@open-agent-toolkit/cli 0.1.27 → 0.1.29

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

@@ -104,14 +104,15 @@ Key behavior:
 - Same pack selection and install flow as `oat init tools`
 - Pack-oriented install subcommands: `core`, `docs`, `ideas`, `workflows`, `utility`, `project-management`, `research`, `brainstorm`
 - 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`, `brainstorm`)
-- The `brainstorm` pack defaults to user scope on fresh installs (driven by `PACK_METADATA[brainstorm].defaultScope = 'user'`); existing project-scope installs still take precedence on re-install so users do not get unexpected scope migrations
-- 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
+- Installing is **additive**: choosing a scope for a pack never removes it from another scope. A user-eligible pack installed at user scope plus a project install ends up at `project + user`, not moved
+- For each user-eligible pack (`ideas`, `docs`, `utility`, `research`, `brainstorm`), the interactive flow offers a per-pack end-state selector (`project`, `user`, or `both`) defaulting to the pack's current placement; leaving the default makes no changes for that pack
+- The `brainstorm` pack defaults to user scope on fresh installs (driven by `PACK_METADATA[brainstorm].defaultScope = 'user'`); existing installs keep their current placement on re-install, so a re-install never moves a pack between scopes
+- Removing a pack from a scope happens only when you explicitly choose a narrower end-state in the interactive flow (e.g. a pack at `both` set to `project` only). All staged removals are shown in a single change summary and applied only after one batch confirmation — declining makes no changes
+- Non-interactive installs (including `--scope project`, `--scope user`, and the default pack set) are strictly additive and never remove a pack from a scope. Removal is interactive-only
 - 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
-- 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
+- Successful installs report the final scope chosen for each pack, including `project + user` when a pack is installed in both, and auto-sync only the scopes actually changed by the install so untouched scopes are never re-synced or pruned
 - 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": "0.1.27",
-  "docs-config": "0.1.27",
-  "docs-theme": "0.1.27",
-  "docs-transforms": "0.1.27"
+  "cli": "0.1.29",
+  "docs-config": "0.1.29",
+  "docs-theme": "0.1.29",
+  "docs-transforms": "0.1.29"
 }

package/assets/templates/docs-app-fuma/next.config.js

@@ -2,6 +2,4 @@ import { createDocsConfig } from '@open-agent-toolkit/docs-config';
 
 const basePath = process.env.NEXT_PUBLIC_BASE_PATH || undefined;
 
-export default createDocsConfig({
-  ...(basePath ? { basePath } : {}),
-});
+export default createDocsConfig(basePath ? { basePath } : {});

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

@@ -52,6 +52,16 @@ export interface InitToolsDependencies {
 interface InitToolsRunMetadata {
     affectedScopes: ConcreteScope[];
 }
+interface PackScopeChange {
+    pack: ToolPack;
+    scope: ConcreteScope;
+}
+/**
+ * Render a batch change summary (`+ pack@scope` adds / `- pack@scope` removes)
+ * for the interactive removal-confirmation gate. Pure for snapshot-friendly
+ * testing.
+ */
+export declare function formatReconcileSummary(adds: PackScopeChange[], removes: PackScopeChange[]): string;
 export declare function consumeInitToolsRunMetadata(): InitToolsRunMetadata | null;
 interface PackScopeInfo {
     pack: ToolPack;

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

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/init/tools/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAI9B,OAAO,EACL,KAAK,mBAAmB,EAGzB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAClB,KAAK,YAAY,EAGlB,MAAM,iCAAiC,CAAC;AAOzC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mCAAmC,CAAC;AAC1E,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAC7D,OAAO,EACL,KAAK,SAAS,EAIf,MAAM,oBAAoB,CAAC;AAG5B,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,OAAO,EAEL,KAAK,wBAAwB,EAC7B,KAAK,uBAAuB,EAC7B,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EAEL,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACvB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAEL,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACvB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAEL,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACxB,MAAM,uBAAuB,CAAC;AAM/B,OAAO,EAEL,KAAK,+BAA+B,EACpC,KAAK,8BAA8B,EACpC,MAAM,iDAAiD,CAAC;AAEzD,OAAO,EAEL,KAAK,sBAAsB,EAC3B,KAAK,qBAAqB,EAC3B,MAAM,6BAA6B,CAAC;AAWrC,OAAO,EAEL,KAAK,qBAAqB,EAC1B,KAAK,oBAAoB,EAC1B,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EAEL,KAAK,uBAAuB,EAC5B,KAAK,sBAAsB,EAC5B,MAAM,+BAA+B,CAAC;AAEvC,KAAK,YAAY,GAAG,SAAS,GAAG,MAAM,CAAC;AACvC,KAAK,iBAAiB,GAAG,YAAY,GAAG,MAAM,CAAC;AAC/C,MAAM,MAAM,QAAQ,GAChB,MAAM,GACN,OAAO,GACP,MAAM,GACN,WAAW,GACX,SAAS,GACT,oBAAoB,GACpB,UAAU,GACV,YAAY,CAAC;AAEjB,MAAM,WAAW,qBAAqB;IACpC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,kBAAkB,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IACrD,gBAAgB,EAAE,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC;IAC7E,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,SAAS,EAAE,CAAC,OAAO,EAAE,gBAAgB,KAAK,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC9D,mBAAmB,EAAE,CAAC,CAAC,SAAS,MAAM,EACpC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAC/B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC;IACzB,eAAe,EAAE,CAAC,CAAC,SAAS,MAAM,EAChC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,EAC1B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;IACvB,WAAW,EAAE,CAAC,OAAO,EAAE,kBAAkB,KAAK,OAAO,CAAC,iBAAiB,CAAC,CAAC;IACzE,WAAW,EAAE,CAAC,OAAO,EAAE,kBAAkB,KAAK,OAAO,CAAC,iBAAiB,CAAC,CAAC;IACzE,YAAY,EAAE,CAAC,OAAO,EAAE,mBAAmB,KAAK,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC5E,gBAAgB,EAAE,CAChB,OAAO,EAAE,uBAAuB,KAC7B,OAAO,CAAC,sBAAsB,CAAC,CAAC;IACrC,cAAc,EAAE,CACd,OAAO,EAAE,qBAAqB,KAC3B,OAAO,CAAC,oBAAoB,CAAC,CAAC;IACnC,wBAAwB,EAAE,CACxB,OAAO,EAAE,+BAA+B,KACrC,OAAO,CAAC,8BAA8B,CAAC,CAAC;IAC7C,eAAe,EAAE,CACf,OAAO,EAAE,sBAAsB,KAC5B,OAAO,CAAC,qBAAqB,CAAC,CAAC;IACpC,iBAAiB,EAAE,CACjB,OAAO,EAAE,wBAAwB,KAC9B,OAAO,CAAC,uBAAuB,CAAC,CAAC;IACtC,iBAAiB,EAAE,CACjB,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,OAAO,KACX,OAAO,CAAC,QAAQ,GAAG,SAAS,GAAG,SAAS,CAAC,CAAC;IAC/C,eAAe,EAAE,CAAC,MAAM,EAAE,MAAM,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IACnD,UAAU,EAAE,CAAC,MAAM,EAAE,MAAM,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IAC9C,aAAa,EAAE,CACb,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EAAE,KACZ,OAAO,CAAC;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,GAAG,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC,CAAC;IACjD,cAAc,EAAE,CACd,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,EAAE,KACjB,OAAO,CAAC;QAAE,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACjC,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,cAAc,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IACvE,iBAAiB,EAAE,CAAC,MAAM,EAAE,SAAS,KAAK,MAAM,EAAE,CAAC;IACnD,qBAAqB,EAAE,CACrB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,KACT,OAAO,CAAC,mBAAmB,CAAC,CAAC;IAClC,qBAAqB,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;CAC5E;AAUD,UAAU,oBAAoB;IAC5B,cAAc,EAAE,aAAa,EAAE,CAAC;CACjC;AAmKD,UAAU,eAAe;IACvB,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,aAAa,CAAC;CACtB;AAED;;;;GAIG;AACH,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,eAAe,EAAE,EACvB,OAAO,EAAE,eAAe,EAAE,GACzB,MAAM,CASR;AA4GD,wBAAgB,2BAA2B,IAAI,oBAAoB,GAAG,IAAI,CAIzE;AAmQD,UAAU,aAAa;IACrB,IAAI,EAAE,QAAQ,CAAC;IACf,KAAK,EAAE,iBAAiB,CAAC;CAC1B;AAED,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,aAAa,EAAE,GAAG,MAAM,CA8CxE;AAED,wBAAsB,YAAY,CAChC,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,qBAAqB,GAClC,OAAO,CAAC,QAAQ,EAAE,CAAC,CAgdrB;AAED,wBAAsB,wBAAwB,CAC5C,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAErB;AAED,wBAAgB,sBAAsB,CACpC,SAAS,GAAE,OAAO,CAAC,qBAAqB,CAAM,GAC7C,OAAO,CA4BT"}

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

@@ -117,6 +117,77 @@ const USER_ELIGIBLE_PACKS = new Set([
 function isUserEligiblePack(pack) {
     return USER_ELIGIBLE_PACKS.has(pack);
 }
+/**
+ * Concrete scopes implied by a desired end-state placement.
+ */
+function scopesForEndState(end) {
+    switch (end) {
+        case 'project':
+            return ['project'];
+        case 'user':
+            return ['user'];
+        case 'both':
+            return ['project', 'user'];
+    }
+}
+/**
+ * Concrete scopes a pack is currently installed at.
+ */
+function scopesForLocation(location) {
+    switch (location) {
+        case 'project':
+            return ['project'];
+        case 'user':
+            return ['user'];
+        case 'both':
+            return ['project', 'user'];
+        default:
+            return [];
+    }
+}
+/**
+ * Pure diff of current placement vs a desired end-state into the set of
+ * scopes to add (install into) and remove (delete from). This is the single
+ * source of truth that the reconciliation loop drives off of, so installs and
+ * removals only ever touch scopes that actually change.
+ */
+function reconcilePackScope(current, desired) {
+    const currentScopes = new Set(scopesForLocation(current));
+    const desiredScopes = new Set(scopesForEndState(desired));
+    const adds = [...desiredScopes].filter((scope) => !currentScopes.has(scope));
+    const removes = [...currentScopes].filter((scope) => !desiredScopes.has(scope));
+    return { adds, removes };
+}
+/**
+ * Render a batch change summary (`+ pack@scope` adds / `- pack@scope` removes)
+ * for the interactive removal-confirmation gate. Pure for snapshot-friendly
+ * testing.
+ */
+export function formatReconcileSummary(adds, removes) {
+    const lines = ['Review pending changes:'];
+    for (const { pack, scope } of adds) {
+        lines.push(`  + ${pack}@${scope}`);
+    }
+    for (const { pack, scope } of removes) {
+        lines.push(`  - ${pack}@${scope}`);
+    }
+    return lines.join('\n');
+}
+/**
+ * Additive union of a pack's current placement with a requested scope. Never
+ * returns a placement narrower than current — installing at one scope can
+ * never remove the pack from another scope.
+ */
+function unionScopeWithCurrent(current, requested) {
+    const scopes = new Set([
+        ...scopesForLocation(current),
+        requested,
+    ]);
+    if (scopes.has('project') && scopes.has('user')) {
+        return 'both';
+    }
+    return scopes.has('user') ? 'user' : 'project';
+}
 async function loadInstalledPackStates(projectRoot, userRoot, assetsRoot, dependencies) {
     const [projectTools, userTools] = await Promise.all([
         dependencies.scanTools({
@@ -191,43 +262,6 @@ function buildPackChoices(installedPackStates) {
         },
     ];
 }
-function buildUserScopeChoices(packs, installedPackStates) {
-    return packs.map((pack) => {
-        const location = installedPackStates[pack].location;
-        // Existing-install detection wins over PACK_METADATA defaultScope so
-        // re-installs of an already-placed pack do not silently migrate the
-        // user across scopes. When the pack is not yet installed at any
-        // scope, fall back to PACK_METADATA[pack]?.defaultScope (defaults
-        // to 'project' when absent).
-        const checked = location === 'user' || location === 'both'
-            ? true
-            : location === 'not-installed'
-                ? resolvePackDefaultScope(pack) === 'user'
-                : false;
-        return {
-            label: location === 'not-installed'
-                ? pack
-                : `${pack} (current: ${formatInstalledLocation(location)})`,
-            value: pack,
-            checked,
-        };
-    });
-}
-async function resolveBothScopeTarget(pack, dependencies, interactive) {
-    const selection = await dependencies.selectWithAbort(`${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;
@@ -258,16 +292,13 @@ async function resolvePackScopes(context, selections, installedPackStates, depen
     if (eligiblePacks.length === 0) {
         return scopes;
     }
-    // Explicit --scope overrides per-pack selection
-    if (context.scope === 'project') {
+    // Explicit --scope is additive: union the requested scope with the pack's
+    // current placement so installing at one scope never removes another. A pack
+    // currently at `user` installed with `--scope project` becomes `both`.
+    if (context.scope === 'project' || context.scope === 'user') {
+        const requested = context.scope;
         for (const pack of eligiblePacks) {
-            scopes[pack] = 'project';
-        }
-        return scopes;
-    }
-    if (context.scope === 'user') {
-        for (const pack of eligiblePacks) {
-            scopes[pack] = 'user';
+            scopes[pack] = unionScopeWithCurrent(installedPackStates[pack].location, requested);
         }
         return scopes;
     }
@@ -298,21 +329,70 @@ async function resolvePackScopes(context, selections, installedPackStates, depen
         }
         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)', buildUserScopeChoices(eligiblePacks, installedPackStates), { interactive: context.interactive })) ?? [];
-    const userScopeSet = new Set(userScopePacks);
+    // Interactive: for each user-eligible pack, choose its desired end-state
+    // placement (project / user / both). The default offered is the pack's
+    // current placement (or its default scope when not yet installed), so
+    // breezing through accepting defaults is a no-op and never removes a scope.
     for (const pack of eligiblePacks) {
-        if (!userScopeSet.has(pack)) {
-            scopes[pack] = 'project';
-            continue;
-        }
-        scopes[pack] =
-            installedPackStates[pack].location === 'both'
-                ? await resolveBothScopeTarget(pack, dependencies, context.interactive)
-                : 'user';
+        const currentLocation = installedPackStates[pack].location;
+        const defaultEndState = resolvePackDefaultEndState(pack, currentLocation);
+        const selection = await dependencies.selectWithAbort(`Where should ${pack} install?`, buildPackEndStateChoices(pack, currentLocation, defaultEndState), { interactive: context.interactive });
+        scopes[pack] = selection ?? defaultEndState;
     }
     return scopes;
 }
+/**
+ * Default end-state offered for a pack in the interactive selector: its
+ * current placement when installed, or its configured default scope when not
+ * yet present.
+ */
+function resolvePackDefaultEndState(pack, currentLocation) {
+    switch (currentLocation) {
+        case 'project':
+            return 'project';
+        case 'user':
+            return 'user';
+        case 'both':
+            return 'both';
+        default:
+            return resolvePackDefaultScope(pack);
+    }
+}
+/**
+ * Per-pack end-state options (project / user / both) for the interactive
+ * selector. The default end-state is listed first so the underlying
+ * single-select highlights it.
+ */
+function buildPackEndStateChoices(pack, currentLocation, defaultEndState) {
+    const currentLabel = currentLocation === 'not-installed'
+        ? 'not installed'
+        : `current: ${formatInstalledLocation(currentLocation)}`;
+    const baseChoices = [
+        {
+            label: `Project scope (${pack})`,
+            value: 'project',
+            description: 'Install at project scope only',
+        },
+        {
+            label: `User scope (${pack})`,
+            value: 'user',
+            description: 'Install at user scope only',
+        },
+        {
+            label: `Project + user (${pack})`,
+            value: 'both',
+            description: 'Install at both scopes',
+        },
+    ];
+    // Annotate the option matching the default so the prompt communicates the
+    // current placement, and order it first so it is the highlighted default.
+    const annotated = baseChoices.map((choice) => choice.value === defaultEndState
+        ? { ...choice, label: `${choice.label} [${currentLabel}]` }
+        : choice);
+    const defaultChoice = annotated.find((choice) => choice.value === defaultEndState);
+    const rest = annotated.filter((choice) => choice.value !== defaultEndState);
+    return defaultChoice ? [defaultChoice, ...rest] : annotated;
+}
 function buildInstalledToolsConfig(selectedPacks, installedPackStates, existingTools) {
     const selectedPackSet = new Set(selectedPacks);
     const tools = { ...existingTools };
@@ -428,37 +508,89 @@ export async function runInitTools(context, dependencies) {
             return [];
         }
         const packScopes = await resolvePackScopes(context, selectedPacks, initialPackStates, dependencies);
-        function packRoot(pack) {
-            return packScopes[pack] === 'user' ? userRoot : projectRoot;
+        function scopeRoot(scope) {
+            return scope === 'user' ? userRoot : projectRoot;
+        }
+        // Reconcile current placement vs the desired end-state per user-eligible
+        // pack into adds/removes. Installs copy idempotently into the full desired
+        // end-state, but only the scopes that actually changed (an add or a
+        // confirmed remove) are recorded in `affectedScopes`, so auto-sync never
+        // prunes a preserved scope.
+        const reconciliationByPack = new Map();
+        for (const pack of selectedPacks) {
+            if (!isUserEligiblePack(pack)) {
+                continue;
+            }
+            reconciliationByPack.set(pack, reconcilePackScope(initialPackStates[pack].location, packScopes[pack]));
         }
+        // Scopes a pack should install into (its full desired end-state for
+        // user-eligible packs; the resolved scope otherwise). Re-installing an
+        // already-present scope is an idempotent copy.
         function packTargets(pack) {
             return packScopes[pack] === 'both'
                 ? [projectRoot, userRoot]
-                : [packRoot(pack)];
+                : [packScopes[pack] === 'user' ? userRoot : projectRoot];
+        }
+        // Only scopes that received a new add for this pack should be auto-synced.
+        function addedScopes(pack) {
+            return new Set(reconciliationByPack.get(pack)?.adds);
         }
         const outdatedSkills = [];
         const affectedScopes = new Set();
-        for (const pack of selectedPacks) {
-            if (!isUserEligiblePack(pack)) {
-                continue;
+        // Collect all staged removals across packs. Removals are interactive-only
+        // and gated behind a single batch confirmation (added in p01-t03);
+        // non-interactive paths are strictly additive and can never remove.
+        const stagedRemovals = [];
+        for (const [pack, reconciliation] of reconciliationByPack) {
+            for (const scope of reconciliation.removes) {
+                stagedRemovals.push({ pack, scope });
             }
-            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');
+        }
+        if (stagedRemovals.length > 0 && !context.interactive) {
+            // Strictly-additive guard: removals must never be applied
+            // non-interactively. This should be unreachable because non-interactive
+            // resolution unions with current placement, but we fail loud rather than
+            // silently delete a user's install.
+            throw new Error('Non-interactive install attempted to remove a pack from a scope; ' +
+                'install is strictly additive in non-interactive mode.');
+        }
+        // Interactive removal gate: if any pack would lose a scope, surface one
+        // batch change summary and require a single confirmation before mutating
+        // anything. Declining aborts with zero changes (no installs, no removals).
+        if (stagedRemovals.length > 0 && context.interactive) {
+            const stagedAdds = [];
+            for (const [pack, reconciliation] of reconciliationByPack) {
+                for (const scope of reconciliation.adds) {
+                    stagedAdds.push({ pack, scope });
                 }
-                continue;
             }
-            if (currentLocation === 'user' || currentLocation === 'both') {
-                await removePackFromScope(pack, userRoot, dependencies);
-                affectedScopes.add('user');
+            context.logger.info(formatReconcileSummary(stagedAdds, stagedRemovals));
+            const confirmation = await dependencies.selectWithAbort('Apply these changes? Removals will delete the listed scoped installs.', [
+                {
+                    label: 'No, cancel (recommended)',
+                    value: 'no',
+                    description: 'Make no changes',
+                },
+                {
+                    label: 'Yes, apply adds and removals',
+                    value: 'yes',
+                    description: 'Install adds and delete the listed removals',
+                },
+            ], { interactive: context.interactive });
+            if (confirmation !== 'yes') {
+                lastRunInitToolsMetadata = { affectedScopes: [] };
+                if (!context.json) {
+                    context.logger.info('No changes applied.');
+                }
+                process.exitCode = 0;
+                return [];
             }
         }
+        // Removals are deferred until after the add phase below: for a confirmed
+        // move (e.g. user -> project), the replacement install must succeed before
+        // the preserved scope is deleted. If any installer throws, the catch
+        // handler aborts and these removals never run, so the pack is never left
+        // installed in neither scope (review I1; design.md:86/114).
         if (selectedPacks.includes('core')) {
             // Core pack always installs at user scope, regardless of userEligibleScope
             affectedScopes.add('user');
@@ -475,8 +607,12 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('ideas')) {
+            const ideasAdded = addedScopes('ideas');
             for (const targetRoot of packTargets('ideas')) {
-                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const targetScope = targetRoot === userRoot ? 'user' : 'project';
+                if (ideasAdded.has(targetScope)) {
+                    affectedScopes.add(targetScope);
+                }
                 const ideasResult = await dependencies.installIdeas({
                     assetsRoot,
                     targetRoot,
@@ -491,8 +627,12 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('docs')) {
+            const docsAdded = addedScopes('docs');
             for (const targetRoot of packTargets('docs')) {
-                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const targetScope = targetRoot === userRoot ? 'user' : 'project';
+                if (docsAdded.has(targetScope)) {
+                    affectedScopes.add(targetScope);
+                }
                 const docsResult = await dependencies.installDocs({
                     assetsRoot,
                     targetRoot,
@@ -557,8 +697,12 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('utility')) {
+            const utilityAdded = addedScopes('utility');
             for (const targetRoot of packTargets('utility')) {
-                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const targetScope = targetRoot === userRoot ? 'user' : 'project';
+                if (utilityAdded.has(targetScope)) {
+                    affectedScopes.add(targetScope);
+                }
                 const utilityResult = await dependencies.installUtility({
                     assetsRoot,
                     targetRoot,
@@ -589,8 +733,12 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('research')) {
+            const researchAdded = addedScopes('research');
             for (const targetRoot of packTargets('research')) {
-                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const targetScope = targetRoot === userRoot ? 'user' : 'project';
+                if (researchAdded.has(targetScope)) {
+                    affectedScopes.add(targetScope);
+                }
                 const researchResult = await dependencies.installResearch({
                     assetsRoot,
                     targetRoot,
@@ -606,8 +754,12 @@ export async function runInitTools(context, dependencies) {
             }
         }
         if (selectedPacks.includes('brainstorm')) {
+            const brainstormAdded = addedScopes('brainstorm');
             for (const targetRoot of packTargets('brainstorm')) {
-                affectedScopes.add(targetRoot === userRoot ? 'user' : 'project');
+                const targetScope = targetRoot === userRoot ? 'user' : 'project';
+                if (brainstormAdded.has(targetScope)) {
+                    affectedScopes.add(targetScope);
+                }
                 const brainstormResult = await dependencies.installBrainstorm({
                     assetsRoot,
                     targetRoot,
@@ -621,6 +773,12 @@ export async function runInitTools(context, dependencies) {
                 }
             }
         }
+        // Apply confirmed removals only after every add has succeeded, so a failed
+        // replacement install can never leave a pack uninstalled in both scopes.
+        for (const { pack, scope } of stagedRemovals) {
+            await removePackFromScope(pack, scopeRoot(scope), dependencies);
+            affectedScopes.add(scope);
+        }
         if (outdatedSkills.length > 0) {
             reportOutdatedSkills(context, outdatedSkills);
             if (context.interactive) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@open-agent-toolkit/cli",
-  "version": "0.1.27",
+  "version": "0.1.29",
   "private": false,
   "description": "Open Agent Toolkit CLI",
   "homepage": "https://github.com/voxmedia/open-agent-toolkit/tree/main/packages/cli",
@@ -34,7 +34,7 @@
     "ora": "^9.0.0",
     "yaml": "2.8.2",
     "zod": "^3.25.76",
-    "@open-agent-toolkit/control-plane": "0.1.27"
+    "@open-agent-toolkit/control-plane": "0.1.29"
   },
   "devDependencies": {
     "@types/node": "^22.10.0",