@detergent-software/atk 8.9.0-dev.4 → 8.9.0-dev.6

package/CHANGELOG.md

@@ -1,3 +1,16 @@
+## [8.9.0-dev.6](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv8.9.0-dev.5&targetVersion=GTv8.9.0-dev.6) (2026-10-18)
+
+### Bug Fixes
+
+* **cli:** check the entrypoint's path and refuse paths naming no file ([3df406e](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/3df406e4b92c865ab50f44c7d46040d4c75126db))
+* **cli:** keep lockfile names and source paths inside their placement ([56979b2](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/56979b25fc14f6361f834d7ad5b5292c3d7bf30d))
+
+## [8.9.0-dev.5](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv8.9.0-dev.4&targetVersion=GTv8.9.0-dev.5) (2026-10-18)
+
+### Bug Fixes
+
+* **cli:** checksum MCP config entries at every depth (ATK-584) ([b0c55f8](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/b0c55f865c3c729486bfe33d82f7823484078837))
+
 ## [8.9.0-dev.4](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv8.9.0-dev.3&targetVersion=GTv8.9.0-dev.4) (2026-10-17)
 
 ### Refactoring

package/build/lib/adapter.js

@@ -6,7 +6,7 @@ import { errorMessage, GuidedError } from './errors.js';
 import { placementForEntrypoint } from './hook-config.js';
 import { parseAndValidate, safeParseJson } from './parse-json.js';
 import { toRelativePosix } from './paths.js';
-import { fromRoot } from './root-path.js';
+import { ASSET_FILE_PATH, fromRoot, isPathInside, PATH_SEGMENT } from './root-path.js';
 import { AdapterSchema } from './schemas/adapter.js';
 import { setupGuidance } from './scope.js';
 const __dirname = dirname(fileURLToPath(import.meta.url));
@@ -328,6 +328,16 @@ export function supportsAssetType(adapter, assetType) {
 export function userConfigDirPath(adapter, dir, root) {
     return resolve(root, dir ?? adapter.userConfigDir?.dir ?? '.');
 }
+/** `relativePath` joined onto `dir`, which it must not leave. */
+function fileInside(dir, relativePath, assetName) {
+    const path = join(dir, relativePath);
+    if (!isPathInside(dir, path))
+        throw fileOutsidePlacement(relativePath, assetName);
+    return path;
+}
+function fileOutsidePlacement(relativePath, assetName) {
+    return new AdapterError(`File "${relativePath}" of ${assetName} resolves outside its placement directory, so ATK won't place or remove it.`, { hint: 'Check the asset entry in .atk-lock.json.' });
+}
 /**
  * The directory `userConfigDir.env` (joined with its `subdir`) moves the tool's user config to,
  * relative to `root` as a POSIX path ('.' for the root itself; absolute when it is on another
@@ -373,6 +383,16 @@ function rebaseUserPath(path, userConfigDir, movedDir) {
  * For additional files, place them relative to the entrypoint's directory.
  */
 function resolveFileInstalledPath(pathTemplate, assetName, projectDir, relativePath, assetType, entrypointName, declaredEntrypoint) {
+    // The lockfile is a committed file anyone can edit in a PR: a name or source path that leaves
+    // the placement's directory would have uninstall and sync delete files outside it.
+    if (!PATH_SEGMENT.test(assetName)) {
+        throw new AdapterError(`Asset name "${assetName}" is not a single path segment, so ATK won't place or remove it.`, {
+            hint: 'Check the asset entry in .atk-lock.json.',
+        });
+    }
+    // Checked for the entrypoint too, which is placed under a fixed name but recorded as it is.
+    if (!ASSET_FILE_PATH.test(relativePath))
+        throw fileOutsidePlacement(relativePath, assetName);
     const resolvedTemplate = pathTemplate.replace(/\{name\}/g, assetName);
     if (entrypointName) {
         // Directory-based placement: path is a directory, entrypoint gets the fixed name
@@ -380,14 +400,14 @@ function resolveFileInstalledPath(pathTemplate, assetName, projectDir, relativeP
         if (isEntrypoint(relativePath, assetType, declaredEntrypoint)) {
             return toRelativePosix(projectDir, join(dirPath, entrypointName));
         }
-        return toRelativePosix(projectDir, join(dirPath, relativePath));
+        return toRelativePosix(projectDir, fileInside(dirPath, relativePath, assetName));
     }
     // Default: single-file placement
     const templatePath = fromRoot(projectDir, resolvedTemplate);
     if (isEntrypoint(relativePath, assetType, declaredEntrypoint)) {
         return toRelativePosix(projectDir, templatePath);
     }
-    return toRelativePosix(projectDir, join(dirname(templatePath), relativePath));
+    return toRelativePosix(projectDir, fileInside(dirname(templatePath), relativePath, assetName));
 }
 /** Whether two placements put an asset's files and config entries at the same paths. */
 function samePlacement(a, b) {

package/build/lib/adapter.js.map

@@ -1 +1 @@
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package/build/lib/atk-api/generated/types.gen.d.ts

@@ -157,7 +157,7 @@ export type DeprecateRequest = {
      */
     undo?: boolean;
     /**
-     * Delete and recreate the branch if it already exists (the CLI's retry behaviour). Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
+     * Point the branch at the new commit if it already exists (the CLI's retry behaviour); 409 `branch_exists` when someone else moved it during the request. Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
      */
     replaceExistingBranch?: boolean;
     /**
@@ -378,7 +378,7 @@ export type PromoteRequest = {
      */
     kind?: 'asset' | 'bundle';
     /**
-     * Delete and recreate the branch if it already exists (the CLI's retry behaviour). Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
+     * Point the branch at the new commit if it already exists (the CLI's retry behaviour); 409 `branch_exists` when someone else moved it during the request. Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
      */
     replaceExistingBranch?: boolean;
     /**
@@ -588,7 +588,7 @@ export type PublishRequest = {
      */
     reviewers?: Array<string> | null;
     /**
-     * Delete and recreate the publish branch if it already exists (the CLI's retry behaviour). Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
+     * Point the publish branch at the new commit if it already exists (the CLI's retry behaviour); 409 `branch_exists` when someone else moved it during the request. Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
      */
     replaceExistingBranch?: boolean;
     /**
@@ -749,7 +749,7 @@ export type UnpublishRequest = {
      */
     version?: string | null;
     /**
-     * Delete and recreate the branch if it already exists (the CLI's retry behaviour). Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
+     * Point the branch at the new commit if it already exists (the CLI's retry behaviour); 409 `branch_exists` when someone else moved it during the request. Default false → 409 `branch_exists`. A branch with an open pull request is never replaced: 409 `pr_open`, either way.
      */
     replaceExistingBranch?: boolean;
     /**

package/build/lib/checksum.d.ts

@@ -1,3 +1,4 @@
+import type { ConfigEntry } from './schemas/lockfile.js';
 /** Describes a single config-entry verification failure. */
 export interface ConfigEntryFailure {
     file: string;
@@ -6,18 +7,30 @@ export interface ConfigEntryFailure {
 }
 /** Reason a config-entry verification can fail. */
 export type ConfigEntryFailureReason = 'CONFIG_CHECKSUM_MISMATCH' | 'CONFIG_FILE_NOT_FOUND' | 'CONFIG_KEY_NOT_FOUND';
+/**
+ * A recorded config entry, as the lockfile holds it, that {@link verifyConfigEntries} can check. Its
+ * `checksumVersion` is {@link CONFIG_CHECKSUM_VERSION} for a deep digest and absent for a legacy one;
+ * hook groups ignore it.
+ */
+export type VerifiableConfigEntry = Omit<ConfigEntry, 'tool'>;
 /** Recursively collect all files in a directory. */
 export declare function collectFilesRecursive(dirPath: string, baseDir: string): Promise<Array<{
     absolutePath: string;
     relativePath: string;
 }>>;
+/**
+ * The lockfile `checksumVersion` of a digest from {@link computeConfigEntryChecksum}. A config entry
+ * without one was recorded by an older CLI with {@link legacyConfigEntryChecksum}.
+ */
+export declare const CONFIG_CHECKSUM_VERSION: 2;
 /**
  * Compute a deterministic SHA-256 checksum for a config entry value.
  *
  * Strips the `_managedBy` metadata key (added by ATK at write time),
- * serializes the remaining keys in sorted order, and returns the hex digest.
- * Both the installer (write path) and the verifier (read path) use this
- * helper so the checksum logic stays in one place.
+ * serializes the rest with keys sorted at every depth (so nested `env` and
+ * `headers` count), and returns the hex digest. Both the installer (write path)
+ * and the verifier (read path) use this helper so the checksum logic stays in
+ * one place.
  */
 export declare function computeConfigEntryChecksum(entry: Record<string, unknown>): string;
 /**
@@ -56,12 +69,19 @@ export declare function hashString(content: string): string;
 export declare function matchesChecksum(content: Uint8Array, expected: string): boolean;
 /**
  * Deterministically serialize a value with object keys sorted recursively.
- * Arrays keep their order; nested object keys are sorted at every level. Unlike
- * the array-replacer used by `computeConfigEntryChecksum` (which only allow-lists
- * top-level keys), this captures deeply-nested fields — required for hook groups
- * whose meaningful data (`command`, `timeout`) lives inside `hooks[]`.
+ * Arrays keep their order; nested object keys are sorted at every level, so
+ * deeply-nested fields count: a hook group's `command` and `timeout` inside
+ * `hooks[]`, an MCP server's `env` and `headers`.
  */
 export declare function stableStringify(value: unknown): string;
+/**
+ * Re-record the config entries an older CLI checksummed with {@link legacyConfigEntryChecksum}, which
+ * can't see nested keys, as {@link computeConfigEntryChecksum} digests of the value the file holds
+ * now. Each entry without a `checksumVersion` whose value matches its legacy digest comes back with
+ * the deep digest and the current version; every other entry comes back as the same object. The
+ * legacy digest can't tell what the nested fields held when it was recorded, so this trusts them once.
+ */
+export declare function upgradeConfigEntryChecksums<T extends VerifiableConfigEntry>(entries: T[], projectDir: string): Promise<T[]>;
 /**
  * Compare a file's current checksum against an expected value (line-ending
  * tolerant; see {@link matchesChecksum}).
@@ -87,7 +107,8 @@ export declare function verifyChecksums(files: Array<{
  *  2. Splits the dot-path key into section/child and looks up the value →
  *     `CONFIG_KEY_NOT_FOUND` if missing.
  *  3. Computes a checksum via `computeConfigEntryChecksum()` and compares →
- *     `CONFIG_CHECKSUM_MISMATCH` on divergence.
+ *     `CONFIG_CHECKSUM_MISMATCH` on divergence. An entry without a
+ *     `checksumVersion` (recorded by an older CLI) also matches its legacy digest.
  *
  * Returns only the entries that failed (empty array = all OK).
  *
@@ -96,10 +117,5 @@ export declare function verifyChecksums(files: Array<{
  * command rather than by an object key, and checksummed via the deep-stable
  * hook-group digest so co-located foreign groups don't affect the result.
  */
-export declare function verifyConfigEntries(entries: Array<{
-    checksum: string;
-    command?: string;
-    file: string;
-    key: string;
-}>, projectDir: string): Promise<ConfigEntryFailure[]>;
+export declare function verifyConfigEntries(entries: VerifiableConfigEntry[], projectDir: string): Promise<ConfigEntryFailure[]>;
 //# sourceMappingURL=checksum.d.ts.map

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

@@ -1 +1 @@
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package/build/lib/checksum.js

@@ -22,19 +22,22 @@ export async function collectFilesRecursive(dirPath, baseDir) {
     }
     return results;
 }
+/**
+ * The lockfile `checksumVersion` of a digest from {@link computeConfigEntryChecksum}. A config entry
+ * without one was recorded by an older CLI with {@link legacyConfigEntryChecksum}.
+ */
+export const CONFIG_CHECKSUM_VERSION = 2;
 /**
  * Compute a deterministic SHA-256 checksum for a config entry value.
  *
  * Strips the `_managedBy` metadata key (added by ATK at write time),
- * serializes the remaining keys in sorted order, and returns the hex digest.
- * Both the installer (write path) and the verifier (read path) use this
- * helper so the checksum logic stays in one place.
+ * serializes the rest with keys sorted at every depth (so nested `env` and
+ * `headers` count), and returns the hex digest. Both the installer (write path)
+ * and the verifier (read path) use this helper so the checksum logic stays in
+ * one place.
  */
 export function computeConfigEntryChecksum(entry) {
-    const cleaned = { ...entry };
-    delete cleaned['_managedBy'];
-    const serialized = JSON.stringify(cleaned, Object.keys(cleaned).sort());
-    return hashString(serialized);
+    return hashString(stableStringify(withoutManagedBy(entry)));
 }
 /**
  * Compute a deterministic SHA-256 checksum for a hook matcher-group.
@@ -99,10 +102,9 @@ export function matchesChecksum(content, expected) {
 }
 /**
  * Deterministically serialize a value with object keys sorted recursively.
- * Arrays keep their order; nested object keys are sorted at every level. Unlike
- * the array-replacer used by `computeConfigEntryChecksum` (which only allow-lists
- * top-level keys), this captures deeply-nested fields — required for hook groups
- * whose meaningful data (`command`, `timeout`) lives inside `hooks[]`.
+ * Arrays keep their order; nested object keys are sorted at every level, so
+ * deeply-nested fields count: a hook group's `command` and `timeout` inside
+ * `hooks[]`, an MCP server's `env` and `headers`.
  */
 export function stableStringify(value) {
     return JSON.stringify(value, (_key, val) => {
@@ -118,6 +120,31 @@ export function stableStringify(value) {
         return val;
     });
 }
+/**
+ * Re-record the config entries an older CLI checksummed with {@link legacyConfigEntryChecksum}, which
+ * can't see nested keys, as {@link computeConfigEntryChecksum} digests of the value the file holds
+ * now. Each entry without a `checksumVersion` whose value matches its legacy digest comes back with
+ * the deep digest and the current version; every other entry comes back as the same object. The
+ * legacy digest can't tell what the nested fields held when it was recorded, so this trusts them once.
+ */
+export async function upgradeConfigEntryChecksums(entries, projectDir) {
+    const upgraded = [];
+    for (const entry of entries) {
+        const config = entry.command === undefined && entry.checksumVersion === undefined
+            ? await readEntryConfig(entry, projectDir)
+            : undefined;
+        const value = config && lookupEntryValue(config, entry.key);
+        if (!value || !matchesLegacyChecksum(entry, value)) {
+            upgraded.push(entry);
+            continue;
+        }
+        const deep = { checksum: computeConfigEntryChecksum(value), checksumVersion: CONFIG_CHECKSUM_VERSION };
+        // Keys in the order an install records them (checksum, checksumVersion, then the rest), so the
+        // committed lockfile doesn't reorder when the entry is next installed.
+        upgraded.push(Object.assign({ ...deep }, entry, deep));
+    }
+    return upgraded;
+}
 /**
  * Compare a file's current checksum against an expected value (line-ending
  * tolerant; see {@link matchesChecksum}).
@@ -153,7 +180,8 @@ export async function verifyChecksums(files) {
  *  2. Splits the dot-path key into section/child and looks up the value →
  *     `CONFIG_KEY_NOT_FOUND` if missing.
  *  3. Computes a checksum via `computeConfigEntryChecksum()` and compares →
- *     `CONFIG_CHECKSUM_MISMATCH` on divergence.
+ *     `CONFIG_CHECKSUM_MISMATCH` on divergence. An entry without a
+ *     `checksumVersion` (recorded by an older CLI) also matches its legacy digest.
  *
  * Returns only the entries that failed (empty array = all OK).
  *
@@ -165,66 +193,28 @@ export async function verifyChecksums(files) {
 export async function verifyConfigEntries(entries, projectDir) {
     const failures = [];
     for (const entry of entries) {
-        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;
-        try {
-            const raw = await readFile(absolutePath, 'utf-8');
-            config = parseConfig(raw, detectConfigFormat(entry.file));
-        }
-        catch {
+        // 1. Read and parse the config file
+        const config = await readEntryConfig(entry, projectDir);
+        if (!config) {
             failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_FILE_NOT_FOUND' });
             continue;
         }
         // Array-element (hook) entry: find the group owned by this asset's command.
         if (entry.command !== undefined) {
-            const failure = verifyHookGroupEntry(config, entry);
+            const failure = verifyHookGroupEntry(config, { ...entry, command: entry.command });
             if (failure) {
                 failures.push(failure);
             }
             continue;
         }
         // 2. Look up the value via dot-path (sectionKey.childKey)
-        const dotIndex = entry.key.indexOf('.');
-        const sectionKey = dotIndex === -1 ? entry.key : entry.key.slice(0, dotIndex);
-        const childKey = dotIndex === -1 ? undefined : entry.key.slice(dotIndex + 1);
-        const section = config[sectionKey];
-        if (childKey === undefined || section === null || section === undefined || typeof section !== 'object') {
-            // No child key means the key format is unexpected, or section missing
-            if (childKey === undefined) {
-                // Single-segment key — look up directly
-                if (!(sectionKey in config)) {
-                    failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_KEY_NOT_FOUND' });
-                    continue;
-                }
-                const value = config[sectionKey];
-                if (value === null || value === undefined || typeof value !== 'object') {
-                    failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_KEY_NOT_FOUND' });
-                    continue;
-                }
-                const actual = computeConfigEntryChecksum(value);
-                if (actual !== entry.checksum) {
-                    failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_CHECKSUM_MISMATCH' });
-                }
-                continue;
-            }
-            failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_KEY_NOT_FOUND' });
-            continue;
-        }
-        const sectionObj = section;
-        if (!(childKey in sectionObj)) {
-            failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_KEY_NOT_FOUND' });
-            continue;
-        }
-        const value = sectionObj[childKey];
-        if (value === null || value === undefined || typeof value !== 'object') {
+        const value = lookupEntryValue(config, entry.key);
+        if (!value) {
             failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_KEY_NOT_FOUND' });
             continue;
         }
         // 3. Compute checksum and compare
-        const actual = computeConfigEntryChecksum(value);
-        if (actual !== entry.checksum) {
+        if (computeConfigEntryChecksum(value) !== entry.checksum && !matchesLegacyChecksum(entry, value)) {
             failures.push({ file: entry.file, key: entry.key, reason: 'CONFIG_CHECKSUM_MISMATCH' });
         }
     }
@@ -232,6 +222,46 @@ export async function verifyConfigEntries(entries, projectDir) {
 }
 const CR = 0x0d;
 const LF = 0x0a;
+function isObject(value) {
+    return value !== null && typeof value === 'object';
+}
+/**
+ * The digest CLIs recorded before {@link CONFIG_CHECKSUM_VERSION}. Its array replacer is an allow-list
+ * of the top-level keys at every depth, so nested objects keep only keys that share a top-level
+ * name (`env` serializes as `{}`). Kept byte for byte so lockfiles those CLIs wrote still verify.
+ */
+function legacyConfigEntryChecksum(entry) {
+    const cleaned = withoutManagedBy(entry);
+    return hashString(JSON.stringify(cleaned, Object.keys(cleaned).sort()));
+}
+/**
+ * The object a config entry's dot-path key (`section.child`, or a single top-level key) names, or
+ * undefined when the key, or the value there, is missing or isn't an object.
+ */
+function lookupEntryValue(config, key) {
+    const dotIndex = key.indexOf('.');
+    const sectionKey = dotIndex === -1 ? key : key.slice(0, dotIndex);
+    const section = config[sectionKey];
+    const value = dotIndex === -1 ? section : isObject(section) ? section[key.slice(dotIndex + 1)] : undefined;
+    return isObject(value) ? value : undefined;
+}
+/** Whether an entry recorded before {@link CONFIG_CHECKSUM_VERSION} holds `value`, by its legacy digest. */
+function matchesLegacyChecksum(entry, value) {
+    return entry.checksumVersion === undefined && legacyConfigEntryChecksum(value) === entry.checksum;
+}
+/**
+ * Read and parse an entry's config file, with the format inferred from its extension (callers only
+ * hold lockfile entries, not the adapter placement), or undefined when it can't be read or parsed.
+ */
+async function readEntryConfig(entry, projectDir) {
+    try {
+        const raw = await readFile(fromRoot(projectDir, entry.file), 'utf-8');
+        return parseConfig(raw, detectConfigFormat(entry.file));
+    }
+    catch {
+        return undefined;
+    }
+}
 /** Expects LF-only input, so every LF gains exactly one CR. */
 function toCrlf(lf) {
     let lines = 0;
@@ -284,4 +314,10 @@ function verifyHookGroupEntry(config, entry) {
     }
     return null;
 }
+/** A copy of a config entry value without the `_managedBy` marker ATK adds at write time. */
+function withoutManagedBy(entry) {
+    const cleaned = { ...entry };
+    delete cleaned['_managedBy'];
+    return cleaned;
+}
 //# sourceMappingURL=checksum.js.map

package/build/lib/checksum.js.map

@@ -1 +1 @@
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package/build/lib/installer.d.ts

@@ -1,7 +1,7 @@
 import type { InstallPlan, InstallPlanEntry } from './resolver.js';
 import type { Adapter } from './schemas/adapter.js';
 import type { RegistryAsset } from './schemas/index.js';
-import type { Lockfile } from './schemas/lockfile.js';
+import type { ConfigEntry, Lockfile } from './schemas/lockfile.js';
 import { ApiCodeError } from './errors.js';
 import { type AssetIdentity } from './lockfile.js';
 import { type Scope } from './scope.js';
@@ -65,12 +65,7 @@ export interface InstallResult {
         org?: string;
         version: string;
     };
-    configEntriesCreated: Array<{
-        checksum: string;
-        command?: string;
-        file: string;
-        key: string;
-    }>;
+    configEntriesCreated: Array<Omit<ConfigEntry, 'tool'>>;
     /** The config files the install created, relative like `configEntriesCreated[].file`; a rollback deletes them once empty. */
     configFilesCreated?: string[];
     /** The names the install added to its placement's enabled list (e.g. `enabledMcpjsonServers`). */

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

@@ -1 +1 @@
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