diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml
index e8737eb..0046067 100644
--- a/.github/workflows/preview.yml
+++ b/.github/workflows/preview.yml
@@ -32,7 +32,6 @@ jobs:
       - uses: dorny/paths-filter@d1c1ffe0248fe513906c8e24db8ea791d46f8590 # v3.0.3
         id: changes
         with:
-          predicate-quantifier: 'every'
           filters: |
             changed:
               - "packages/**"
diff --git a/packages/pnpm-plugin-skills/README.md b/packages/pnpm-plugin-skills/README.md
index 3a30e25..54e9626 100644
--- a/packages/pnpm-plugin-skills/README.md
+++ b/packages/pnpm-plugin-skills/README.md
@@ -26,12 +26,17 @@ Then create a `skills.json` in your project root:
 {
   "installDir": ".agents/skills",
   "linkTargets": [".claude/skills"],
+  "pnpmPlugin": {
+    "removePnpmfileChecksum": true
+  },
   "skills": {
     "my-skill": "https://github.com/owner/repo.git#path:/skills/my-skill"
   }
 }
 ```
 
+`pnpmPlugin.removePnpmfileChecksum` is a temporary compatibility switch for repositories that need `pnpm-plugin-skills` to remove `pnpmfileChecksum` from `pnpm-lock.yaml` in `afterAllResolved`.
+
 Now `pnpm install` will automatically install your skills.
 
 ## Architecture
diff --git a/packages/pnpm-plugin-skills/pnpmfile.cjs b/packages/pnpm-plugin-skills/pnpmfile.cjs
index 1e90c88..2c74ba3 100644
--- a/packages/pnpm-plugin-skills/pnpmfile.cjs
+++ b/packages/pnpm-plugin-skills/pnpmfile.cjs
@@ -1,8 +1,9 @@
 // pnpm v10
-const { preResolution } = require('./dist/index.js')
+const { afterAllResolved, preResolution } = require('./dist/index.js')
 
 module.exports = {
   hooks: {
+    afterAllResolved,
     preResolution,
   },
 }
diff --git a/packages/pnpm-plugin-skills/pnpmfile.mjs b/packages/pnpm-plugin-skills/pnpmfile.mjs
index a61d3f6..7c67bac 100644
--- a/packages/pnpm-plugin-skills/pnpmfile.mjs
+++ b/packages/pnpm-plugin-skills/pnpmfile.mjs
@@ -1,4 +1,4 @@
 // pnpm v11
-import { preResolution } from './dist/index.mjs'
+import { afterAllResolved, preResolution } from './dist/index.mjs'
 
-export const hooks = { preResolution }
+export const hooks = { afterAllResolved, preResolution }
diff --git a/packages/pnpm-plugin-skills/src/index.ts b/packages/pnpm-plugin-skills/src/index.ts
index 5ac06b9..5de5316 100644
--- a/packages/pnpm-plugin-skills/src/index.ts
+++ b/packages/pnpm-plugin-skills/src/index.ts
@@ -1,4 +1,19 @@
-import { installCommand } from 'skills-package-manager'
+import { readFileSync } from 'node:fs'
+import path from 'node:path'
+import { installCommand, type SkillsManifest } from 'skills-package-manager'
+
+function readPluginManifest(rootDir: string): SkillsManifest | null {
+  const filePath = path.join(rootDir, 'skills.json')
+
+  try {
+    const parsed = JSON.parse(readFileSync(filePath, 'utf8')) as {
+      pnpmPlugin?: SkillsManifest['pnpmPlugin']
+    }
+    return parsed as SkillsManifest
+  } catch {
+    return null
+  }
+}
 
 export async function preResolution(
   options: { lockfileDir?: string; workspaceRoot?: string } = {},
@@ -11,3 +26,28 @@ export async function preResolution(
   await installCommand({ cwd: lockfileDir })
   return undefined
 }
+
+export function afterAllResolved(
+  lockfile: Record<string, unknown>,
+  context: { lockfileDir?: string; workspaceDir?: string } = {},
+) {
+  const manifestRoot = context.lockfileDir ?? context.workspaceDir
+  if (!manifestRoot) {
+    return lockfile
+  }
+
+  const manifest = readPluginManifest(manifestRoot)
+  if (!manifest) {
+    return lockfile
+  }
+
+  if (manifest.pnpmPlugin?.removePnpmfileChecksum !== true) {
+    return lockfile
+  }
+
+  if ('pnpmfileChecksum' in lockfile) {
+    delete lockfile.pnpmfileChecksum
+  }
+
+  return lockfile
+}
diff --git a/packages/pnpm-plugin-skills/test/index.test.ts b/packages/pnpm-plugin-skills/test/index.test.ts
index ebc822b..f59076b 100644
--- a/packages/pnpm-plugin-skills/test/index.test.ts
+++ b/packages/pnpm-plugin-skills/test/index.test.ts
@@ -65,3 +65,50 @@ describe('preResolution', () => {
     expect(existsSync(path.join(root, '.claude/skills/hello-skill'))).toBe(true)
   })
 })
+
+describe('afterAllResolved', () => {
+  it('removes pnpmfileChecksum when enabled in skills.json', async () => {
+    const { afterAllResolved } = await import('../src/index')
+    const root = mkdtempSync(path.join(tmpdir(), 'pnpm-plugin-skills-config-'))
+
+    writeFileSync(
+      path.join(root, 'skills.json'),
+      JSON.stringify(
+        {
+          installDir: '.agents/skills',
+          linkTargets: [],
+          pnpmPlugin: {
+            removePnpmfileChecksum: true,
+          },
+          skills: {},
+        },
+        null,
+        2,
+      ),
+    )
+
+    const lockfile = {
+      lockfileVersion: '9.0',
+      pnpmfileChecksum: 'checksum-to-remove',
+    }
+
+    const result = afterAllResolved(lockfile, { lockfileDir: root })
+
+    expect(result).toBe(lockfile)
+    expect(result).not.toHaveProperty('pnpmfileChecksum')
+  })
+
+  it('keeps pnpmfileChecksum by default', async () => {
+    const { afterAllResolved } = await import('../src/index')
+
+    const lockfile = {
+      lockfileVersion: '9.0',
+      pnpmfileChecksum: 'checksum-to-keep',
+    }
+
+    const result = afterAllResolved(lockfile, {})
+
+    expect(result).toBe(lockfile)
+    expect(result).toHaveProperty('pnpmfileChecksum', 'checksum-to-keep')
+  })
+})
diff --git a/packages/skills-package-manager/src/config/schema.ts b/packages/skills-package-manager/src/config/schema.ts
index 76fbfca..c60a27f 100644
--- a/packages/skills-package-manager/src/config/schema.ts
+++ b/packages/skills-package-manager/src/config/schema.ts
@@ -16,6 +16,17 @@ export const skillsManifestSchema = z
       .default([])
       .describe('Directories where skill symlinks will be created'),
     selfSkill: z.boolean().optional().describe('Whether this project is itself a skill'),
+    pnpmPlugin: z
+      .object({
+        removePnpmfileChecksum: z
+          .boolean()
+          .optional()
+          .describe(
+            'Temporarily remove pnpmfileChecksum from pnpm lockfiles in pnpm-plugin-skills afterAllResolved',
+          ),
+      })
+      .optional()
+      .describe('pnpm-plugin-skills specific compatibility settings'),
     skills: z
       .record(z.string(), z.string())
       .default({})
diff --git a/packages/skills-package-manager/src/config/skillsManifest.ts b/packages/skills-package-manager/src/config/skillsManifest.ts
index 09616ac..3b1494f 100644
--- a/packages/skills-package-manager/src/config/skillsManifest.ts
+++ b/packages/skills-package-manager/src/config/skillsManifest.ts
@@ -49,6 +49,7 @@ export function normalizeSkillsManifest(manifest: Partial<SkillsManifest>): Skil
     installDir: manifest.installDir ?? '.agents/skills',
     linkTargets: manifest.linkTargets ?? [],
     selfSkill: manifest.selfSkill ?? false,
+    pnpmPlugin: manifest.pnpmPlugin,
     skills: manifest.skills ?? {},
   }
 }
diff --git a/packages/skills-package-manager/src/config/writeSkillsManifest.ts b/packages/skills-package-manager/src/config/writeSkillsManifest.ts
index 04934bd..d5ed14f 100644
--- a/packages/skills-package-manager/src/config/writeSkillsManifest.ts
+++ b/packages/skills-package-manager/src/config/writeSkillsManifest.ts
@@ -24,6 +24,10 @@ export async function writeSkillsManifest(
     nextManifest.selfSkill = manifest.selfSkill
   }
 
+  if (manifest.pnpmPlugin !== undefined) {
+    nextManifest.pnpmPlugin = manifest.pnpmPlugin
+  }
+
   try {
     await writeFile(filePath, `${JSON.stringify(nextManifest, null, 2)}\n`, 'utf8')
   } catch (error) {
diff --git a/packages/skills-package-manager/test/manifest.test.ts b/packages/skills-package-manager/test/manifest.test.ts
index d6266d7..633ce39 100644
--- a/packages/skills-package-manager/test/manifest.test.ts
+++ b/packages/skills-package-manager/test/manifest.test.ts
@@ -18,10 +18,36 @@ describe('manifest io', () => {
       $schema: DEFAULT_SCHEMA_URL,
       installDir: '.agents/skills',
       linkTargets: [],
+      pnpmPlugin: undefined,
       skills: { hello: 'link:./skills/hello' },
     })
   })
 
+  it('reads pnpmPlugin config from skills.json', async () => {
+    const root = mkdtempSync(path.join(tmpdir(), 'skills-pm-manifest-pnpm-plugin-'))
+    writeFileSync(
+      path.join(root, 'skills.json'),
+      JSON.stringify(
+        {
+          installDir: '.agents/skills',
+          linkTargets: [],
+          pnpmPlugin: {
+            removePnpmfileChecksum: true,
+          },
+          skills: {},
+        },
+        null,
+        2,
+      ),
+    )
+
+    const manifest = await readSkillsManifest(root)
+
+    expect(manifest?.pnpmPlugin).toEqual({
+      removePnpmfileChecksum: true,
+    })
+  })
+
   it('defaults selfSkill to undefined when omitted from skills.json', async () => {
     const root = mkdtempSync(path.join(tmpdir(), 'skills-pm-manifest-default-self-'))
     writeFileSync(
@@ -104,6 +130,9 @@ describe('manifest validation', () => {
       installDir: '.custom/skills',
       linkTargets: ['.claude/skills'],
       selfSkill: true,
+      pnpmPlugin: {
+        removePnpmfileChecksum: true,
+      },
       skills: { test: 'link:./test' },
     }
 
@@ -123,6 +152,7 @@ describe('manifest validation', () => {
       expect(result.data.installDir).toBe('.agents/skills')
       expect(result.data.linkTargets).toEqual([])
       expect(result.data.selfSkill).toBeUndefined()
+      expect(result.data.pnpmPlugin).toBeUndefined()
       expect(result.data.skills).toEqual({})
     }
   })
diff --git a/website/docs/architecture/pnpm-plugin.mdx b/website/docs/architecture/pnpm-plugin.mdx
index cae9d46..ceea722 100644
--- a/website/docs/architecture/pnpm-plugin.mdx
+++ b/website/docs/architecture/pnpm-plugin.mdx
@@ -24,12 +24,17 @@ Then add the following to the workspace root:
 {
   "installDir": ".agents/skills",
   "linkTargets": [".claude/skills"],
+  "pnpmPlugin": {
+    "removePnpmfileChecksum": true
+  },
   "skills": {
     "my-skill": "https://github.com/owner/repo.git#path:/skills/my-skill"
   }
 }
 ```
 
+`pnpmPlugin.removePnpmfileChecksum` is a temporary compatibility option for `pnpm-plugin-skills`. When enabled, the plugin removes `pnpmfileChecksum` from `pnpm-lock.yaml` in `afterAllResolved` to work around tools that run `pnpm install --ignore-pnpmfile`.
+
 ## Suitable team scenarios
 
 - You want developers to run only `pnpm install` without remembering extra skill installation commands