@open-agent-toolkit/cli 0.0.35 → 0.0.36

package/assets/docs/cli-utilities/tool-packs.md

@@ -73,10 +73,14 @@ Key behavior:
 
 - Same pack selection and install flow as `oat init tools`
 - Pack-oriented install subcommands: `core`, `docs`, `ideas`, `workflows`, `utility`, `project-management`, `research`
+- Interactive installs show each pack's current install location in the picker so already-installed packs are visible before you submit
+- User-scope follow-up choices are prepopulated from the current install state for user-eligible packs (`ideas`, `docs`, `utility`, `research`)
+- If a user-eligible pack is already installed in both project and user scope, the installer asks whether to keep both installs or normalize the pack to user scope before it makes any cleanup changes
+- Changing a user-eligible pack from project scope to user scope, or back again, is treated as a migration: the old canonical copy is removed so the pack ends in the selected scope instead of accumulating duplicate installs
 - Tracks installed vs bundled skill versions and reports outdated skills
 - Records installed pack state in shared repo config as `tools.<pack>: true` so other OAT workflows can detect installed capabilities without relying on filesystem heuristics
 - Interactive runs can prompt to update selected outdated skills
-- Auto-sync runs automatically after successful install (provider views are updated)
+- Successful installs report the final scope chosen for each pack, including `project + user` when both installs are preserved, and auto-sync every scope touched by the install or migration
 - Install-triggered auto-sync limits removal planning to the canonical entries from the pack that was just installed, so stale manifest drift in unrelated packs does not delete other provider views
 - Use `--no-sync` to skip auto-sync
 

package/assets/public-package-versions.json

@@ -1,6 +1,6 @@
 {
-  "cli": "0.0.35",
-  "docs-config": "0.0.35",
-  "docs-theme": "0.0.35",
-  "docs-transforms": "0.0.35"
+  "cli": "0.0.36",
+  "docs-config": "0.0.36",
+  "docs-theme": "0.0.36",
+  "docs-transforms": "0.0.36"
 }

package/dist/commands/init/tools/index.d.ts

@@ -1,7 +1,10 @@
 import { type CommandContext, type GlobalOptions } from '../../../app/command-context.js';
 import { type UpsertSectionResult } from '../../shared/agents-md.js';
 import { type MultiSelectChoice, type PromptContext, type SelectChoice } from '../../shared/shared.prompts.js';
+import type { ScanToolsOptions } from '../../tools/shared/scan-tools.js';
+import type { ToolInfo } from '../../tools/shared/types.js';
 import { type OatConfig } from '../../../config/oat-config.js';
+import type { ConcreteScope } from '../../../shared/types.js';
 import { Command } from 'commander';
 import { type InstallCoreOptions, type InstallCoreResult } from './core/install-core.js';
 import { type InstallDocsOptions, type InstallDocsResult } from './docs/install-docs.js';
@@ -11,12 +14,14 @@ import { type InstallResearchOptions, type InstallResearchResult } from './resea
 import { type InstallUtilityOptions, type InstallUtilityResult } from './utility/install-utility.js';
 import { type InstallWorkflowsOptions, type InstallWorkflowsResult } from './workflows/install-workflows.js';
 type InstallScope = 'project' | 'user';
+type PackInstallTarget = InstallScope | 'both';
 export type ToolPack = 'core' | 'ideas' | 'docs' | 'workflows' | 'utility' | 'project-management' | 'research';
-interface InitToolsDependencies {
+export interface InitToolsDependencies {
     buildCommandContext: (options: GlobalOptions) => CommandContext;
     resolveProjectRoot: (cwd: string) => Promise<string>;
     resolveScopeRoot: (scope: InstallScope, cwd: string, home: string) => string;
     resolveAssetsRoot: () => Promise<string>;
+    scanTools: (options: ScanToolsOptions) => Promise<ToolInfo[]>;
     selectManyWithAbort: <T extends string>(message: string, choices: MultiSelectChoice<T>[], ctx: PromptContext) => Promise<T[] | null>;
     selectWithAbort: <T extends string>(message: string, choices: SelectChoice<T>[], ctx: PromptContext) => Promise<T | null>;
     installCore: (options: InstallCoreOptions) => Promise<InstallCoreResult>;
@@ -27,6 +32,8 @@ interface InitToolsDependencies {
     installProjectManagement: (options: InstallProjectManagementOptions) => Promise<InstallProjectManagementResult>;
     installResearch: (options: InstallResearchOptions) => Promise<InstallResearchResult>;
     copyDirWithStatus: (source: string, destination: string, force: boolean) => Promise<'copied' | 'updated' | 'skipped'>;
+    removeDirectory: (target: string) => Promise<void>;
+    removeFile: (target: string) => Promise<void>;
     addLocalPaths: (repoRoot: string, paths: string[]) => Promise<{
         added: string[];
         all: string[];
@@ -40,9 +47,13 @@ interface InitToolsDependencies {
     upsertAgentsMdSection: (repoRoot: string, key: string, body: string) => Promise<UpsertSectionResult>;
     removeAgentsMdSection: (repoRoot: string, key: string) => Promise<boolean>;
 }
+interface InitToolsRunMetadata {
+    affectedScopes: ConcreteScope[];
+}
+export declare function consumeInitToolsRunMetadata(): InitToolsRunMetadata | null;
 interface PackScopeInfo {
     pack: ToolPack;
-    scope: InstallScope;
+    scope: PackInstallTarget;
 }
 export declare function buildToolPacksSectionBody(packs: PackScopeInfo[]): string;
 export declare function runInitTools(context: CommandContext, dependencies: InitToolsDependencies): Promise<ToolPack[]>;

package/dist/commands/init/tools/index.d.ts.map

@@ -1 +1 @@
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package/dist/commands/init/tools/index.js

@@ -1,3 +1,4 @@
+import { rm, unlink } from 'node:fs/promises';
 import { join } from 'node:path';
 import { buildCommandContext, } from '../../../app/command-context.js';
 import { copyDirWithStatus } from '../../init/tools/shared/copy-helpers.js';
@@ -7,6 +8,7 @@ import { removeAgentsMdSection, upsertAgentsMdSection, } from '../../shared/agen
 import { selectManyWithAbort, selectWithAbort, } from '../../shared/shared.prompts.js';
 import { readGlobalOptions } from '../../shared/shared.utils.js';
 import { canonicalPathsForPacks, setInstalledCanonicalPaths, } from '../../tools/shared/install-sync-context.js';
+import { scanTools } from '../../tools/shared/scan-tools.js';
 import { readOatConfig, resolveLocalPaths, writeOatConfig, } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
 import { resolveProjectRoot, resolveScopeRoot } from '../../../fs/paths.js';
@@ -14,38 +16,56 @@ import { Command } from 'commander';
 import { createInitToolsCoreCommand } from './core/index.js';
 import { installCore as defaultInstallCore, } from './core/install-core.js';
 import { createInitToolsDocsCommand } from './docs/index.js';
-import { DOCS_SKILLS, installDocs as defaultInstallDocs, } from './docs/install-docs.js';
+import { installDocs as defaultInstallDocs, } from './docs/install-docs.js';
 import { createInitToolsIdeasCommand } from './ideas/index.js';
 import { installIdeas as defaultInstallIdeas, } from './ideas/install-ideas.js';
+import { buildPackInstallStateMap, } from './install-state.js';
 import { createInitToolsProjectManagementCommand } from './project-management/index.js';
 import { installProjectManagement as defaultInstallProjectManagement, } from './project-management/install-project-management.js';
 import { createInitToolsResearchCommand } from './research/index.js';
-import { installResearch as defaultInstallResearch, RESEARCH_SKILLS, } from './research/install-research.js';
+import { installResearch as defaultInstallResearch, } from './research/install-research.js';
+import { DOCS_SKILLS, IDEA_SKILLS, RESEARCH_AGENTS, RESEARCH_SKILLS, UTILITY_SKILLS, } from './shared/skill-manifest.js';
 import { createInitToolsUtilityCommand } from './utility/index.js';
-import { installUtility as defaultInstallUtility, UTILITY_SKILLS, } from './utility/install-utility.js';
+import { installUtility as defaultInstallUtility, } from './utility/install-utility.js';
 import { createInitToolsWorkflowsCommand } from './workflows/index.js';
 import { installWorkflows as defaultInstallWorkflows, } from './workflows/install-workflows.js';
 function formatVersionForDisplay(version) {
     return version ?? '(unversioned)';
 }
-const PACK_CHOICES = [
-    { label: 'Core [user]', value: 'core', checked: true },
-    { label: 'Ideas [project|user]', value: 'ideas', checked: true },
-    { label: 'Docs [project|user]', value: 'docs', checked: true },
-    {
-        label: 'Project Management [project]',
-        value: 'project-management',
-        checked: false,
-    },
-    { label: 'Workflows [project]', value: 'workflows', checked: true },
-    { label: 'Utility [project|user]', value: 'utility', checked: true },
-    { label: 'Research [project|user]', value: 'research', checked: true },
+const ALL_TOOL_PACKS = [
+    'core',
+    'ideas',
+    'docs',
+    'workflows',
+    'utility',
+    'project-management',
+    'research',
 ];
+const USER_ELIGIBLE_PACK_MEMBERS = {
+    ideas: {
+        skills: IDEA_SKILLS,
+        agents: [],
+    },
+    docs: {
+        skills: DOCS_SKILLS,
+        agents: [],
+    },
+    utility: {
+        skills: UTILITY_SKILLS,
+        agents: [],
+    },
+    research: {
+        skills: RESEARCH_SKILLS,
+        agents: RESEARCH_AGENTS,
+    },
+};
+let lastRunInitToolsMetadata = null;
 const DEFAULT_DEPENDENCIES = {
     buildCommandContext,
     resolveProjectRoot,
     resolveScopeRoot,
     resolveAssetsRoot,
+    scanTools,
     selectManyWithAbort,
     selectWithAbort,
     installCore: defaultInstallCore,
@@ -56,6 +76,21 @@ const DEFAULT_DEPENDENCIES = {
     installProjectManagement: defaultInstallProjectManagement,
     installResearch: defaultInstallResearch,
     copyDirWithStatus,
+    removeDirectory: async (target) => {
+        await rm(target, { recursive: true, force: true });
+    },
+    removeFile: async (target) => {
+        try {
+            await unlink(target);
+        }
+        catch (error) {
+            if (!(error instanceof Error) ||
+                !('code' in error) ||
+                error.code !== 'ENOENT') {
+                throw error;
+            }
+        }
+    },
     addLocalPaths,
     applyGitignore,
     readOatConfig,
@@ -70,7 +105,120 @@ const USER_ELIGIBLE_PACKS = new Set([
     'utility',
     'research',
 ]);
-async function resolvePackScopes(context, selections, dependencies) {
+function isUserEligiblePack(pack) {
+    return USER_ELIGIBLE_PACKS.has(pack);
+}
+async function loadInstalledPackStates(projectRoot, userRoot, assetsRoot, dependencies) {
+    const [projectTools, userTools] = await Promise.all([
+        dependencies.scanTools({
+            scope: 'project',
+            scopeRoot: projectRoot,
+            assetsRoot,
+        }),
+        dependencies.scanTools({
+            scope: 'user',
+            scopeRoot: userRoot,
+            assetsRoot,
+        }),
+    ]);
+    return buildPackInstallStateMap(ALL_TOOL_PACKS, [
+        ...projectTools,
+        ...userTools,
+    ]);
+}
+function formatInstalledLocation(location) {
+    switch (location) {
+        case 'project':
+            return 'project';
+        case 'user':
+            return 'user';
+        case 'both':
+            return 'project + user';
+        default:
+            return 'not installed';
+    }
+}
+function buildPackChoices(installedPackStates) {
+    return [
+        {
+            label: `Core [user]${installedPackStates.core.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.core.location)})`}`,
+            value: 'core',
+            checked: true,
+        },
+        {
+            label: `Ideas [project|user]${installedPackStates.ideas.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.ideas.location)})`}`,
+            value: 'ideas',
+            checked: true,
+        },
+        {
+            label: `Docs [project|user]${installedPackStates.docs.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.docs.location)})`}`,
+            value: 'docs',
+            checked: true,
+        },
+        {
+            label: `Project Management [project]${installedPackStates['project-management'].location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates['project-management'].location)})`}`,
+            value: 'project-management',
+            checked: false,
+        },
+        {
+            label: `Workflows [project]${installedPackStates.workflows.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.workflows.location)})`}`,
+            value: 'workflows',
+            checked: true,
+        },
+        {
+            label: `Utility [project|user]${installedPackStates.utility.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.utility.location)})`}`,
+            value: 'utility',
+            checked: true,
+        },
+        {
+            label: `Research [project|user]${installedPackStates.research.location === 'not-installed' ? '' : ` (installed: ${formatInstalledLocation(installedPackStates.research.location)})`}`,
+            value: 'research',
+            checked: true,
+        },
+    ];
+}
+function buildUserScopeChoices(packs, installedPackStates) {
+    return packs.map((pack) => {
+        const location = installedPackStates[pack].location;
+        return {
+            label: location === 'not-installed'
+                ? pack
+                : `${pack} (current: ${formatInstalledLocation(location)})`,
+            value: pack,
+            checked: location === 'user' || location === 'both',
+        };
+    });
+}
+async function resolveBothScopeTarget(pack, dependencies, interactive) {
+    const selection = await dependencies.selectWithAbort(`${pack} is currently installed in project and user scope. Keep both installs or normalize to user scope?`, [
+        {
+            label: 'Keep project + user (recommended)',
+            value: 'both',
+            description: 'Preserve both installed copies',
+        },
+        {
+            label: 'User only',
+            value: 'user',
+            description: 'Remove the project-scoped copy',
+        },
+    ], { interactive });
+    return selection ?? 'both';
+}
+export function consumeInitToolsRunMetadata() {
+    const metadata = lastRunInitToolsMetadata;
+    lastRunInitToolsMetadata = null;
+    return metadata;
+}
+async function removePackFromScope(pack, root, dependencies) {
+    const members = USER_ELIGIBLE_PACK_MEMBERS[pack];
+    for (const skill of members.skills) {
+        await dependencies.removeDirectory(join(root, '.agents', 'skills', skill));
+    }
+    for (const agent of members.agents) {
+        await dependencies.removeFile(join(root, '.agents', 'agents', agent));
+    }
+}
+async function resolvePackScopes(context, selections, installedPackStates, dependencies) {
     const scopes = {};
     // Workflows is always project-only
     for (const pack of selections) {
@@ -82,7 +230,7 @@ async function resolvePackScopes(context, selections, dependencies) {
     if (selections.includes('core')) {
         scopes.core = 'user';
     }
-    const eligiblePacks = selections.filter((pack) => USER_ELIGIBLE_PACKS.has(pack));
+    const eligiblePacks = selections.filter((pack) => isUserEligiblePack(pack));
     if (eligiblePacks.length === 0) {
         return scopes;
     }
@@ -107,31 +255,45 @@ async function resolvePackScopes(context, selections, dependencies) {
         return scopes;
     }
     // Interactive: let user pick which packs go to user scope
-    const userScopePacks = (await dependencies.selectManyWithAbort('Which packs should install at user scope? (unselected go to project scope)', eligiblePacks.map((pack) => ({
-        label: pack,
-        value: pack,
-        checked: false,
-    })), { interactive: context.interactive })) ?? [];
+    const userScopePacks = (await dependencies.selectManyWithAbort('Which packs should install at user scope? (unselected go to project scope)', buildUserScopeChoices(eligiblePacks, installedPackStates), { interactive: context.interactive })) ?? [];
     const userScopeSet = new Set(userScopePacks);
     for (const pack of eligiblePacks) {
-        scopes[pack] = userScopeSet.has(pack) ? 'user' : 'project';
+        if (!userScopeSet.has(pack)) {
+            scopes[pack] = 'project';
+            continue;
+        }
+        scopes[pack] =
+            installedPackStates[pack].location === 'both'
+                ? await resolveBothScopeTarget(pack, dependencies, context.interactive)
+                : 'user';
     }
     return scopes;
 }
-function reportSuccess(context, selectedPacks, utilityScope) {
+function buildInstalledToolsConfig(selectedPacks, installedPackStates, existingTools) {
+    const selectedPackSet = new Set(selectedPacks);
+    const tools = { ...existingTools };
+    for (const pack of ALL_TOOL_PACKS) {
+        tools[pack] =
+            selectedPackSet.has(pack) ||
+                installedPackStates[pack].location !== 'not-installed';
+    }
+    return tools;
+}
+function reportSuccess(context, packs, syncScopes) {
     if (context.json) {
         context.logger.json({
             status: 'ok',
-            selectedPacks,
-            utilityScope,
+            installedPacks: packs,
+            syncScopes,
         });
         return;
     }
-    context.logger.info(`Installed tool packs: ${selectedPacks.join(', ')}`);
-    context.logger.info(`User-eligible pack scope: ${utilityScope}`);
-    context.logger.info('Run: oat sync --scope project');
-    if (utilityScope === 'user') {
-        context.logger.info('Also run: oat sync --scope user');
+    context.logger.info(`Installed tool packs: ${packs.map(({ pack, scope }) => `${pack} (${formatInstalledLocation(scope)})`).join(', ')}`);
+    syncScopes.forEach((scope, index) => {
+        context.logger.info(`${index === 0 ? 'Run' : 'Also run'}: oat sync --scope ${scope}`);
+    });
+    if (syncScopes.length === 0) {
+        context.logger.info('No sync needed.');
     }
 }
 function reportOutdatedSkills(context, outdatedSkills) {
@@ -140,7 +302,7 @@ function reportOutdatedSkills(context, outdatedSkills) {
     }
     context.logger.info('Outdated skills:');
     for (const skill of outdatedSkills) {
-        context.logger.info(`  ${skill.name}  ${formatVersionForDisplay(skill.installed)} -> ${formatVersionForDisplay(skill.bundled)}`);
+        context.logger.info(`  ${skill.name} (${skill.targetRoot})  ${formatVersionForDisplay(skill.installed)} -> ${formatVersionForDisplay(skill.bundled)}`);
     }
 }
 async function updateOutdatedSkills(outdatedSkills, assetsRoot, dependencies) {
@@ -163,7 +325,7 @@ const PACK_DESCRIPTIONS = {
     research: 'Research, analysis, verification, and synthesis',
 };
 export function buildToolPacksSectionBody(packs) {
-    const userPacks = packs.filter((p) => p.scope === 'user');
+    const userPacks = packs.filter((p) => p.scope === 'user' || p.scope === 'both');
     const hasWorkflows = packs.some((p) => p.pack === 'workflows');
     const lines = [
         '## Tool Packs',
@@ -179,7 +341,11 @@ export function buildToolPacksSectionBody(packs) {
     }
     lines.push('', '### Installed Packs', '');
     for (const { pack, scope } of packs) {
-        const suffix = scope === 'user' ? ' _(user scope)_' : '';
+        const suffix = scope === 'user'
+            ? ' _(user scope)_'
+            : scope === 'both'
+                ? ' _(project + user scope)_'
+                : '';
         lines.push(`- **${pack}** — ${PACK_DESCRIPTIONS[pack]}${suffix}`);
     }
     if (hasWorkflows) {
@@ -188,66 +354,118 @@ export function buildToolPacksSectionBody(packs) {
     return lines.join('\n');
 }
 export async function runInitTools(context, dependencies) {
+    lastRunInitToolsMetadata = null;
     try {
+        const projectRoot = await dependencies.resolveProjectRoot(context.cwd);
+        const userRoot = dependencies.resolveScopeRoot('user', context.cwd, context.home);
+        const assetsRoot = await dependencies.resolveAssetsRoot();
+        const initialPackStates = await loadInstalledPackStates(projectRoot, userRoot, assetsRoot, dependencies);
         const selectedPacks = context.interactive
-            ? ((await dependencies.selectManyWithAbort('Select tool packs to install', PACK_CHOICES, { interactive: context.interactive })) ?? [])
+            ? ((await dependencies.selectManyWithAbort('Select tool packs to install', buildPackChoices(initialPackStates), { interactive: context.interactive })) ?? [])
             : ['core', 'ideas', 'docs', 'workflows', 'utility', 'research'];
         if (!context.interactive) {
             selectedPacks.push('project-management');
         }
         if (selectedPacks.length === 0) {
+            lastRunInitToolsMetadata = { affectedScopes: [] };
             if (!context.json) {
                 context.logger.info('No tool packs selected.');
             }
             process.exitCode = 0;
             return [];
         }
-        const projectRoot = await dependencies.resolveProjectRoot(context.cwd);
-        const userRoot = dependencies.resolveScopeRoot('user', context.cwd, context.home);
-        const packScopes = await resolvePackScopes(context, selectedPacks, dependencies);
+        const packScopes = await resolvePackScopes(context, selectedPacks, initialPackStates, dependencies);
         function packRoot(pack) {
             return packScopes[pack] === 'user' ? userRoot : projectRoot;
         }
-        const assetsRoot = await dependencies.resolveAssetsRoot();
+        function packTargets(pack) {
+            return packScopes[pack] === 'both'
+                ? [projectRoot, userRoot]
+                : [packRoot(pack)];
+        }
         const outdatedSkills = [];
+        const affectedScopes = new Set();
+        for (const pack of selectedPacks) {
+            if (!isUserEligiblePack(pack)) {
+                continue;
+            }
+            const desiredScope = packScopes[pack];
+            const currentLocation = initialPackStates[pack].location;
+            if (desiredScope === 'both') {
+                continue;
+            }
+            if (desiredScope === 'user') {
+                if (currentLocation === 'project' || currentLocation === 'both') {
+                    await removePackFromScope(pack, projectRoot, dependencies);
+                    affectedScopes.add('project');
+                }
+                continue;
+            }
+            if (currentLocation === 'user' || currentLocation === 'both') {
+                await removePackFromScope(pack, userRoot, dependencies);
+                affectedScopes.add('user');
+            }
+        }
         if (selectedPacks.includes('core')) {
             // Core pack always installs at user scope, regardless of userEligibleScope
+            affectedScopes.add('user');
             const coreResult = await dependencies.installCore({
                 assetsRoot,
                 targetRoot: userRoot,
             });
             for (const skill of coreResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot: userRoot });
+                outdatedSkills.push({
+                    ...skill,
+                    targetRoot: userRoot,
+                    selectionKey: `${skill.name}:${userRoot}`,
+                });
             }
         }
         if (selectedPacks.includes('ideas')) {
-            const targetRoot = packRoot('ideas');
-            const ideasResult = await dependencies.installIdeas({
-                assetsRoot,
-                targetRoot,
-            });
-            for (const skill of ideasResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot });
+            for (const targetRoot of packTargets('ideas')) {
+                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const ideasResult = await dependencies.installIdeas({
+                    assetsRoot,
+                    targetRoot,
+                });
+                for (const skill of ideasResult.outdatedSkills) {
+                    outdatedSkills.push({
+                        ...skill,
+                        targetRoot,
+                        selectionKey: `${skill.name}:${targetRoot}`,
+                    });
+                }
             }
         }
         if (selectedPacks.includes('docs')) {
-            const targetRoot = packRoot('docs');
-            const docsResult = await dependencies.installDocs({
-                assetsRoot,
-                targetRoot,
-                skills: [...DOCS_SKILLS],
-            });
-            for (const skill of docsResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot });
+            for (const targetRoot of packTargets('docs')) {
+                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const docsResult = await dependencies.installDocs({
+                    assetsRoot,
+                    targetRoot,
+                    skills: [...DOCS_SKILLS],
+                });
+                for (const skill of docsResult.outdatedSkills) {
+                    outdatedSkills.push({
+                        ...skill,
+                        targetRoot,
+                        selectionKey: `${skill.name}:${targetRoot}`,
+                    });
+                }
             }
         }
         if (selectedPacks.includes('workflows')) {
+            affectedScopes.add('project');
             const workflowsResult = await dependencies.installWorkflows({
                 assetsRoot,
                 targetRoot: projectRoot,
             });
             for (const skill of workflowsResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot: projectRoot });
+                outdatedSkills.push({
+                    ...skill,
+                    targetRoot: projectRoot,
+                    selectionKey: `${skill.name}:${projectRoot}`,
+                });
             }
             const resolvedRoot = workflowsResult.resolvedProjectsRoot || '.oat/projects/shared';
             const projectsBase = resolvedRoot.replace(/\/[^/]+$/, '');
@@ -286,47 +504,64 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('utility')) {
-            const targetRoot = packRoot('utility');
-            const utilityResult = await dependencies.installUtility({
-                assetsRoot,
-                targetRoot,
-                skills: [...UTILITY_SKILLS],
-            });
-            for (const skill of utilityResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot });
+            for (const targetRoot of packTargets('utility')) {
+                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const utilityResult = await dependencies.installUtility({
+                    assetsRoot,
+                    targetRoot,
+                    skills: [...UTILITY_SKILLS],
+                });
+                for (const skill of utilityResult.outdatedSkills) {
+                    outdatedSkills.push({
+                        ...skill,
+                        targetRoot,
+                        selectionKey: `${skill.name}:${targetRoot}`,
+                    });
+                }
             }
         }
         if (selectedPacks.includes('project-management')) {
             const targetRoot = projectRoot;
+            affectedScopes.add('project');
             const projectManagementResult = await dependencies.installProjectManagement({
                 assetsRoot,
                 targetRoot,
             });
             for (const skill of projectManagementResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot });
+                outdatedSkills.push({
+                    ...skill,
+                    targetRoot,
+                    selectionKey: `${skill.name}:${targetRoot}`,
+                });
             }
         }
         if (selectedPacks.includes('research')) {
-            const targetRoot = packRoot('research');
-            const researchResult = await dependencies.installResearch({
-                assetsRoot,
-                targetRoot,
-                skills: [...RESEARCH_SKILLS],
-            });
-            for (const skill of researchResult.outdatedSkills) {
-                outdatedSkills.push({ ...skill, targetRoot });
+            for (const targetRoot of packTargets('research')) {
+                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const researchResult = await dependencies.installResearch({
+                    assetsRoot,
+                    targetRoot,
+                    skills: [...RESEARCH_SKILLS],
+                });
+                for (const skill of researchResult.outdatedSkills) {
+                    outdatedSkills.push({
+                        ...skill,
+                        targetRoot,
+                        selectionKey: `${skill.name}:${targetRoot}`,
+                    });
+                }
             }
         }
         if (outdatedSkills.length > 0) {
             reportOutdatedSkills(context, outdatedSkills);
             if (context.interactive) {
                 const selectedNames = (await dependencies.selectManyWithAbort('Update outdated skills?', outdatedSkills.map((skill) => ({
-                    label: `${skill.name} (${skill.installed} -> ${skill.bundled})`,
-                    value: skill.name,
+                    label: `${skill.name} (${skill.targetRoot}) (${skill.installed} -> ${skill.bundled})`,
+                    value: skill.selectionKey,
                     checked: true,
                 })), { interactive: context.interactive })) ?? [];
                 const selectedSet = new Set(selectedNames);
-                const selectedOutdated = outdatedSkills.filter((skill) => selectedSet.has(skill.name));
+                const selectedOutdated = outdatedSkills.filter((skill) => selectedSet.has(skill.selectionKey));
                 const updatedNames = await updateOutdatedSkills(selectedOutdated, assetsRoot, dependencies);
                 if (updatedNames.length > 0) {
                     context.logger.info(`Updated outdated skills: ${updatedNames.join(', ')}`);
@@ -349,17 +584,18 @@ export async function runInitTools(context, dependencies) {
             context.logger.info(`AGENTS.md tool packs section ${sectionResult.action}.`);
         }
         const config = await dependencies.readOatConfig(projectRoot);
-        const tools = { ...config.tools };
-        for (const pack of selectedPacks) {
-            tools[pack] = true;
-        }
+        const tools = buildInstalledToolsConfig(selectedPacks, initialPackStates, config.tools);
         await dependencies.writeOatConfig(projectRoot, { ...config, tools });
-        const hasUserScope = selectedPacks.some((pack) => packScopes[pack] === 'user');
-        reportSuccess(context, selectedPacks, hasUserScope ? 'user' : 'project');
+        const affectedScopesList = [...affectedScopes];
+        lastRunInitToolsMetadata = {
+            affectedScopes: affectedScopesList,
+        };
+        reportSuccess(context, packScopeInfo, affectedScopesList);
         process.exitCode = 0;
         return selectedPacks;
     }
     catch (error) {
+        lastRunInitToolsMetadata = null;
         const message = error instanceof Error ? error.message : String(error);
         if (context.json) {
             context.logger.json({ status: 'error', message });

package/dist/commands/init/tools/install-state.d.ts

@@ -0,0 +1,10 @@
+import type { PackName, ToolInfo } from '../../tools/shared/types.js';
+export type PackInstallLocation = 'not-installed' | 'project' | 'user' | 'both';
+export interface PackInstallState {
+    project: boolean;
+    user: boolean;
+    location: PackInstallLocation;
+}
+export declare function resolvePackInstallLocation(project: boolean, user: boolean): PackInstallLocation;
+export declare function buildPackInstallStateMap<TPack extends PackName>(packs: readonly TPack[], tools: ToolInfo[]): Record<TPack, PackInstallState>;
+//# sourceMappingURL=install-state.d.ts.map

package/dist/commands/init/tools/install-state.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"install-state.d.ts","sourceRoot":"","sources":["../../../../src/commands/init/tools/install-state.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAEvE,MAAM,MAAM,mBAAmB,GAAG,eAAe,GAAG,SAAS,GAAG,MAAM,GAAG,MAAM,CAAC;AAEhF,MAAM,WAAW,gBAAgB;IAC/B,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,OAAO,CAAC;IACd,QAAQ,EAAE,mBAAmB,CAAC;CAC/B;AAED,wBAAgB,0BAA0B,CACxC,OAAO,EAAE,OAAO,EAChB,IAAI,EAAE,OAAO,GACZ,mBAAmB,CAcrB;AAED,wBAAgB,wBAAwB,CAAC,KAAK,SAAS,QAAQ,EAC7D,KAAK,EAAE,SAAS,KAAK,EAAE,EACvB,KAAK,EAAE,QAAQ,EAAE,GAChB,MAAM,CAAC,KAAK,EAAE,gBAAgB,CAAC,CA8BjC"}

package/dist/commands/init/tools/install-state.js

@@ -0,0 +1,36 @@
+export function resolvePackInstallLocation(project, user) {
+    if (project && user) {
+        return 'both';
+    }
+    if (project) {
+        return 'project';
+    }
+    if (user) {
+        return 'user';
+    }
+    return 'not-installed';
+}
+export function buildPackInstallStateMap(packs, tools) {
+    const state = Object.fromEntries(packs.map((pack) => [
+        pack,
+        {
+            project: false,
+            user: false,
+            location: 'not-installed',
+        },
+    ]));
+    for (const tool of tools) {
+        if (tool.pack === 'custom' || !(tool.pack in state)) {
+            continue;
+        }
+        const packState = state[tool.pack];
+        if (tool.scope === 'project') {
+            packState.project = true;
+        }
+        else {
+            packState.user = true;
+        }
+        packState.location = resolvePackInstallLocation(packState.project, packState.user);
+    }
+    return state;
+}

package/dist/commands/tools/install/index.d.ts

@@ -1,4 +1,5 @@
+import { type InitToolsDependencies } from '../../init/tools/index.js';
 import { type AutoSyncDependencies } from '../../tools/shared/auto-sync.js';
 import type { Command } from 'commander';
-export declare function createToolsInstallCommand(syncDependencies?: AutoSyncDependencies, createBaseCommand?: () => Command): Command;
+export declare function createToolsInstallCommand(syncDependencies?: AutoSyncDependencies, initOverrides?: Partial<InitToolsDependencies>, createBaseCommand?: () => Command): Command;
 //# sourceMappingURL=index.d.ts.map

package/dist/commands/tools/install/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/install/index.ts"],"names":[],"mappings":"AAQA,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAE1C,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwBzC,wBAAgB,yBAAyB,CACvC,gBAAgB,GAAE,oBAA8C,EAChE,iBAAiB,GAAE,MAAM,OAAgC,GACxD,OAAO,CA2BT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/tools/install/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAGL,KAAK,qBAAqB,EAC3B,MAAM,sBAAsB,CAAC;AAK9B,OAAO,EACL,KAAK,oBAAoB,EAE1B,MAAM,kCAAkC,CAAC;AAE1C,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwBzC,wBAAgB,yBAAyB,CACvC,gBAAgB,GAAE,oBAA8C,EAChE,aAAa,GAAE,OAAO,CAAC,qBAAqB,CAAM,EAClD,iBAAiB,CAAC,EAAE,MAAM,OAAO,GAChC,OAAO,CAoCT"}

package/dist/commands/tools/install/index.js

@@ -1,6 +1,6 @@
 import { execFile } from 'node:child_process';
 import { buildCommandContext } from '../../../app/command-context.js';
-import { createInitToolsCommand } from '../../init/tools/index.js';
+import { consumeInitToolsRunMetadata, createInitToolsCommand, } from '../../init/tools/index.js';
 import { readGlobalOptions, resolveConcreteScopes, } from '../../shared/shared.utils.js';
 import { autoSync, } from '../../tools/shared/auto-sync.js';
 import { getInstalledCanonicalPaths as getInstallSyncCanonicalPaths } from '../../tools/shared/install-sync-context.js';
@@ -26,8 +26,10 @@ const defaultSyncDependencies = {
         });
     },
 };
-export function createToolsInstallCommand(syncDependencies = defaultSyncDependencies, createBaseCommand = createInitToolsCommand) {
-    const cmd = createBaseCommand();
+export function createToolsInstallCommand(syncDependencies = defaultSyncDependencies, initOverrides = {}, createBaseCommand) {
+    const cmd = createBaseCommand === undefined
+        ? createInitToolsCommand(initOverrides)
+        : createBaseCommand();
     cmd.name('install');
     cmd.option('--no-sync', 'Skip auto-sync after install');
     cmd.hook('postAction', async (thisCommand, actionCommand) => {
@@ -37,8 +39,12 @@ export function createToolsInstallCommand(syncDependencies = defaultSyncDependen
         if (opts.sync === false)
             return;
         const globalOptions = readGlobalOptions(actionCommand);
-        const context = buildCommandContext(globalOptions);
-        const scopes = resolveConcreteScopes(context.scope);
+        const buildContext = initOverrides.buildCommandContext ?? buildCommandContext;
+        const context = buildContext(globalOptions);
+        const metadata = consumeInitToolsRunMetadata();
+        const scopes = metadata === null
+            ? resolveConcreteScopes(context.scope)
+            : metadata.affectedScopes;
         const installedCanonicalPaths = getInstallSyncCanonicalPaths(actionCommand);
         await autoSync(scopes, context.cwd, context.home, context.logger, syncDependencies, { installedCanonicalPaths });
     });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@open-agent-toolkit/cli",
-  "version": "0.0.35",
+  "version": "0.0.36",
   "private": false,
   "description": "Open Agent Toolkit CLI",
   "homepage": "https://github.com/voxmedia/open-agent-toolkit/tree/main/packages/cli",
@@ -33,7 +33,7 @@
     "ora": "^9.0.0",
     "yaml": "2.8.2",
     "zod": "^3.25.76",
-    "@open-agent-toolkit/control-plane": "0.0.35"
+    "@open-agent-toolkit/control-plane": "0.0.36"
   },
   "devDependencies": {
     "@types/node": "^22.10.0",