#388 Filter stale entries from manifest on partial uninstall

packages/agents/src/commands/__tests__/uninstall.test.ts

@@ -1,13 +1,13 @@
+import assert from 'node:assert';
 import { existsSync } from 'node:fs';
 import { mkdir, readFile, rm, writeFile } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import path from 'node:path';
 
 import { afterEach, beforeEach, describe, expect, it } from 'vitest';
 
-import { readManifest } from '../../lib/manifest.js';
-import { getManifestPath } from '../../lib/manifest.js';
-import type { InstallOptions } from '../../lib/types.js';
+import { computeContentHash, getManifestPath, readManifest, writeManifest } from '../../lib/manifest.js';
+import type { AgentsManifest, InstallOptions } from '../../lib/types.js';
 import { installCommand } from '../install.js';
 import { uninstallCommand } from '../uninstall.js';
 
@@ -91,6 +91,76 @@ describe('uninstallCommand', () => {
     expect(manifest.platforms.claude).toBeDefined();
   });
 
+  it('should retain only skipped entries in platform manifest after partial uninstall', async () => {
+    const claudeHome = path.join(tempDir, '.claude');
+    await mkdir(path.join(claudeHome, 'skills'), { recursive: true });
+    await mkdir(path.join(claudeHome, 'agents'), { recursive: true });
+
+    // Install
+    await installCommand(makeInstallOptions(), tempDir);
+
+    // Modify one installed subagent file
+    const agentFile = path.join(claudeHome, 'agents', 'orchestrated-coder.md');
+    const original = await readFile(agentFile, 'utf8');
+    await writeFile(agentFile, original + '\n<!-- user modification -->', 'utf8');
+
+    // Uninstall without force — modified file is skipped, others are removed
+    await uninstallCommand({ platform: 'claude', force: false }, tempDir);
+
+    // Platform manifest should contain only the skipped entry
+    const manifest = await readManifest(getManifestPath(tempDir));
+    const claudeEntries = manifest.platforms.claude?.entries;
+    assert.ok(claudeEntries, 'Expected claude platform entries to be defined');
+    expect(claudeEntries).toHaveLength(1);
+    expect(claudeEntries[0]?.relativePath).toBe('agents/orchestrated-coder.md');
+  });
+
+  it('should retain only skipped entries in shared manifest after partial uninstall', async () => {
+    const sharedHome = path.join(tempDir, '.agents');
+    await mkdir(sharedHome, { recursive: true });
+
+    // Create two shared guidance files on disk
+    const fileA = path.join(sharedHome, 'AGENTS.md');
+    const fileB = path.join(sharedHome, 'EXTRA.md');
+    await writeFile(fileA, 'original content A', 'utf8');
+    await writeFile(fileB, 'original content B', 'utf8');
+
+    // Write a synthetic manifest with two shared entries
+    const hashA = await computeContentHash(fileA);
+    const hashB = await computeContentHash(fileB);
+    const manifest: AgentsManifest = {
+      schemaVersion: 1,
+      shared: {
+        version: '0.0.0',
+        installedAt: new Date().toISOString(),
+        entries: [
+          { relativePath: 'AGENTS.md', contentHash: hashA, linked: false },
+          { relativePath: 'EXTRA.md', contentHash: hashB, linked: false },
+        ],
+      },
+      platforms: {},
+    };
+    await writeManifest(getManifestPath(tempDir), manifest);
+
+    // Modify one file so it gets skipped
+    await writeFile(fileA, 'modified content A', 'utf8');
+
+    // Uninstall without force — AGENTS.md is skipped, EXTRA.md is removed
+    await uninstallCommand({ platform: 'claude', force: false }, tempDir);
+
+    // Shared manifest should contain only the skipped entry
+    const updated = await readManifest(getManifestPath(tempDir));
+    const sharedEntries = updated.shared?.entries;
+    assert.ok(sharedEntries, 'Expected shared entries to be defined');
+    expect(sharedEntries).toHaveLength(1);
+    expect(sharedEntries[0]?.relativePath).toBe('AGENTS.md');
+
+    // EXTRA.md should be deleted from disk
+    expect(existsSync(fileB)).toBe(false);
+    // AGENTS.md should still exist
+    expect(existsSync(fileA)).toBe(true);
+  });
+
   it('should remove modified files when force is true', async () => {
     const claudeHome = path.join(tempDir, '.claude');
     await mkdir(path.join(claudeHome, 'skills'), { recursive: true });

packages/agents/src/commands/uninstall.ts

@@ -1,7 +1,7 @@
 import { removeItem } from '../lib/installer.js';
 import { detectDrift, getManifestPath, readManifest, resolveSharedHome, writeManifest } from '../lib/manifest.js';
 import { resolvePlatformIds, resolvePlatformPaths } from '../lib/platform.js';
-import type { AgentsManifest, InstallOptions, SharedManifest } from '../lib/types.js';
+import type { AgentsManifest, InstallOptions, ManifestEntry, SharedManifest } from '../lib/types.js';
 
 /**
  * Executes the uninstall command, removing installed skills, subagents, and guidance files.
@@ -36,7 +36,7 @@ export async function uninstallCommand(
     console.info(`\nUninstalling for platform: ${platformId}`);
     const paths = resolvePlatformPaths(platformId, baseDir);
     let removedCount = 0;
-    let skippedCount = 0;
+    const skippedEntries: ManifestEntry[] = [];
 
     for (const entry of platformManifest.entries) {
       const drift = await detectDrift(entry, paths.platformHome);
@@ -49,7 +49,7 @@ export async function uninstallCommand(
 
       if (drift === 'modified' && !options.force) {
         console.warn(`  Skipping modified file: ${entry.relativePath}`);
-        skippedCount++;
+        skippedEntries.push(entry);
         continue;
       }
 
@@ -58,13 +58,18 @@ export async function uninstallCommand(
       removedCount++;
     }
 
-    // Only remove platform from manifest when all entries were successfully removed
-    if (skippedCount === 0) {
+    // Remove platform from manifest or retain only skipped entries
+    if (skippedEntries.length === 0) {
       const { [platformId]: _removed, ...rest } = remainingPlatforms;
       remainingPlatforms = rest;
+    } else {
+      remainingPlatforms = {
+        ...remainingPlatforms,
+        [platformId]: { ...platformManifest, entries: skippedEntries },
+      };
     }
 
-    console.info(`  Removed ${removedCount} items, skipped ${skippedCount} modified items`);
+    console.info(`  Removed ${removedCount} items, skipped ${skippedEntries.length} modified items`);
   }
 
   const updatedManifest: AgentsManifest = {
@@ -94,7 +99,7 @@ async function uninstallSharedGuidance(
   console.info('\nUninstalling shared guidance');
   const sharedHome = resolveSharedHome(baseDir);
   let removedCount = 0;
-  let skippedCount = 0;
+  const skippedEntries: ManifestEntry[] = [];
 
   for (const entry of sharedManifest.entries) {
     const drift = await detectDrift(entry, sharedHome);
@@ -106,7 +111,7 @@ async function uninstallSharedGuidance(
 
     if (drift === 'modified' && !options.force) {
       console.warn(`  Skipping modified file: ~/.agents/${entry.relativePath}`);
-      skippedCount++;
+      skippedEntries.push(entry);
       continue;
     }
 
@@ -115,11 +120,11 @@ async function uninstallSharedGuidance(
     removedCount++;
   }
 
-  console.info(`  Removed ${removedCount} items, skipped ${skippedCount} modified items`);
+  console.info(`  Removed ${removedCount} items, skipped ${skippedEntries.length} modified items`);
 
-  // Retain shared manifest only if some entries were skipped
-  if (skippedCount > 0) {
-    return sharedManifest;
+  // Retain shared manifest only with the entries that were skipped
+  if (skippedEntries.length > 0) {
+    return { ...sharedManifest, entries: skippedEntries };
   }
   return undefined;
 }