From 192d67bef0d24e976ad8e1a67f36ad6a2d996611 Mon Sep 17 00:00:00 2001
From: Rayan Salhab <r.salhab@aiyexpertsolutions.com>
Date: Sun, 3 May 2026 01:02:35 +0300
Subject: [PATCH] fix(clean): ignore lockfile setting unless flag is passed
 (#11431)

Keep pnpm clean from removing pnpm-lock.yaml just because the workspace config sets lockfile: true. The lockfile cleanup now follows the command-line --lockfile option.

Co-authored-by: cyphercodes <cyphercodes@users.noreply.github.com>
---
 .changeset/clean-lockfile-cli-option.md |  5 +++++
 pnpm/src/cmd/clean.ts                   |  7 +++++--
 pnpm/test/clean.ts                      | 14 ++++++++++++++
 3 files changed, 24 insertions(+), 2 deletions(-)
 create mode 100644 .changeset/clean-lockfile-cli-option.md

diff --git a/.changeset/clean-lockfile-cli-option.md b/.changeset/clean-lockfile-cli-option.md
new file mode 100644
index 0000000000..1fe4977798
--- /dev/null
+++ b/.changeset/clean-lockfile-cli-option.md
@@ -0,0 +1,5 @@
+---
+"pnpm": patch
+---
+
+Do not remove `pnpm-lock.yaml` during `pnpm clean` when `lockfile: true` is configured in `pnpm-workspace.yaml`. The lockfile is only removed when the `--lockfile` option is passed to `pnpm clean`.
diff --git a/pnpm/src/cmd/clean.ts b/pnpm/src/cmd/clean.ts
index 48db8c1113..4c7204552b 100644
--- a/pnpm/src/cmd/clean.ts
+++ b/pnpm/src/cmd/clean.ts
@@ -13,7 +13,7 @@ export const commandNames = ['clean', 'purge']
 
 export const overridableByScript = true
 
-export const rcOptionsTypes = cliOptionsTypes
+export const rcOptionsTypes = (): Record<string, unknown> => ({})
 
 export function cliOptionsTypes (): Record<string, unknown> {
   return {
@@ -58,11 +58,14 @@ export async function handler (
     virtualStoreDir?: string
     workspaceDir?: string
     workspacePackagePatterns?: string[]
+    cliOptions?: {
+      lockfile?: boolean
+    }
   }
 ): Promise<void> {
   const modulesDir = opts.modulesDir ?? 'node_modules'
   const rootDir = opts.workspaceDir ?? opts.dir
-  const cleanOpts = { modulesDir, removeLockfile: opts.lockfile }
+  const cleanOpts = { modulesDir, removeLockfile: opts.cliOptions?.lockfile === true }
   const dirs = await getProjectDirs(opts)
   await Promise.all(dirs.map(cleanProjectDir.bind(null, cleanOpts)))
   if (opts.virtualStoreDir) {
diff --git a/pnpm/test/clean.ts b/pnpm/test/clean.ts
index 572097b7d1..ab8e74510b 100644
--- a/pnpm/test/clean.ts
+++ b/pnpm/test/clean.ts
@@ -70,6 +70,20 @@ test('pnpm clean preserves lockfile by default', () => {
   expect(fs.existsSync('pnpm-lock.yaml')).toBe(true)
 })
 
+test('pnpm clean preserves lockfile when pnpm-workspace.yaml sets lockfile', () => {
+  tempDir()
+  fs.writeFileSync('package.json', '{}', 'utf8')
+  writeYamlFileSync('pnpm-workspace.yaml', { lockfile: true })
+  fs.writeFileSync('pnpm-lock.yaml', 'lockfileVersion: 9')
+  fs.mkdirSync('node_modules/.pnpm', { recursive: true })
+
+  const result = execPnpmSync(['clean'])
+  expect(result.status).toBe(0)
+
+  expect(fs.existsSync('node_modules/.pnpm')).toBe(false)
+  expect(fs.existsSync('pnpm-lock.yaml')).toBe(true)
+})
+
 test('pnpm clean --lockfile removes lockfile', () => {
   tempDir()
   fs.writeFileSync('package.json', '{}', 'utf8')