@detergent-software/atk 8.6.2-dev.1 → 8.7.0-dev.10

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.
@@ -48,22 +63,32 @@ 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`).
  */
-export async function writeConfigFile(filePath, data, format, onProgress) {
+export async function writeConfigFile(filePath, data, format, onProgress, options = {}) {
     if (format === 'json') {
-        await writeJsonFile(filePath, data);
+        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);
+    await writeTomlFile(filePath, data, options);
 }
 /** Recursively drop null/undefined members from plain objects (arrays are mapped, not filtered). */
 function stripNullish(value) {

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

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

@@ -0,0 +1,22 @@
+import type { PlacementConfig } from './schemas/adapter.js';
+/**
+ * The lock to hold while writing `file` (relative to `root`): the placement's `configLockFile`,
+ * kept where it sits relative to `configFile`, when `file` is a copy of the placement's
+ * `configFile` (the same file name). That also covers one recorded before `CLAUDE_CONFIG_DIR`
+ * moved the file. Otherwise none.
+ */
+export declare function configLockPath(placement: Pick<PlacementConfig, 'configFile' | 'configLockFile'> | undefined, root: string, file: string): string | undefined;
+/**
+ * Run `fn` holding a tool's own config lock (a placement's `configLockFile`, such as Claude
+ * Code's `.claude.json.lock`), so a read-merge-write of a file the tool rewrites while it runs
+ * doesn't interleave with one of its own writes.
+ *
+ * The lock is a directory made with `mkdir`, the way the tool's `proper-lockfile` takes it.
+ * It is best effort: the tool doesn't wait for it either (ATK-324), so a lock still held after
+ * `waitMs` is left alone and `fn` runs without it. Only a lock this call made is removed.
+ * Without a `lockPath`, `fn` just runs.
+ */
+export declare function withConfigLock<T>(lockPath: string | undefined, fn: () => Promise<T>, { waitMs }?: {
+    waitMs?: number;
+}): Promise<T>;
+//# sourceMappingURL=config-lock.d.ts.map

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

@@ -0,0 +1 @@
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package/build/lib/config-lock.js

@@ -0,0 +1,67 @@
+import { mkdir, rmdir } from 'node:fs/promises';
+import { join, posix } from 'node:path';
+import { setTimeout as sleep } from 'node:timers/promises';
+import { normalizeConfigPath } from './config-entries.js';
+import { fromRoot } from './root-path.js';
+/** How long a held lock is waited for before going ahead without it. */
+const LOCK_WAIT_MS = 1000;
+const LOCK_RETRY_MS = 50;
+/**
+ * The lock to hold while writing `file` (relative to `root`): the placement's `configLockFile`,
+ * kept where it sits relative to `configFile`, when `file` is a copy of the placement's
+ * `configFile` (the same file name). That also covers one recorded before `CLAUDE_CONFIG_DIR`
+ * moved the file. Otherwise none.
+ */
+export function configLockPath(placement, root, file) {
+    if (!placement?.configLockFile || !placement.configFile) {
+        return undefined;
+    }
+    const configFile = normalizeConfigPath(placement.configFile);
+    const recorded = normalizeConfigPath(file);
+    if (posix.basename(recorded) !== posix.basename(configFile)) {
+        return undefined;
+    }
+    const lockFromConfig = posix.relative(posix.dirname(configFile), normalizeConfigPath(placement.configLockFile));
+    return join(fromRoot(root, posix.dirname(recorded)), lockFromConfig);
+}
+/**
+ * Run `fn` holding a tool's own config lock (a placement's `configLockFile`, such as Claude
+ * Code's `.claude.json.lock`), so a read-merge-write of a file the tool rewrites while it runs
+ * doesn't interleave with one of its own writes.
+ *
+ * The lock is a directory made with `mkdir`, the way the tool's `proper-lockfile` takes it.
+ * It is best effort: the tool doesn't wait for it either (ATK-324), so a lock still held after
+ * `waitMs` is left alone and `fn` runs without it. Only a lock this call made is removed.
+ * Without a `lockPath`, `fn` just runs.
+ */
+export async function withConfigLock(lockPath, fn, { waitMs = LOCK_WAIT_MS } = {}) {
+    if (lockPath === undefined) {
+        return fn();
+    }
+    const acquired = await tryLock(lockPath, waitMs);
+    try {
+        return await fn();
+    }
+    finally {
+        if (acquired) {
+            await rmdir(lockPath).catch(() => undefined);
+        }
+    }
+}
+/** Make the lock directory, retrying while another process holds it, until `waitMs` has passed. */
+async function tryLock(lockPath, waitMs) {
+    const deadline = Date.now() + waitMs;
+    for (;;) {
+        try {
+            await mkdir(lockPath);
+            return true;
+        }
+        catch (error) {
+            if (error.code !== 'EEXIST' || Date.now() >= deadline) {
+                return false;
+            }
+        }
+        await sleep(LOCK_RETRY_MS);
+    }
+}
+//# sourceMappingURL=config-lock.js.map

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

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package/build/lib/cross-scope.d.ts

@@ -0,0 +1,50 @@
+import type { AssetType } from './schemas/index.js';
+import type { InstalledAsset } from './schemas/lockfile.js';
+import { type Notice } from './notices.js';
+import { type ScopeClash } from './schemas/adapter.js';
+import { type ResolvedScope, type Scope } from './scope.js';
+/** Which copy one tool uses of an asset installed at both scopes. */
+export interface CrossScopeClash {
+    displayName: string;
+    tool: string;
+    uses: ScopeClash;
+}
+/** An asset being installed at one scope that the other scope already has. */
+export interface CrossScopeInstall {
+    /** Each tool that has both copies and a known rule, and the copy it uses. */
+    clash: CrossScopeClash[];
+    name: string;
+    org?: string;
+    /** The other scope's root. */
+    root: string;
+    /** The scope that already has it. */
+    scope: Scope;
+    type: AssetType;
+    /** The version the other scope has. */
+    version: string;
+}
+/**
+ * The `CrossScopeInstall` for `installed`, an entry of the other scope's lockfile: its version
+ * there, and the clash rule of each of `tools` (the tools that have both copies) that has one.
+ */
+export declare function crossScopeInstall(installed: InstalledAsset, { root, scope }: ResolvedScope, tools: string[]): Promise<CrossScopeInstall>;
+/** The one `cross-scope` notice for an install's duplicates, which all sit at the same other scope. */
+export declare function crossScopeNotice(installs: [CrossScopeInstall, ...CrossScopeInstall[]]): Notice;
+/** The tools' rules for which copy they use, as one clause: `Claude Code uses the user copy; …`. */
+export declare function describeClashes(clash: CrossScopeClash[]): string;
+/** One line on an asset installed at both scopes: where the other copy is, its version, and each tool's rule. */
+export declare function describeCrossScope(install: CrossScopeInstall): string;
+/**
+ * The assets among `assets` that the other scope already has: the user scope for a project install,
+ * and the cwd's project for a user-scope install (none when the cwd is in no project but the user
+ * root). Matched on (type, org, name). `tools` are the install's tools; each result's rules are for
+ * those that have both copies. An asset's `excludedTools` (from the lockfile, after an install) and
+ * the other entry's leave out the tools a copy isn't placed for, and a copy placed for none of its
+ * scope's tools doesn't count. The other scope is optional, so one that is missing or can't be read
+ * gives none, never an error.
+ */
+export declare function findCrossScopeInstalls(assets: ReadonlyArray<Pick<InstalledAsset, 'excludedTools' | 'name' | 'org' | 'type'>>, { scope, tools }: {
+    scope: Scope;
+    tools: string[];
+}): Promise<CrossScopeInstall[]>;
+//# sourceMappingURL=cross-scope.d.ts.map

package/build/lib/cross-scope.d.ts.map

@@ -0,0 +1 @@
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package/build/lib/cross-scope.js

@@ -0,0 +1,132 @@
+import { existsSync } from 'node:fs';
+import { loadAdapter } from './adapter.js';
+import { isExcludedForTool, isExcludedForTools } from './asset-tools.js';
+import { identityKey, lockfileExists, readLockfile } from './lockfile.js';
+import {} from './notices.js';
+import { formatOrgName } from './org.js';
+import { findProjectRoot } from './paths.js';
+import {} from './schemas/adapter.js';
+import { isUserRoot, loadScopeConfig, resolveUserRoot, scopedCommand, } from './scope.js';
+/**
+ * The `CrossScopeInstall` for `installed`, an entry of the other scope's lockfile: its version
+ * there, and the clash rule of each of `tools` (the tools that have both copies) that has one.
+ */
+export async function crossScopeInstall(installed, { root, scope }, tools) {
+    return {
+        clash: await clashRules(installed.type, tools),
+        name: installed.name,
+        ...(installed.org ? { org: installed.org } : {}),
+        root,
+        scope,
+        type: installed.type,
+        version: installed.version,
+    };
+}
+/** The one `cross-scope` notice for an install's duplicates, which all sit at the same other scope. */
+export function crossScopeNotice(installs) {
+    if (installs.length === 1) {
+        const [install] = installs;
+        return { command: uninstallCommand(install), kind: 'cross-scope', text: describeCrossScope(install) };
+    }
+    const list = installs.map((i) => `${formatOrgName(i.org, i.name)} (${i.type}) v${i.version}`).join(', ');
+    return {
+        command: 'atk list',
+        kind: 'cross-scope',
+        text: `${installs.length} assets are also installed ${scopePhrase(installs[0].scope)}: ${list}. Each tool that has both copies follows its own rule for which one it uses.`,
+    };
+}
+/** The tools' rules for which copy they use, as one clause: `Claude Code uses the user copy; …`. */
+export function describeClashes(clash) {
+    return clash
+        .map(({ displayName, uses }) => uses === 'both' ? `${displayName} loads both copies` : `${displayName} uses the ${uses} copy`)
+        .join('; ');
+}
+/** One line on an asset installed at both scopes: where the other copy is, its version, and each tool's rule. */
+export function describeCrossScope(install) {
+    const head = `${formatOrgName(install.org, install.name)} (${install.type}) is also installed ${scopePhrase(install.scope)} (v${install.version})`;
+    return install.clash.length === 0 ? `${head}.` : `${head}. ${describeClashes(install.clash)}.`;
+}
+/**
+ * The assets among `assets` that the other scope already has: the user scope for a project install,
+ * and the cwd's project for a user-scope install (none when the cwd is in no project but the user
+ * root). Matched on (type, org, name). `tools` are the install's tools; each result's rules are for
+ * those that have both copies. An asset's `excludedTools` (from the lockfile, after an install) and
+ * the other entry's leave out the tools a copy isn't placed for, and a copy placed for none of its
+ * scope's tools doesn't count. The other scope is optional, so one that is missing or can't be read
+ * gives none, never an error.
+ */
+export async function findCrossScopeInstalls(assets, { scope, tools }) {
+    const other = await otherScope(scope);
+    if (!other)
+        return [];
+    let otherAssets;
+    let otherTools;
+    try {
+        otherAssets = (await readLockfile(other.root)).assets ?? [];
+        // Without a config, the other scope names no tools, so no rule applies (as in `atk doctor`).
+        otherTools = (await loadScopeConfig(other.root))?.tools ?? [];
+    }
+    catch {
+        return [];
+    }
+    const byKey = new Map(otherAssets.map((a) => [identityKey(a), a]));
+    const seen = new Set();
+    const installs = [];
+    for (const asset of assets) {
+        const key = identityKey(asset);
+        const installed = byKey.get(key);
+        if (!installed || seen.has(key))
+            continue;
+        if (isExcludedForTools(asset, tools) || isExcludedForTools(installed, otherTools))
+            continue;
+        seen.add(key);
+        const shared = tools.filter((t) => otherTools.includes(t) && !isExcludedForTool(asset, t) && !isExcludedForTool(installed, t));
+        installs.push(await crossScopeInstall(installed, other, shared));
+    }
+    return installs;
+}
+/** Each tool's rule for `type`; a tool without one, or whose adapter doesn't load, is left out. */
+async function clashRules(type, tools) {
+    const rules = [];
+    for (const tool of tools) {
+        try {
+            const adapter = await loadAdapter(tool);
+            const uses = adapter.scopeClash?.[type];
+            if (uses) {
+                rules.push({ displayName: adapter.displayName, tool, uses });
+            }
+        }
+        catch {
+            // The install itself reports an adapter that doesn't load.
+        }
+    }
+    return rules;
+}
+/** The scope opposite `scope`, when it exists and has a lockfile. */
+async function otherScope(scope) {
+    let root;
+    try {
+        if (scope === 'project') {
+            root = await resolveUserRoot();
+        }
+        else {
+            root = findProjectRoot();
+            if (await isUserRoot(root))
+                return undefined;
+        }
+    }
+    catch {
+        return undefined;
+    }
+    if (!existsSync(root) || !lockfileExists(root))
+        return undefined;
+    return { root, scope: scope === 'project' ? 'user' : 'project' };
+}
+function scopePhrase(scope) {
+    return scope === 'user' ? 'at the user scope' : 'in the project';
+}
+/** The command that removes the other scope's copy. */
+function uninstallCommand({ name, org, scope, type }) {
+    return scopedCommand(`atk uninstall ${name} --type ${type}${org ? ` --org ${org}` : ''}`, scope);
+}
+//# sourceMappingURL=cross-scope.js.map

package/build/lib/cross-scope.js.map

@@ -0,0 +1 @@
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package/build/lib/diagnostics.d.ts

@@ -3,11 +3,24 @@ import type { ProjectConfig } from './schemas/config.js';
 import type { Registry } from './schemas/index.js';
 import type { InstalledAsset } from './schemas/lockfile.js';
 import { type Scope } from './scope.js';
+/**
+ * Check for assets installed both in the project and at the user scope, with the version at each and
+ * which copy each tool that has both uses. A copy uninstalled for every tool of its scope doesn't
+ * count. Returns undefined when there are none.
+ */
+export declare function checkBothScopes(project: {
+    assets: InstalledAsset[];
+    tools: string[];
+}, user: {
+    assets: InstalledAsset[];
+    root: string;
+    tools: string[];
+}): Promise<DiagnosticCheck | undefined>;
 /**
  * Check that the hook scripts a configured tool runs directly are executable. Returns
  * undefined when there is nothing to check: on Windows, which has no exec bit, or when
- * no installed hook places a script for any configured tool. The sync command it suggests runs in
- * `scope`.
+ * no installed hook places a script for any configured tool. Scripts are looked for where `scope`
+ * places them, and the sync command it suggests runs in `scope`.
  */
 export declare function checkHookScripts(projectDir: string, tools: string[], assets: InstalledAsset[], platform?: NodeJS.Platform, scope?: Scope): Promise<DiagnosticCheck | undefined>;
 /**

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

@@ -1 +1 @@
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+{"version":3,"file":"diagnostics.d.ts","sourceRoot":"","sources":["../../src/lib/diagnostics.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AAE9D,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAgB5D,OAAO,EAAkD,KAAK,KAAK,EAAiB,MAAM,YAAY,CAAC;AAEvG;;;;GAIG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE;IAAE,MAAM,EAAE,cAAc,EAAE,CAAC;IAAC,KAAK,EAAE,MAAM,EAAE,CAAA;CAAE,EACtD,IAAI,EAAE;IAAE,MAAM,EAAE,cAAc,EAAE,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,EAAE,CAAA;CAAE,GAChE,OAAO,CAAC,eAAe,GAAG,SAAS,CAAC,CAyBtC;AAED;;;;;GAKG;AACH,wBAAsB,gBAAgB,CACpC,UAAU,EAAE,MAAM,EAClB,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,EAAE,cAAc,EAAE,EACxB,QAAQ,GAAE,MAAM,CAAC,QAA2B,EAC5C,KAAK,CAAC,EAAE,KAAK,GACZ,OAAO,CAAC,eAAe,GAAG,SAAS,CAAC,CA0CtC;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAC9B,aAAa,EAAE,aAAa,EAC5B,MAAM,EAAE,cAAc,EAAE,EACxB,QAAQ,EAAE,QAAQ,EAClB,KAAK,CAAC,EAAE,KAAK,GACZ,eAAe,GAAG,SAAS,CAmB7B;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,eAAe,CAqBjE;AAED;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAClC,QAAQ,EAAE,CAAC,OAAO,EAAE,MAAM,KAAK,IAAI,EACnC,EAAE,WAAW,EAAE,IAAI,EAAE,GAAE;IAAE,WAAW,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAA;CAAO,GACnE,OAAO,CAAC,eAAe,EAAE,CAAC,CAsM5B"}

package/build/lib/diagnostics.js

@@ -1,23 +1,53 @@
 import { existsSync } from 'node:fs';
-import { join } from 'node:path';
-import { loadAdapter } from './adapter.js';
+import { adapterForScope, loadAdapter } from './adapter.js';
 import { resolveApiUrl } from './api-client.js';
-import { isExcludedAtVersion, isExcludedForTool, isUndeclaredForTool } from './asset-tools.js';
+import { isExcludedAtVersion, isExcludedForTool, isExcludedForTools, isUndeclaredForTool } from './asset-tools.js';
 import { getCredential, getLastEntraSession, validateToken } from './auth.js';
 import { isFrozenInConfig, loadConfig } from './config.js';
+import { crossScopeInstall, describeClashes } from './cross-scope.js';
 import { detectTools, getAdapterDiagnostics } from './detector.js';
 import { getEntraCachePath } from './entra.js';
 import { errorMessage } from './errors.js';
 import { hookScriptPath, lacksExecBit } from './hook-script.js';
-import { lockfileExists, readLockfile } from './lockfile.js';
+import { identityKey, lockfileExists, readLockfile } from './lockfile.js';
 import { formatOrgName } from './org.js';
 import { fetchRegistry, versionTools } from './registry.js';
-import { loadScopeConfig, resolveScope, scopedCommand } from './scope.js';
+import { fromRoot } from './root-path.js';
+import { loadScopeConfig, resolveScope, resolveUserRoot, scopedCommand } from './scope.js';
+/**
+ * Check for assets installed both in the project and at the user scope, with the version at each and
+ * which copy each tool that has both uses. A copy uninstalled for every tool of its scope doesn't
+ * count. Returns undefined when there are none.
+ */
+export async function checkBothScopes(project, user) {
+    const projectByKey = new Map(project.assets.map((a) => [identityKey(a), a]));
+    const lines = [];
+    for (const userAsset of user.assets) {
+        const projectAsset = projectByKey.get(identityKey(userAsset));
+        if (!projectAsset)
+            continue;
+        if (isExcludedForTools(projectAsset, project.tools) || isExcludedForTools(userAsset, user.tools))
+            continue;
+        const tools = project.tools.filter((t) => user.tools.includes(t) && !isExcludedForTool(projectAsset, t) && !isExcludedForTool(userAsset, t));
+        const { clash } = await crossScopeInstall(userAsset, { root: user.root, scope: 'user' }, tools);
+        const rules = clash.length > 0 ? ` (${describeClashes(clash)})` : '';
+        lines.push(`${formatOrgName(userAsset.org, userAsset.name)} (${userAsset.type}): project v${projectAsset.version}, user v${userAsset.version}${rules}`);
+    }
+    if (lines.length === 0)
+        return undefined;
+    const one = lines.length === 1;
+    return {
+        detail: `${lines.join('; ')}. Run \`atk uninstall <name> --type <type>\` (with \`--org <org>\` for an org asset), adding \`--user\` for the user copy, to keep one copy.`,
+        message: `${lines.length} asset${one ? ' is' : 's are'} installed at both scopes`,
+        name: 'Both scopes',
+        status: 'warn',
+    };
+}
 /**
  * Check that the hook scripts a configured tool runs directly are executable. Returns
  * undefined when there is nothing to check: on Windows, which has no exec bit, or when
- * no installed hook places a script for any configured tool. The sync command it suggests runs in
- * `scope`.
+ * no installed hook places a script for any configured tool. Scripts are looked for where `scope`
+ * places them, and the sync command it suggests runs in `scope`.
  */
 export async function checkHookScripts(projectDir, tools, assets, platform = process.platform, scope) {
     if (platform === 'win32')
@@ -26,7 +56,7 @@ export async function checkHookScripts(projectDir, tools, assets, platform = pro
     for (const tool of tools) {
         let adapter;
         try {
-            adapter = await loadAdapter(tool);
+            adapter = adapterForScope(await loadAdapter(tool), scope ?? 'project', projectDir);
         }
         catch {
             // The Adapters check already reports adapters that fail to load.
@@ -36,7 +66,7 @@ export async function checkHookScripts(projectDir, tools, assets, platform = pro
             if (isExcludedForTool(asset, tool))
                 continue;
             const scriptPath = hookScriptPath(adapter.placements[asset.type], asset.name);
-            if (scriptPath && existsSync(join(projectDir, scriptPath))) {
+            if (scriptPath && existsSync(fromRoot(projectDir, scriptPath))) {
                 scripts.add(scriptPath);
             }
         }
@@ -45,7 +75,7 @@ export async function checkHookScripts(projectDir, tools, assets, platform = pro
         return undefined;
     const notExecutable = [];
     for (const scriptPath of scripts) {
-        if (await lacksExecBit(join(projectDir, scriptPath), platform)) {
+        if (await lacksExecBit(fromRoot(projectDir, scriptPath), platform)) {
             notExecutable.push(scriptPath);
         }
     }
@@ -228,6 +258,12 @@ export async function runDiagnostics(progress, { projectRoot, user } = {}) {
             status: 'pass',
         });
     }
+    // The user root: the user scope's own root with --user, else checked with the user scope below
+    progress('Checking user root...');
+    const userRoot = await checkUserRoot(config);
+    if (scope === 'user') {
+        checks.push(userRoot.check);
+    }
     // Check the scope's config: the project's .atkrc.json, or the user scope's tools in the user config
     const configName = scope === 'user' ? 'User scope config' : 'Project config';
     const setup = scopedCommand('atk setup', scope);
@@ -304,6 +340,112 @@ export async function runDiagnostics(progress, { projectRoot, user } = {}) {
     if (liftedHooks) {
         checks.push(liftedHooks);
     }
+    // In a project, the user scope's installs sit beside the project's, so check them too
+    if (scope === 'project') {
+        progress('Checking user scope...');
+        checks.push(userRoot.check);
+        if (userRoot.root) {
+            checks.push(...(await checkUserScope(userRoot.root, registry, { assets: installedAssets, tools: configuredTools })));
+        }
+    }
+    return checks;
+}
+/**
+ * Report the user root: its path, where it comes from (`ATK_USER_ROOT`, the `userRoot` config key
+ * or the home directory), and a warning when it doesn't exist. `root` is set when it can be checked.
+ */
+async function checkUserRoot(config) {
+    let root;
+    try {
+        root = await resolveUserRoot();
+    }
+    catch (err) {
+        return { check: { message: errorMessage(err), name: 'User root', status: 'warn' } };
+    }
+    const source = process.env['ATK_USER_ROOT']
+        ? 'From ATK_USER_ROOT'
+        : config?.userRoot
+            ? 'From userRoot in config'
+            : 'The home directory';
+    if (!existsSync(root)) {
+        return {
+            check: {
+                detail: `${source}. Create it, or point ATK_USER_ROOT or the userRoot config key at an existing directory.`,
+                message: `${root} does not exist`,
+                name: 'User root',
+                status: 'warn',
+            },
+        };
+    }
+    return { check: { detail: source, message: root, name: 'User root', status: 'pass' }, root };
+}
+/**
+ * The user scope's checks for a project's doctor run: its config (tools), its lockfile, its hooks,
+ * and the assets it shares with `project`. The user scope is optional, so one that isn't set up
+ * passes; one that can't be read warns.
+ */
+async function checkUserScope(userRoot, registry, project) {
+    const checks = [];
+    let userConfig = null;
+    try {
+        userConfig = await loadScopeConfig(userRoot);
+        checks.push(userConfig
+            ? {
+                message: userConfig.tools.length === 0
+                    ? 'Loaded (no tools configured)'
+                    : `Loaded (tools: ${userConfig.tools.join(', ')})`,
+                name: 'User scope config',
+                status: 'pass',
+            }
+            : {
+                detail: 'Run `atk setup --user` to install assets at the user scope.',
+                message: 'Not set up',
+                name: 'User scope config',
+                status: 'pass',
+            });
+    }
+    catch (err) {
+        checks.push({
+            detail: 'Run `atk setup --user` to initialize user scope config.',
+            message: errorMessage(err),
+            name: 'User scope config',
+            status: 'warn',
+        });
+    }
+    let userAssets = [];
+    if (!lockfileExists(userRoot)) {
+        checks.push({ message: 'None (no user installs)', name: 'User lockfile', status: 'pass' });
+    }
+    else {
+        try {
+            userAssets = (await readLockfile(userRoot)).assets ?? [];
+            checks.push({
+                message: `Found .atk-lock.json (${userAssets.length} asset${userAssets.length === 1 ? '' : 's'})`,
+                name: 'User lockfile',
+                status: 'pass',
+            });
+        }
+        catch (err) {
+            checks.push({
+                detail: 'Run `atk setup --user` to re-initialize',
+                message: errorMessage(err),
+                name: 'User lockfile',
+                status: 'warn',
+            });
+        }
+    }
+    const userTools = userConfig?.tools ?? [];
+    const hookScripts = await checkHookScripts(userRoot, userTools, userAssets, process.platform, 'user');
+    const liftedHooks = registry && userConfig && checkLiftedHooks(userConfig, userAssets, registry, 'user');
+    for (const check of [hookScripts, liftedHooks]) {
+        if (check) {
+            checks.push({ ...check, name: `User ${check.name.toLowerCase()}` });
+        }
+    }
+    const bothScopes = await checkBothScopes(project, { assets: userAssets, root: userRoot, tools: userTools });
+    if (bothScopes) {
+        checks.push(bothScopes);
+    }
     return checks;
 }
 const SOURCE_LABELS = {