refactor(cli): drop the MCP exclusion no command could reach

cli/.claude/skills/framework/SKILL.md

@@ -24,7 +24,7 @@ disk is exactly the job that needs all three.
 
 | Concept | Location |
 |---|---|
-| The manifest aggregate and its members | `domain/manifest.ts`, `domain/manifest/` (tool-entry, tracked-files, merge-files, mcp-exclusions, native-registrations) |
+| The manifest aggregate and its members | `domain/manifest.ts`, `domain/manifest/` (tool-entry, tracked-files, merge-files, native-registrations) |
 | A plugin's declared state | `domain/plugins/` (installed-plugin, source-resolver, requested-version-policy) |
 | The diagnosis shape | `domain/doctor.ts` |
 | Setup orchestration state | `domain/setup-flow.ts` |

cli/src/contexts/framework/application/uninstall/uninstall-use-case.ts

@@ -10,14 +10,12 @@ import type { ToolId } from "../../../../kernel/tool.js";
 import { VALID_TOOL_IDS } from "../../../../kernel/tool.js";
 import type { Manifest } from "../../domain/manifest.js";
 import type { ManifestRepository } from "../../domain/ports/manifest-repository.js";
-import { UninstallMcpExclusionUseCase } from "./uninstall-mcp-exclusion-use-case.js";
 import { UninstallPluginUseCase } from "./uninstall-plugin-use-case.js";
 import { UninstallToolsUseCase } from "./uninstall-tools-use-case.js";
 
 interface UninstallOptions {
   toolIds: ToolId[];
   projectRoot: string;
-  mcpFilter: string[];
   pluginName?: string;
 }
 
@@ -30,7 +28,6 @@ interface UninstallToolResult {
 export class UninstallUseCase {
   private readonly pluginUninstall: UninstallPluginUseCase;
   private readonly toolsUninstall: UninstallToolsUseCase;
-  private readonly mcpExclusion: UninstallMcpExclusionUseCase;
 
   constructor(
     fs: FileReader & FileWriter,
@@ -39,11 +36,10 @@ export class UninstallUseCase {
   ) {
     this.pluginUninstall = new UninstallPluginUseCase(fs, manifestRepo);
     this.toolsUninstall = new UninstallToolsUseCase(fs, logger);
-    this.mcpExclusion = new UninstallMcpExclusionUseCase(fs, logger);
   }
 
   async execute(options: UninstallOptions): Promise<UninstallToolResult[]> {
-    const { toolIds, projectRoot, mcpFilter, pluginName } = options;
+    const { toolIds, projectRoot, pluginName } = options;
 
     if (pluginName !== undefined) {
       return this.pluginUninstall.execute({ pluginName, toolIds, projectRoot });
@@ -57,10 +53,7 @@ export class UninstallUseCase {
 
     const manifest = await this.loadAndValidate(toolIds);
 
-    const results =
-      mcpFilter.length > 0
-        ? await this.runMcpExclusions(toolIds, manifest, projectRoot, mcpFilter)
-        : await this.toolsUninstall.execute({ toolIds, manifest, projectRoot });
+    const results = await this.toolsUninstall.execute({ toolIds, manifest, projectRoot });
 
     await this.manifestRepo.save(manifest);
     return results;
@@ -74,17 +67,4 @@ export class UninstallUseCase {
     }
     return manifest;
   }
-
-  private async runMcpExclusions(
-    toolIds: ToolId[],
-    manifest: Manifest,
-    projectRoot: string,
-    mcpFilter: string[]
-  ): Promise<UninstallToolResult[]> {
-    const results: UninstallToolResult[] = [];
-    for (const toolId of toolIds) {
-      results.push(await this.mcpExclusion.execute({ toolId, manifest, projectRoot, mcpFilter }));
-    }
-    return results;
-  }
 }

cli/src/contexts/framework/domain/manifest.ts

@@ -3,8 +3,6 @@ import type { FileHash, InstallationFile } from "../../../kernel/file.js";
 import type { MergeFileEntry } from "../../../kernel/merge.js";
 import { AIDD_DIR, MANIFEST_FILENAME } from "../../../kernel/paths.js";
 import type { ToolId } from "../../../kernel/tool.js";
-import type { McpExclusion } from "../../tools/domain/mcp-exclusion.js";
-import { addExclusions, removeExclusions } from "./manifest/mcp-exclusions.js";
 import type { NativeRegistrations } from "./manifest/native-registrations.js";
 import {
   addPluginToEntry,
@@ -59,8 +57,7 @@ export class Manifest {
     toolId: ToolId,
     version: string,
     files: InstallationFile[],
-    mergeFiles: MergeFileEntry[] = [],
-    excludedMcp: McpExclusion[] = []
+    mergeFiles: MergeFileEntry[] = []
   ): void {
     const existing = this._tools.get(toolId);
     this._tools.set(
@@ -70,7 +67,6 @@ export class Manifest {
         version,
         files,
         mergeFiles,
-        excludedMcp,
         existingPlugins: existing?.plugins ?? [],
       })
     );
@@ -109,34 +105,6 @@ export class Manifest {
     return tracked;
   }
 
-  getExcludedMcp(toolId: ToolId): readonly McpExclusion[] {
-    return this._tools.get(toolId)?.excludedMcp ?? [];
-  }
-
-  addExcludedMcp(toolId: ToolId, exclusions: McpExclusion[]): void {
-    const entry = this._tools.get(toolId);
-    if (!entry) throw new ToolNotInManifestError(toolId);
-    this._tools.set(toolId, {
-      ...entry,
-      excludedMcp: addExclusions(entry.excludedMcp, exclusions),
-    });
-  }
-
-  removeExcludedMcp(toolId: ToolId, exclusions: McpExclusion[]): void {
-    const entry = this._tools.get(toolId);
-    if (!entry) throw new ToolNotInManifestError(toolId);
-    this._tools.set(toolId, {
-      ...entry,
-      excludedMcp: removeExclusions(entry.excludedMcp, exclusions),
-    });
-  }
-
-  clearExcludedMcp(toolId: ToolId): void {
-    const entry = this._tools.get(toolId);
-    if (!entry) throw new ToolNotInManifestError(toolId);
-    this._tools.set(toolId, { ...entry, excludedMcp: [] });
-  }
-
   updateTrackedFileHash(toolId: ToolId, relativePath: string, hash: FileHash): void {
     const entry = this._tools.get(toolId);
     if (!entry) return;
@@ -146,18 +114,10 @@ export class Manifest {
     });
   }
 
-  updateToolMergeFiles(
-    toolId: ToolId,
-    mergeFiles: MergeFileEntry[],
-    excludedMcp?: McpExclusion[]
-  ): void {
+  updateToolMergeFiles(toolId: ToolId, mergeFiles: MergeFileEntry[]): void {
     const entry = this._tools.get(toolId);
     if (!entry) throw new ToolNotInManifestError(toolId);
-    this._tools.set(toolId, {
-      ...entry,
-      mergeFiles,
-      ...(excludedMcp !== undefined && { excludedMcp }),
-    });
+    this._tools.set(toolId, { ...entry, mergeFiles });
   }
 
   removeTool(toolId: ToolId): void {

cli/src/contexts/framework/domain/manifest/tool-entry.ts

@@ -2,13 +2,7 @@ import { DuplicatePluginError, PluginNotFoundError } from "../../../../kernel/er
 import type { InstallationFile } from "../../../../kernel/file.js";
 import type { MergeFileEntry } from "../../../../kernel/merge.js";
 import type { ToolId } from "../../../../kernel/tool.js";
-import type { McpExclusion } from "../../../tools/domain/mcp-exclusion.js";
 import { InstalledPlugin, type PluginEntryData } from "../plugins/installed-plugin.js";
-import {
-  type McpExclusionData,
-  parseMcpExclusionData,
-  toMcpExclusionData,
-} from "./mcp-exclusions.js";
 import {
   type MergeFileEntryData,
   parseMergeFileEntries,
@@ -33,7 +27,6 @@ export interface ToolEntry {
   readonly version: string;
   readonly files: readonly TrackedFile[];
   readonly mergeFiles: readonly MergeFileEntry[];
-  readonly excludedMcp: readonly McpExclusion[];
   readonly plugins: readonly InstalledPlugin[];
   /** What this tool's own CLI was asked to register, or `undefined` for a tool with
    * no `nativeActivation` — see {@link NativeRegistrations}. */
@@ -45,7 +38,6 @@ export interface ToolEntryData {
   version: string;
   files: TrackedFileData[];
   mergeFiles?: MergeFileEntryData[];
-  excludedMcp?: McpExclusionData[];
   plugins?: PluginEntryData[];
   nativeRegistrations?: NativeRegistrationsData;
 }
@@ -55,15 +47,13 @@ export function createToolEntry(params: {
   version: string;
   files: InstallationFile[];
   mergeFiles: readonly MergeFileEntry[];
-  excludedMcp: readonly McpExclusion[];
   existingPlugins: readonly InstalledPlugin[];
 }): ToolEntry {
   return {
     toolId: params.toolId,
     version: params.version,
     files: toTrackedFiles(params.files),
     mergeFiles: params.mergeFiles,
-    excludedMcp: params.excludedMcp,
     plugins: params.existingPlugins,
   };
 }
@@ -104,7 +94,6 @@ export function serializeToolEntry(entry: ToolEntry): ToolEntryData {
     version: entry.version,
     files: toTrackedFileData(entry.files),
     mergeFiles: toMergeFileEntryData(entry.mergeFiles),
-    ...(entry.excludedMcp.length > 0 && { excludedMcp: toMcpExclusionData(entry.excludedMcp) }),
     ...(entry.plugins.length > 0 && { plugins: entry.plugins.map((p) => p.toJSON()) }),
     ...(entry.nativeRegistrations !== undefined && {
       nativeRegistrations: toNativeRegistrationsData(entry.nativeRegistrations),
@@ -118,7 +107,6 @@ export function parseToolEntry(toolId: ToolId, data: ToolEntryData): ToolEntry {
     version: data.version,
     files: parseTrackedFiles(data.files),
     mergeFiles: parseMergeFileEntries(data.mergeFiles ?? []),
-    excludedMcp: parseMcpExclusionData(data.excludedMcp ?? []),
     plugins: (data.plugins ?? []).map((p) => InstalledPlugin.fromJSON(p)),
     nativeRegistrations: parseNativeRegistrations(data.nativeRegistrations),
   };

cli/src/contexts/tools/domain/mcp-exclusion.ts

@@ -28,12 +28,3 @@ function transformMcpForWin32(content: string): string {
 export function transformFor(platform: string): ((content: string) => string) | undefined {
   return platform === "win32" ? transformMcpForWin32 : undefined;
 }
-
-export interface McpExclusion {
-  readonly configPath: string;
-  readonly entryKey: string;
-}
-
-export function mcpExclusionEquals(a: McpExclusion, b: McpExclusion): boolean {
-  return a.configPath === b.configPath && a.entryKey === b.entryKey;
-}

cli/src/presentation/commands/framework.ts

@@ -102,7 +102,6 @@ async function runFrameworkRemove(
     const results = await deps.uninstallUseCase.execute({
       toolIds: [toolId],
       projectRoot,
-      mcpFilter: [],
     });
     const totalFileCount = results.reduce((sum, r) => sum + r.fileCount, 0);
     printToolRemoved(output, results[0].toolId, totalFileCount);

cli/tests/contexts/framework/application/uninstall-plugin.unit.test.ts

@@ -48,7 +48,6 @@ describe("UninstallUseCase — plugin scope", () => {
     await new UninstallUseCase(deps.fs, deps.manifestRepo, deps.logger).execute({
       toolIds: [],
       projectRoot: PROJECT_ROOT,
-      mcpFilter: [],
       pluginName: "sample-plugin",
     });
 
@@ -65,7 +64,6 @@ describe("UninstallUseCase — plugin scope", () => {
       new UninstallUseCase(deps.fs, deps.manifestRepo, deps.logger).execute({
         toolIds: [],
         projectRoot: PROJECT_ROOT,
-        mcpFilter: [],
         pluginName: "nonexistent",
       })
     ).rejects.toThrow(PluginNotFoundError);