemas/adapter.js';
@@ -16,16 +17,41 @@ export interface AdapterLoadFailure {
 export declare class AdapterError extends GuidedError {
     name: string;
 }
+/**
+ * The adapter as it placed `asset`: a user-scope adapter whose user config directory moved since
+ * (see {@link configDirMove}) comes back with its placements in the directory the asset recorded
+ * for the tool, so its copy is found, and removed, where ATK wrote it. Any other comes back as is.
+ */
+export declare function adapterAsPlaced(adapter: Adapter, asset: Pick<InstalledAsset, 'type' | 'userConfigDirs'>): Adapter;
 /**
  * The adapter as the scope sees it. At the user scope its placements are the adapter's
  * `userPlacements` (none when it has none), so every reader of `placements` places assets,
  * and finds their config entries, the user-scope way.
+ *
+ * While the adapter's `userConfigDir.env` is set (Claude Code's `CLAUDE_CONFIG_DIR`, Codex's
+ * `CODEX_HOME`, Copilot's `XDG_CONFIG_HOME`: an absolute path), the user placements under
+ * `userConfigDir.dir`, and its `files`, move into that directory, or into its `subdir` (Copilot's
+ * `$XDG_CONFIG_HOME/.copilot`). Those under a `keep` prefix stay (Copilot's hooks). They stay
+ * relative to `root`, the user root (with `..` when the directory is outside it), so the
+ * lockfile records where each was written and every reader still resolves them against the
+ * root ({@link fromRoot}). On another drive than the root they are absolute POSIX paths.
  */
-export declare function adapterForScope(adapter: Adapter, scope: Scope): Adapter;
+export declare function adapterForScope(adapter: Adapter, scope: Scope, root: string): Adapter;
 /**
  * Clear the adapter cache (useful for testing).
  */
 export declare function clearAdapterCache(): void;
+/**
+ * Where a user-scope adapter's tool has its copy of `asset` (`from`, the directory `userConfigDirs`
+ * recorded) and where the tool reads it now (`to`), when its `userConfigDir.env` moved the asset
+ * type's placement in between; undefined when it didn't. Each is undefined for the tool's default
+ * directory. A move that leaves the placement where it was (`CODEX_HOME=~/.codex`, Copilot's kept
+ * hooks, a skill when `CLAUDE_CONFIG_DIR=~/.claude`) isn't one.
+ */
+export declare function configDirMove(adapter: Adapter, asset: Pick<InstalledAsset, 'type' | 'userConfigDirs'>): undefined | {
+    from: string | undefined;
+    to: string | undefined;
+};
 /**
  * Get the placement config for an asset type from an adapter.
  * Returns undefined if the adapter has no placement for that type.
@@ -47,8 +73,9 @@ export declare function isEntrypoint(relativePath: string, assetType: string, de
 /**
  * Load a tool adapter by tool name.
  * Looks for `tool-adapters/{tool}.json` bundled with the repo.
+ * `root` is the scope the tool was configured in, so a missing adapter names that scope's setup.
  */
-export declare function loadAdapter(tool: string): Promise<Adapter>;
+export declare function loadAdapter(tool: string, root?: string): Promise<Adapter>;
 /**
  * Load all adapter JSON files from the tool-adapters directory.
  * Reads all `.json` files (excluding files starting with `_`),
@@ -66,6 +93,13 @@ export declare function loadAllAdaptersWithDiagnostics(): Promise<{
     adapters: Adapter[];
     diagnostics: AdapterDiagnostics;
 }>;
+/**
+ * The `userConfigDirs` to record after placing an asset for the adapter's tool: other tools' carry
+ * over from `previous`, and this tool's is the directory its user placements are in now (none for
+ * its default directory). Off the user scope, `previous` is kept as it is. Keys are sorted, so the
+ * lockfile doesn't reorder with the tool that last wrote it.
+ */
+export declare function recordUserConfigDir(previous: InstalledAsset['userConfigDirs'], adapter: Adapter): InstalledAsset['userConfigDirs'];
 /**
  * Resolve the installed file paths and config entries for an asset, given the adapter
  * and project directory. This is the single source of truth for where an asset's files
@@ -102,4 +136,9 @@ export declare function resolvePlacementPath(placement: PlacementConfig, assetNa
  * Check if an adapter supports a given asset type.
  */
 export declare function supportsAssetType(adapter: Adapter, assetType: AssetType): boolean;
+/**
+ * The absolute path of a user-scope adapter's user config directory, from the user-root-relative
+ * `dir` of {@link configDirMove} (undefined for the tool's default directory).
+ */
+export declare function userConfigDirPath(adapter: Adapter, dir: string | undefined, root: string): string;
 //# sourceMappingURL=adapter.d.ts.map

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package/build/lib/adapter.js

@@ -1,11 +1,13 @@
 import { existsSync } from 'node:fs';
 import { readdir, readFile } from 'node:fs/promises';
-import { dirname, join } from 'node:path';
+import { dirname, isAbsolute, join, posix, resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 import { errorMessage, GuidedError } from './errors.js';
 import { parseAndValidate, safeParseJson } from './parse-json.js';
 import { toRelativePosix } from './paths.js';
+import { fromRoot } from './root-path.js';
 import { AdapterSchema } from './schemas/adapter.js';
+import { setupGuidance } from './scope.js';
 const __dirname = dirname(fileURLToPath(import.meta.url));
 /** Resolve tool-adapters directory relative to the package root (works both in dev and when installed via npm). */
 const ADAPTERS_DIR = join(__dirname, '..', '..', 'tool-adapters');
@@ -14,13 +16,34 @@ export class AdapterError extends GuidedError {
 }
 /** Cache loaded adapters by tool name. */
 const adapterCache = new Map();
+/**
+ * The adapter as it placed `asset`: a user-scope adapter whose user config directory moved since
+ * (see {@link configDirMove}) comes back with its placements in the directory the asset recorded
+ * for the tool, so its copy is found, and removed, where ATK wrote it. Any other comes back as is.
+ */
+export function adapterAsPlaced(adapter, asset) {
+    const move = configDirMove(adapter, asset);
+    return move ? userScopeAdapter(adapter, move.from) : adapter;
+}
 /**
  * The adapter as the scope sees it. At the user scope its placements are the adapter's
  * `userPlacements` (none when it has none), so every reader of `placements` places assets,
  * and finds their config entries, the user-scope way.
+ *
+ * While the adapter's `userConfigDir.env` is set (Claude Code's `CLAUDE_CONFIG_DIR`, Codex's
+ * `CODEX_HOME`, Copilot's `XDG_CONFIG_HOME`: an absolute path), the user placements under
+ * `userConfigDir.dir`, and its `files`, move into that directory, or into its `subdir` (Copilot's
+ * `$XDG_CONFIG_HOME/.copilot`). Those under a `keep` prefix stay (Copilot's hooks). They stay
+ * relative to `root`, the user root (with `..` when the directory is outside it), so the
+ * lockfile records where each was written and every reader still resolves them against the
+ * root ({@link fromRoot}). On another drive than the root they are absolute POSIX paths.
  */
-export function adapterForScope(adapter, scope) {
-    return scope === 'user' ? { ...adapter, placements: adapter.userPlacements ?? {} } : adapter;
+export function adapterForScope(adapter, scope, root) {
+    if (scope !== 'user') {
+        return adapter;
+    }
+    const movedDir = adapter.userConfigDir && movedUserConfigDir(adapter.userConfigDir, root);
+    return userScopeAdapter(adapter, movedDir);
 }
 /**
  * Clear the adapter cache (useful for testing).
@@ -28,6 +51,26 @@ export function adapterForScope(adapter, scope) {
 export function clearAdapterCache() {
     adapterCache.clear();
 }
+/**
+ * Where a user-scope adapter's tool has its copy of `asset` (`from`, the directory `userConfigDirs`
+ * recorded) and where the tool reads it now (`to`), when its `userConfigDir.env` moved the asset
+ * type's placement in between; undefined when it didn't. Each is undefined for the tool's default
+ * directory. A move that leaves the placement where it was (`CODEX_HOME=~/.codex`, Copilot's kept
+ * hooks, a skill when `CLAUDE_CONFIG_DIR=~/.claude`) isn't one.
+ */
+export function configDirMove(adapter, asset) {
+    if (!adapter.userScope || !adapter.userConfigDir) {
+        return undefined;
+    }
+    const from = asset.userConfigDirs?.[adapter.tool];
+    const to = adapter.userScope.movedDir;
+    if (from === to) {
+        return undefined;
+    }
+    const placed = userScopeAdapter(adapter, from).placements[asset.type];
+    const current = adapter.placements[asset.type];
+    return samePlacement(placed, current) ? undefined : { from, to };
+}
 /**
  * Get the placement config for an asset type from an adapter.
  * Returns undefined if the adapter has no placement for that type.
@@ -71,8 +114,9 @@ export function isEntrypoint(relativePath, assetType, declaredEntrypoint) {
 /**
  * Load a tool adapter by tool name.
  * Looks for `tool-adapters/{tool}.json` bundled with the repo.
+ * `root` is the scope the tool was configured in, so a missing adapter names that scope's setup.
  */
-export async function loadAdapter(tool) {
+export async function loadAdapter(tool, root) {
     const cached = adapterCache.get(tool);
     if (cached) {
         return cached;
@@ -80,7 +124,7 @@ export async function loadAdapter(tool) {
     const filePath = join(ADAPTERS_DIR, `${tool}.json`);
     if (!existsSync(filePath)) {
         throw new AdapterError(`No adapter found for tool "${tool}". Expected file at: ${filePath}`, {
-            command: 'atk setup',
+            command: root === undefined ? 'atk setup' : (await setupGuidance(root)).command,
             hint: 'The configured tool is not recognized. Re-run setup to pick a supported tool.',
         });
     }
@@ -190,6 +234,22 @@ export async function loadAllAdaptersWithDiagnostics() {
     }
     return { adapters, diagnostics };
 }
+/**
+ * The `userConfigDirs` to record after placing an asset for the adapter's tool: other tools' carry
+ * over from `previous`, and this tool's is the directory its user placements are in now (none for
+ * its default directory). Off the user scope, `previous` is kept as it is. Keys are sorted, so the
+ * lockfile doesn't reorder with the tool that last wrote it.
+ */
+export function recordUserConfigDir(previous, adapter) {
+    if (!adapter.userScope || !adapter.userConfigDir) {
+        return previous;
+    }
+    const { movedDir } = adapter.userScope;
+    const dirs = Object.entries(previous ?? {}).filter(([tool]) => tool !== adapter.tool);
+    if (movedDir !== undefined)
+        dirs.push([adapter.tool, movedDir]);
+    return dirs.length > 0 ? Object.fromEntries(dirs.sort(([a], [b]) => a.localeCompare(b))) : undefined;
+}
 /**
  * Resolve the installed file paths and config entries for an asset, given the adapter
  * and project directory. This is the single source of truth for where an asset's files
@@ -252,7 +312,7 @@ export function resolveInstalledPaths(asset, adapter, projectDir) {
  */
 export function resolvePlacementPath(placement, assetName, basePath) {
     const resolvedPath = placement.path.replace(/\{name\}/g, assetName);
-    return join(basePath, resolvedPath);
+    return fromRoot(basePath, resolvedPath);
 }
 /**
  * Check if an adapter supports a given asset type.
@@ -260,6 +320,51 @@ export function resolvePlacementPath(placement, assetName, basePath) {
 export function supportsAssetType(adapter, assetType) {
     return assetType in adapter.placements;
 }
+/**
+ * The absolute path of a user-scope adapter's user config directory, from the user-root-relative
+ * `dir` of {@link configDirMove} (undefined for the tool's default directory).
+ */
+export function userConfigDirPath(adapter, dir, root) {
+    return resolve(root, dir ?? adapter.userConfigDir?.dir ?? '.');
+}
+/**
+ * The directory `userConfigDir.env` (joined with its `subdir`) moves the tool's user config to,
+ * relative to `root` as a POSIX path ('.' for the root itself; absolute when it is on another
+ * drive), or undefined while the variable is unset or empty.
+ */
+function movedUserConfigDir(userConfigDir, root) {
+    const value = process.env[userConfigDir.env];
+    if (!value) {
+        return undefined;
+    }
+    if (!isAbsolute(value)) {
+        throw new AdapterError(`${userConfigDir.env} (${value}) is a relative path, so where it points depends on the directory a command runs from.`, { hint: `Set ${userConfigDir.env} to an absolute path.` });
+    }
+    const dir = resolve(value, userConfigDir.subdir ?? '');
+    // On another drive than the root there is no relative path, so this is the absolute one, its
+    // drive letter in one case so `z:` and `Z:` record the same directory.
+    const relativeDir = toRelativePosix(resolve(root), dir).replace(/^[a-z](?=:)/, (letter) => letter.toUpperCase());
+    if (relativeDir.startsWith('//')) {
+        throw new AdapterError(`${userConfigDir.env} (${resolve(value)}) is a network share path, which ATK can't record its paths under.`, { hint: `Map the share to a drive letter and point ${userConfigDir.env} at it.` });
+    }
+    return relativeDir === '' ? '.' : relativeDir;
+}
+/**
+ * A user placement path moved into `movedDir` when it is under `userConfigDir.dir` or one of its
+ * `files`, unless it is under one of its `keep` prefixes.
+ */
+function rebaseUserPath(path, userConfigDir, movedDir) {
+    if (userConfigDir.keep?.some((prefix) => path.startsWith(prefix))) {
+        return path;
+    }
+    if (path.startsWith(`${userConfigDir.dir}/`)) {
+        return posix.join(movedDir, path.slice(userConfigDir.dir.length + 1));
+    }
+    if (userConfigDir.files?.includes(path)) {
+        return posix.join(movedDir, path);
+    }
+    return path;
+}
 /**
  * Resolve the destination file path for an asset file, returning a project-relative POSIX path.
  * For directory-based placement (entrypointName set), the path is a directory template.
@@ -270,17 +375,47 @@ function resolveFileInstalledPath(pathTemplate, assetName, projectDir, relativeP
     const resolvedTemplate = pathTemplate.replace(/\{name\}/g, assetName);
     if (entrypointName) {
         // Directory-based placement: path is a directory, entrypoint gets the fixed name
-        const dirPath = resolvedTemplate;
+        const dirPath = fromRoot(projectDir, resolvedTemplate);
         if (isEntrypoint(relativePath, assetType, declaredEntrypoint)) {
-            return toRelativePosix(projectDir, join(projectDir, dirPath, entrypointName));
+            return toRelativePosix(projectDir, join(dirPath, entrypointName));
         }
-        return toRelativePosix(projectDir, join(projectDir, dirPath, relativePath));
+        return toRelativePosix(projectDir, join(dirPath, relativePath));
     }
     // Default: single-file placement
-    const templateDir = dirname(resolvedTemplate);
+    const templatePath = fromRoot(projectDir, resolvedTemplate);
     if (isEntrypoint(relativePath, assetType, declaredEntrypoint)) {
-        return toRelativePosix(projectDir, join(projectDir, resolvedTemplate));
+        return toRelativePosix(projectDir, templatePath);
+    }
+    return toRelativePosix(projectDir, join(dirname(templatePath), relativePath));
+}
+/** Whether two placements put an asset's files and config entries at the same paths. */
+function samePlacement(a, b) {
+    return (a?.path === b?.path &&
+        a?.configFile === b?.configFile &&
+        a?.configLockFile === b?.configLockFile &&
+        a?.enabledListFile === b?.enabledListFile);
+}
+/**
+ * The adapter's user placements, in `movedDir` when it is set (see {@link adapterForScope}), marked
+ * with the directory they are in.
+ */
+function userScopeAdapter(adapter, movedDir) {
+    const placements = adapter.userPlacements ?? {};
+    const { userConfigDir } = adapter;
+    if (!userConfigDir || movedDir === undefined) {
+        return { ...adapter, placements, userScope: {} };
     }
-    return toRelativePosix(projectDir, join(projectDir, templateDir, relativePath));
+    const rebase = (path) => rebaseUserPath(path, userConfigDir, movedDir);
+    const rebased = Object.fromEntries(Object.entries(placements).map(([type, placement]) => [
+        type,
+        {
+            ...placement,
+            path: rebase(placement.path),
+            ...(placement.configFile && { configFile: rebase(placement.configFile) }),
+            ...(placement.configLockFile && { configLockFile: rebase(placement.configLockFile) }),
+            ...(placement.enabledListFile && { enabledListFile: rebase(placement.enabledListFile) }),
+        },
+    ]));
+    return { ...adapter, placements: rebased, userScope: { movedDir } };
 }
 //# sourceMappingURL=adapter.js.map

package/build/lib/adapter.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"checksum.d.ts","sourceRoot":"","sources":["../../src/lib/checksum.ts"],"names":[],"mappings":"AAQA,4DAA4D;AAC5D,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,MAAM,EAAE,wBAAwB,CAAC;CAClC;AAED,mDAAmD;AACnD,MAAM,MAAM,wBAAwB,GAAG,0BAA0B,GAAG,uBAAuB,GAAG,sBAAsB,CAAC;AAErH,oDAAoD;AACpD,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,KAAK,CAAC;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,YAAY,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAgBhE;AAED;;;;;;;GAOG;AACH,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAMjF;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,CAE/D;AAED;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,UAAU,GAAG,MAAM,CAErD;AAED;;;GAGG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAcpE;AAED;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAGhE;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAElD;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAK9E;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,CAatD;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAAC,QAAQ,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAEjG;AAED;;;GAGG;AACH,wBAAsB,eAAe,CACnC,KAAK,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,GAC/C,OAAO,CAAC,KAAK,CAAC;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAgBpE;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAAC,EACjF,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CA8E/B"}
+{"version":3,"file":"checksum.d.ts","sourceRoot":"","sources":["../../src/lib/checksum.ts"],"names":[],"mappings":"AASA,4DAA4D;AAC5D,MAAM,WAAW,kBAAkB;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,MAAM,EAAE,wBAAwB,CAAC;CAClC;AAED,mDAAmD;AACnD,MAAM,MAAM,wBAAwB,GAAG,0BAA0B,GAAG,uBAAuB,GAAG,sBAAsB,CAAC;AAErH,oDAAoD;AACpD,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,KAAK,CAAC;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,YAAY,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAgBhE;AAED;;;;;;;GAOG;AACH,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAMjF;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,CAE/D;AAED;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,UAAU,GAAG,MAAM,CAErD;AAED;;;GAGG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAcpE;AAED;;;GAGG;AACH,wBAAsB,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAGhE;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAElD;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAK9E;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,CAatD;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAAC,QAAQ,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAEjG;AAED;;;GAGG;AACH,wBAAsB,eAAe,CACnC,KAAK,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,GAC/C,OAAO,CAAC,KAAK,CAAC;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAgBpE;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAAC,EACjF,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CA8E/B"}

package/build/lib/checksum.js

@@ -4,6 +4,7 @@ import { join } from 'node:path';
 import { detectConfigFormat, parseConfig } from './config-file.js';
 import { errorMessage } from './errors.js';
 import { hookGroupOwnsCommand } from './hook-config.js';
+import { fromRoot } from './root-path.js';
 /** Recursively collect all files in a directory. */
 export async function collectFilesRecursive(dirPath, baseDir) {
     const results = [];
@@ -164,7 +165,7 @@ export async function verifyChecksums(files) {
 export async function verifyConfigEntries(entries, projectDir) {
     const failures = [];
     for (const entry of entries) {
-        const absolutePath = join(projectDir, entry.file);
+        const absolutePath = fromRoot(projectDir, entry.file);
         // 1. Read and parse the config file (format inferred from the extension —
         //    callers only hold lockfile entries, not the adapter placement)
         let config;

package/build/lib/checksum.js.map

@@ -1 +1 @@
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package/build/lib/config-entries.d.ts

@@ -37,9 +37,11 @@ export declare function getOtherToolsConfigEntries(asset: AssetConfigEntries | u
 export declare function mergeConfigEntriesForTool(previous: AssetConfigEntries | undefined, adapter: Adapter, fresh: Array<Omit<ConfigEntry, 'tool'>>): ConfigEntry[];
 /**
  * Whether an asset is missing its config registration for the given tool: the adapter
- * registers this asset type in a config file, the asset has recorded entries for some
- * other tool, but none for this one. This repairs multi-tool projects where only one
- * tool's registration was ever recorded.
+ * registers this asset type in a config file, the asset has recorded entries, but none
+ * for this tool in that file. This repairs multi-tool projects where only one tool's
+ * registration was ever recorded, and moves a tool's entries out of a config file its
+ * adapter no longer uses (copilot-cli's mcp-config once went to `copilot/mcp-config.json`,
+ * which Copilot never reads).
  *
  * Assets with no recorded entries at all are left alone — a hook with no event
  * bindings, a legacy lockfile, or a memory-template legitimately has none, and

package/build/lib/config-entries.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config-entries.d.ts","sourceRoot":"","sources":["../../src/lib/config-entries.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AACpD,OAAO,KAAK,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAEzE;;;;;;;;;;;;;;GAcG;AAEH,KAAK,kBAAkB,GAAG,IAAI,CAAC,cAAc,EAAE,eAAe,GAAG,MAAM,CAAC,CAAC;AAEzE;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,GAAG,OAAO,CAWzG;AAED,mFAAmF;AACnF,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,kBAAkB,EAAE,OAAO,EAAE,OAAO,GAAG,WAAW,EAAE,CAElG;AAED,kGAAkG;AAClG,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,kBAAkB,GAAG,SAAS,EAAE,OAAO,EAAE,OAAO,GAAG,WAAW,EAAE,CAKjH;AAED;;;;;;;GAOG;AACH,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,kBAAkB,GAAG,SAAS,EACxC,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,CAAC,CAAC,GACtC,WAAW,EAAE,CAQf;AAED;;;;;;;;;GASG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,kBAAkB,EAAE,OAAO,EAAE,OAAO,GAAG,OAAO,CAS5F;AAED,kGAAkG;AAClG,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAMxD"}
+{"version":3,"file":"config-entries.d.ts","sourceRoot":"","sources":["../../src/lib/config-entries.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AACpD,OAAO,KAAK,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAEzE;;;;;;;;;;;;;;GAcG;AAEH,KAAK,kBAAkB,GAAG,IAAI,CAAC,cAAc,EAAE,eAAe,GAAG,MAAM,CAAC,CAAC;AAEzE;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,GAAG,OAAO,CAWzG;AAED,mFAAmF;AACnF,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,kBAAkB,EAAE,OAAO,EAAE,OAAO,GAAG,WAAW,EAAE,CAElG;AAED,kGAAkG;AAClG,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,kBAAkB,GAAG,SAAS,EAAE,OAAO,EAAE,OAAO,GAAG,WAAW,EAAE,CAKjH;AAED;;;;;;;GAOG;AACH,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,kBAAkB,GAAG,SAAS,EACxC,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,CAAC,CAAC,GACtC,WAAW,EAAE,CAQf;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,kBAAkB,EAAE,OAAO,EAAE,OAAO,GAAG,OAAO,CAU5F;AAED,kGAAkG;AAClG,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAMxD"}

package/build/lib/config-entries.js

@@ -42,9 +42,11 @@ export function mergeConfigEntriesForTool(previous, adapter, fresh) {
 }
 /**
  * Whether an asset is missing its config registration for the given tool: the adapter
- * registers this asset type in a config file, the asset has recorded entries for some
- * other tool, but none for this one. This repairs multi-tool projects where only one
- * tool's registration was ever recorded.
+ * registers this asset type in a config file, the asset has recorded entries, but none
+ * for this tool in that file. This repairs multi-tool projects where only one tool's
+ * registration was ever recorded, and moves a tool's entries out of a config file its
+ * adapter no longer uses (copilot-cli's mcp-config once went to `copilot/mcp-config.json`,
+ * which Copilot never reads).
  *
  * Assets with no recorded entries at all are left alone — a hook with no event
  * bindings, a legacy lockfile, or a memory-template legitimately has none, and
@@ -58,7 +60,8 @@ export function needsConfigRegistration(asset, adapter) {
     if ((asset.configEntries?.length ?? 0) === 0) {
         return false;
     }
-    return getConfigEntriesForTool(asset, adapter).length === 0;
+    const configFile = normalizeConfigPath(placement.configFile);
+    return !getConfigEntriesForTool(asset, adapter).some((e) => normalizeConfigPath(e.file) === configFile);
 }
 /** Normalize a project-relative config path for comparison: POSIX separators, no leading `./`. */
 export function normalizeConfigPath(path) {

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

@@ -1 +1 @@
-{"version":3,"file":"config-entries.js","sourceRoot":"","sources":["../../src/lib/config-entries.ts"],"names":[],"mappings":"AAqBA;;;;GAIG;AACH,MAAM,UAAU,wBAAwB,CAAC,KAAkB,EAAE,OAAgB,EAAE,SAAiB;IAC9F,IAAI,KAAK,CAAC,IAAI,KAAK,SAAS,EAAE,CAAC;QAC7B,OAAO,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,IAAI,CAAC;IACrC,CAAC;IAED,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,CAAC,SAAwC,CAAC,CAAC;IAC/E,IAAI,CAAC,SAAS,EAAE,UAAU,EAAE,CAAC;QAC3B,OAAO,KAAK,CAAC;IACf,CAAC;IAED,OAAO,mBAAmB,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,mBAAmB,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;AACvF,CAAC;AAED,mFAAmF;AACnF,MAAM,UAAU,uBAAuB,CAAC,KAAyB,EAAE,OAAgB;IACjF,OAAO,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,wBAAwB,CAAC,CAAC,EAAE,OAAO,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;AACrG,CAAC;AAED,kGAAkG;AAClG,MAAM,UAAU,0BAA0B,CAAC,KAAqC,EAAE,OAAgB;IAChG,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,wBAAwB,CAAC,CAAC,EAAE,OAAO,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;AACtG,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAAwC,EACxC,OAAgB,EAChB,KAAuC;IAEvC,MAAM,MAAM,GAAkB;QAC5B,GAAG,0BAA0B,CAAC,QAAQ,EAAE,OAAO,CAAC;QAChD,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC;KACpD,CAAC;IAEF,sFAAsF;IACtF,OAAO,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC;AAC3E,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,uBAAuB,CAAC,KAAyB,EAAE,OAAgB;IACjF,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,IAAmC,CAAC,CAAC;IAChF,IAAI,CAAC,SAAS,EAAE,UAAU,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,CAAC;QACnD,OAAO,KAAK,CAAC;IACf,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,aAAa,EAAE,MAAM,IAAI,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;QAC7C,OAAO,KAAK,CAAC;IACf,CAAC;IACD,OAAO,uBAAuB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC;AAC9D,CAAC;AAED,kGAAkG;AAClG,MAAM,UAAU,mBAAmB,CAAC,IAAY;IAC9C,IAAI,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAC1C,OAAO,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QACnC,UAAU,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC"}
+{"version":3,"file":"config-entries.js","sourceRoot":"","sources":["../../src/lib/config-entries.ts"],"names":[],"mappings":"AAqBA;;;;GAIG;AACH,MAAM,UAAU,wBAAwB,CAAC,KAAkB,EAAE,OAAgB,EAAE,SAAiB;IAC9F,IAAI,KAAK,CAAC,IAAI,KAAK,SAAS,EAAE,CAAC;QAC7B,OAAO,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,IAAI,CAAC;IACrC,CAAC;IAED,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,CAAC,SAAwC,CAAC,CAAC;IAC/E,IAAI,CAAC,SAAS,EAAE,UAAU,EAAE,CAAC;QAC3B,OAAO,KAAK,CAAC;IACf,CAAC;IAED,OAAO,mBAAmB,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,mBAAmB,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;AACvF,CAAC;AAED,mFAAmF;AACnF,MAAM,UAAU,uBAAuB,CAAC,KAAyB,EAAE,OAAgB;IACjF,OAAO,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,wBAAwB,CAAC,CAAC,EAAE,OAAO,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;AACrG,CAAC;AAED,kGAAkG;AAClG,MAAM,UAAU,0BAA0B,CAAC,KAAqC,EAAE,OAAgB;IAChG,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,wBAAwB,CAAC,CAAC,EAAE,OAAO,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;AACtG,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAAwC,EACxC,OAAgB,EAChB,KAAuC;IAEvC,MAAM,MAAM,GAAkB;QAC5B,GAAG,0BAA0B,CAAC,QAAQ,EAAE,OAAO,CAAC;QAChD,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC;KACpD,CAAC;IAEF,sFAAsF;IACtF,OAAO,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC;AAC3E,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,uBAAuB,CAAC,KAAyB,EAAE,OAAgB;IACjF,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,IAAmC,CAAC,CAAC;IAChF,IAAI,CAAC,SAAS,EAAE,UAAU,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,CAAC;QACnD,OAAO,KAAK,CAAC;IACf,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,aAAa,EAAE,MAAM,IAAI,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;QAC7C,OAAO,KAAK,CAAC;IACf,CAAC;IACD,MAAM,UAAU,GAAG,mBAAmB,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;IAC7D,OAAO,CAAC,uBAAuB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,UAAU,CAAC,CAAC;AAC1G,CAAC;AAED,kGAAkG;AAClG,MAAM,UAAU,mBAAmB,CAAC,IAAY;IAC9C,IAAI,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAC1C,OAAO,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QACnC,UAAU,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC"}

package/build/lib/config-file.d.ts

@@ -34,6 +34,11 @@ export declare function parseConfig(raw: string, format: ConfigFormat): Record<s
  * like `readFile` — callers keep their own existence guards.
  */
 export declare function readConfigFile(filePath: string, format: ConfigFormat): Promise<Record<string, unknown>>;
+/**
+ * Delete a config file that removing ATK's entries left with no keys. A TOML file that still holds
+ * the user's comments is kept instead, with only ATK's tables taken out of it.
+ */
+export declare function removeEmptiedConfigFile(filePath: string, format: ConfigFormat, options?: WriteOptions): Promise<void>;
 /**
  * Resolve the format for a placement's config file: an explicit
  * `configFormat` wins, otherwise the file extension decides.
@@ -42,9 +47,11 @@ export declare function resolveConfigFormat(filePath: string, placement?: Pick<P
 /**
  * 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.
+ * An existing TOML file is edited in place ({@link editTomlTables}): only the tables that changed
+ * are rewritten, so the user's comments and formatting stay. When the change can't be made that way
+ * (it isn't one of the `section.child` tables ATK writes, or the file defines one inline), the whole
+ * document is re-serialized, which drops the comments; a one-line warning is then emitted through
+ * `onProgress` so the loss is visible rather than silent.
  *
  * `options.atomic` writes through a temp file and a rename, for a file the tool rewrites while it
  * runs (a placement with `configLockFile`).

package/build/lib/config-file.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config-file.d.ts","sourceRoot":"","sources":["../../src/lib/config-file.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AAE5D,OAAO,EAAiB,KAAK,YAAY,EAAiB,MAAM,iBAAiB,CAAC;AAElF;;;;;;;;GAQG;AAEH,6DAA6D;AAC7D,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,MAAM,CAAC;AAE3C;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,YAAY,CAEjE;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,YAAY,GAAG,CAAC,CAKvE;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAEtF;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAG7G;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,SAAS,CAAC,EAAE,IAAI,CAAC,eAAe,EAAE,cAAc,CAAC,GAAG,SAAS,GAC5D,YAAY,CAEd;AAED;;;;;;;;;GASG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,YAAY,EACpB,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,EACtC,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,IAAI,CAAC,CAcf"}
+{"version":3,"file":"config-file.d.ts","sourceRoot":"","sources":["../../src/lib/config-file.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AAG5D,OAAO,EAAiB,KAAK,YAAY,EAAgC,MAAM,iBAAiB,CAAC;AAEjG;;;;;;;;GAQG;AAEH,6DAA6D;AAC7D,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,MAAM,CAAC;AAE3C;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,YAAY,CAEjE;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,YAAY,GAAG,CAAC,CAKvE;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAEtF;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAG7G;AAED;;;GAGG;AACH,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,YAAY,EACpB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,IAAI,CAAC,CASf;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,SAAS,CAAC,EAAE,IAAI,CAAC,eAAe,EAAE,cAAc,CAAC,GAAG,SAAS,GAC5D,YAAY,CAEd;AAED;;;;;;;;;;;GAWG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,YAAY,EACpB,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,EACtC,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,IAAI,CAAC,CAmBf"}

package/build/lib/config-file.js

@@ -1,8 +1,9 @@
 import { existsSync } from 'node:fs';
-import { readFile } from 'node:fs/promises';
+import { readFile, unlink } from 'node:fs/promises';
 import { extname } from 'node:path';
 import { parse as parseToml } from 'smol-toml';
-import { writeJsonFile, writeTomlFile } from './write-file.js';
+import { editTomlTables } from './toml-edit.js';
+import { writeJsonFile, writeTextFile, 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
@@ -38,6 +39,20 @@ export async function readConfigFile(filePath, format) {
     const raw = await readFile(filePath, 'utf-8');
     return parseConfig(raw, format);
 }
+/**
+ * Delete a config file that removing ATK's entries left with no keys. A TOML file that still holds
+ * the user's comments is kept instead, with only ATK's tables taken out of it.
+ */
+export async function removeEmptiedConfigFile(filePath, format, options = {}) {
+    if (format === 'toml') {
+        const remaining = editTomlTables(await readFile(filePath, 'utf-8'), {});
+        if (remaining !== undefined && remaining.trim() !== '') {
+            await writeTextFile(filePath, remaining, options);
+            return;
+        }
+    }
+    await unlink(filePath);
+}
 /**
  * Resolve the format for a placement's config file: an explicit
  * `configFormat` wins, otherwise the file extension decides.
@@ -48,9 +63,11 @@ export function resolveConfigFormat(filePath, placement) {
 /**
  * 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.
+ * An existing TOML file is edited in place ({@link editTomlTables}): only the tables that changed
+ * are rewritten, so the user's comments and formatting stay. When the change can't be made that way
+ * (it isn't one of the `section.child` tables ATK writes, or the file defines one inline), the whole
+ * document is re-serialized, which drops the comments; a one-line warning is then emitted through
+ * `onProgress` so the loss is visible rather than silent.
  *
  * `options.atomic` writes through a temp file and a rename, for a file the tool rewrites while it
  * runs (a placement with `configLockFile`).
@@ -60,10 +77,15 @@ export async function writeConfigFile(filePath, data, format, onProgress, option
         await writeJsonFile(filePath, data, options);
         return;
     }
-    if (onProgress && existsSync(filePath)) {
+    if (existsSync(filePath)) {
         const existing = await readFile(filePath, 'utf-8');
+        const edited = editTomlTables(existing, data);
+        if (edited !== undefined) {
+            await writeTextFile(filePath, edited, options);
+            return;
+        }
         if (/^\s*#/m.test(existing)) {
-            onProgress(`Warning: rewriting ${filePath} — TOML comments and custom formatting are not preserved`);
+            onProgress?.(`Warning: rewriting ${filePath} — TOML comments and custom formatting are not preserved`);
         }
     }
     await writeTomlFile(filePath, data, options);