@open-agent-toolkit/cli 0.0.35 → 0.0.37

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 - Tracks installed vs bundled skill versions and reports outdated skills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 - Interactive runs can prompt to update selected outdated skills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/docs/docs-tooling/workflows.md

@@ -27,6 +27,11 @@ Install the workflow skills with `oat tools install docs` (preferred) or
   contributor guidance, and docs-app contract issues
 - `oat-docs-apply` consumes the analysis artifact and applies only approved,
   evidence-backed recommendations
+- `oat-project-document` performs post-implementation docs sync for a tracked project,
+  including finding missing coverage for newly shipped capability areas and
+  recommending new docs pages or directories when existing docs do not provide
+  a natural home. See the [project lifecycle post-implementation flow](../workflows/projects/lifecycle.md#post-implementation-flow)
+  for where this runs in the tracked project flow.
 
 ## Contract model
 

package/assets/docs/workflows/projects/lifecycle.md

@@ -18,7 +18,7 @@ OAT lifecycle order:
 7. Summary (`oat-project-summary`) — generates `summary.md` as institutional memory; `oat-project-pr-final` and `oat-project-complete` auto-refresh it when missing or stale
 8. PR (`oat-project-pr-progress` / `oat-project-pr-final`) — sets `pr_open` status
 9. Revision loop (`oat-project-revise`) — optional; accepts post-PR feedback
-10. Documentation sync (`oat-project-document`) — optional; reads project artifacts to identify docs needing updates, checks `tools.project-management`, and auto-runs `oat-pjm-update-repo-reference` before scanning docs when the project-management pack is installed
+10. Documentation sync (`oat-project-document`) — optional; reads project artifacts and code evidence to identify docs needing updates, checks for missing coverage of newly shipped capability areas, checks `tools.project-management`, and auto-runs `oat-pjm-update-repo-reference` before scanning docs when the project-management pack is installed
 11. Complete (`oat-project-complete`)
 
 **Shortcut:** `oat-project-next` reads project state and invokes the correct next skill automatically — use it instead of remembering which skill comes next. Complements `oat-project-progress` (which is read-only diagnostic).
@@ -49,7 +49,7 @@ flowchart LR
 After implementation and final review pass:
 
 1. **Summary** (`oat-project-summary`) — generates `summary.md` as institutional memory from project artifacts; PR-final and completion will auto-refresh it if you have not already run it or if it is stale
-2. **Documentation** (`oat-project-document`) — optional sync of project docs; now uses the shared `tools.project-management` config signal to decide whether repo-reference refresh should run before docs analysis
+2. **Documentation** (`oat-project-document`) — optional sync of project docs; now uses the shared `tools.project-management` config signal to decide whether repo-reference refresh should run before docs analysis, and should recommend new docs pages/directories when the shipped work introduces a capability area that the docs app does not already cover
 3. **PR** (`oat-project-pr-final`) — creates PR description (auto-refreshes `summary.md` first when needed, then uses it as source), sets `oat_phase_status: pr_open`, and tracks actual PR existence with `oat_pr_status` / `oat_pr_url`
 4. **Revision loop** (`oat-project-revise`) — accepts post-PR feedback:
    - Inline feedback creates `p-revN` revision phases with `prevN-tNN` task IDs

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": "0.0.37",
+  "docs-config": "0.0.37",
+  "docs-theme": "0.0.37",
+  "docs-transforms": "0.0.37"
 }

package/assets/skills/oat-project-document/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: oat-project-document
-version: 1.2.0
+version: 1.3.0
 description: Run when implementation is complete and documentation needs updating. Analyzes project artifacts to produce documentation update recommendations, then applies approved changes before project completion.
 argument-hint: '[project-path] [--auto]'
 disable-model-invocation: true
@@ -195,9 +195,9 @@ These will be verified against actual code in Step 3.
 - Quick-mode projects may lack spec.md and design.md — extract what's available
 - If only plan.md exists (no implementation.md), the project may not have started implementation yet — still proceed, but note that documentation recommendations will be based on planned work rather than verified implementation
 
-### Step 3: Verify Against Code
+### Step 3: Verify Against Code and Build a Capability Inventory
 
-Read source files referenced in artifacts to confirm what actually shipped.
+Read source files referenced in artifacts to confirm what actually shipped, then do a targeted capability-discovery pass so the skill can catch newly introduced documentation surfaces rather than only updating already-documented ones.
 
 **For each referenced source file:**
 
@@ -211,11 +211,31 @@ Read source files referenced in artifacts to confirm what actually shipped.
 
 - Add code-verified details that artifacts didn't capture
 - Note any discrepancies between artifacts and code (informational — include in delta plan as context, not as blocking issues)
+- Organize the verified implementation into **capability areas** (for example: new app surface, CI/CD pipeline, release automation flow, deployment target, integration surface, CLI/config workflow)
+
+**Targeted capability discovery pass:**
+
+After verifying artifact-referenced files, inspect the strongest adjacent signals for newly shipped capability surfaces even when the exact docs target does not already exist.
+
+Prioritize evidence from:
+
+- new apps/packages/directories called out by the artifacts
+- workflow/config files tied to shipped behavior (`.github/workflows`, release configs, deploy configs, mobile build/release files, etc.)
+- entrypoints, route registration files, service modules, and schemas that define user- or operator-facing behavior
+- package manifests and scripts that expose new setup, release, or operational workflows
+
+For each significant capability area, capture:
+
+- capability name
+- concrete repo evidence proving it shipped
+- likely audience (`developer`, `operator`, `integrator`, `end user`)
+- whether the capability represents a new docs surface versus an addition to an existing surface
 
 **Scope control:**
 
-- Focus on files directly referenced in artifacts — don't scan the entire codebase
-- If artifacts reference many files (>20), prioritize: new files first, then modified files with the most changes
+- Start with files directly referenced in artifacts, then inspect only the highest-signal adjacent files needed to understand the shipped capability areas
+- Do not scan the entire codebase blindly; stay anchored to the implementation areas surfaced by the project artifacts
+- If artifacts reference many files (>20), prioritize: new files first, then modified files with the most changes, then only the adjacent files needed to confirm docs impact
 - Read file contents, not just check existence — the skill needs to understand what the code does to make good documentation recommendations
 
 ### Step 4: Discover Documentation Surfaces
@@ -228,6 +248,8 @@ Scan the repository for all documentation and instruction surfaces.
    - Read the docs tooling config (e.g., `$DOCS_CONFIG`) to understand nav structure
    - List all files in `$DOCS_ROOT` recursively
    - Read existing docs files that could be affected by the project
+   - Identify the parent section or directory where each uncovered capability area would naturally live
+   - Note when no existing page or directory is a good fit — this is a strong signal for a `CREATE` recommendation, not a reason to force the content into an unrelated existing page
 
 2. **Root README.md:**
    - Always check — read current content
@@ -270,7 +292,38 @@ Scan the repository for all documentation and instruction surfaces.
 
 Compare "what was built" (from Steps 2-3) against "what's documented" (from Step 4) to produce recommendations.
 
-**5a. Documentation surface assessment:**
+**5a. Capability coverage assessment (required):**
+
+Before recommending file-level edits, evaluate coverage for each significant capability area in the "what was built" model.
+
+For each capability area, classify the documentation state as:
+
+- **adequately covered** — existing docs already explain the shipped behavior accurately
+- **thin coverage** — the area is mentioned, but important setup, workflow, or usage details are missing
+- **no coverage** — no existing docs surface meaningfully covers the capability
+
+For each capability with **thin coverage** or **no coverage**, determine the best docs home:
+
+- **Expand an existing page** when a clear, discoverable page already owns the topic
+- **Create a new page** when the topic is distinct enough to deserve its own entrypoint
+- **Create a new docs directory** (with `index.md` entrypoint, where that is the local convention) when the shipped work introduces a new top-level capability area with multiple likely subtopics
+
+Bias rules:
+
+- If a docs app exists and the shipped work represents a new major capability area, do **not** default to stuffing the information into `README.md`, `roadmap.md`, or `current-state.md`
+- Examples that often warrant `CREATE` recommendations: new mobile apps, CI/CD and release automation, new deployment targets, new integration surfaces, or new operator workflows
+- If no existing docs section is a natural fit, prefer recommending a new page or directory rather than forcing an `UPDATE` on a loosely related page
+
+Each coverage-gap finding should capture:
+
+- capability area
+- current docs state (`thin coverage` or `no coverage`)
+- evidence proving the capability shipped
+- likely audience
+- suggested docs location (`existing page`, `new page`, or `new directory`)
+- why that location is the right home
+
+**5b. Documentation surface assessment:**
 
 For each documentation surface relevant to the project, determine one of:
 
@@ -283,6 +336,7 @@ For each documentation surface relevant to the project, determine one of:
   - Proposed file path
   - Proposed content outline (section headings, key points)
   - Why this warrants a new file (evidence)
+  - If inside a docs app, note any parent index/nav follow-on work that will be needed
 
 - **SPLIT:** Existing doc would become too large with additions. Specify:
   - Current file path and approximate size
@@ -291,7 +345,13 @@ For each documentation surface relevant to the project, determine one of:
 
 - **No change:** Surface is already accurate — skip from delta plan.
 
-**5b. Instruction surface assessment (strong signals only):**
+When deciding between `UPDATE` and `CREATE`, prefer `CREATE` if:
+
+- the capability currently has **no coverage**
+- the docs app has no discoverable home for that topic
+- the proposed addition would otherwise bury a new major workflow inside an unrelated page
+
+**5c. Instruction surface assessment (strong signals only):**
 
 Only recommend instruction changes when there is a clear trigger:
 
@@ -305,14 +365,17 @@ Only recommend instruction changes when there is a clear trigger:
 
 If no strong signal is present for an instruction surface, skip it.
 
-**5c. Per recommendation, capture:**
+**5d. Per recommendation, capture:**
 
 ```
 - Target: {file path — existing or proposed}
 - Action: {UPDATE | CREATE | SPLIT}
 - Summary: {1-2 sentences on what changes and why}
-- Evidence: {artifact reference — e.g., "spec.md §3", "plan.md p02-t03", "implementation.md p01-t01 outcome"}
+- Evidence: {artifact/code reference — e.g., "spec.md §3", "plan.md p02-t03", "implementation.md p01-t01 outcome", "workflow file X proves release automation shipped"}
+- Audience: {developer | operator | integrator | end user}
 - Content guidance: {specific content to add or outline for new files}
+- Coverage state: {adequately covered | thin coverage | no coverage}
+- Parent docs impact: {parent index/nav updates needed, or "none"}
 ```
 
 ### Step 6: Present Delta Plan
@@ -378,7 +441,8 @@ Execute the approved documentation updates.
 2. **CREATE:**
    - Create parent directories if needed (`mkdir -p`)
    - Write the new file with the content outlined in the recommendation
-   - For docs directory files: follow the existing docs conventions (e.g., index.md structure for MkDocs)
+   - For docs directory files: follow the existing docs conventions for entrypoints and local navigation (for example, `index.md` entrypoints and `## Contents` sections where that is the local pattern)
+   - If the recommendation created a new docs directory, add the required entrypoint file for that directory as part of the same change
 
 3. **SPLIT:**
    - Create the new file with the content being moved
@@ -475,7 +539,9 @@ Next steps:
 ## Success Criteria
 
 - All documentation surfaces relevant to the project are scanned
+- Significant capability areas from the "what was built" model are classified as `adequately covered`, `thin coverage`, or `no coverage` before file-level recommendations are chosen
 - Recommendations are evidence-based (every recommendation cites artifact/code sources)
+- `CREATE` actions are recommended when no existing docs surface is a natural fit, including new docs pages or directories when the shipped work introduces a new capability area
 - Interactive approval flow works correctly (all/individual/skip)
 - `--auto` mode applies all changes without user interaction
 - New files and splits are handled correctly

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": "0.0.37",
   "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": "0.0.37"
   },
   "devDependencies": {
     "@types/node": "^22.10.0",