verifyDepsBeforeRun reinstalls before every run when dedupePeers is true and a pnpmfile is active (12.15.0 regression) #17322

Last pnpm version that worked

12.14.0

pnpm version

12.15.0

Code to reproduce the issue

package.json:

{
  "name": "repro",
  "private": true,
  "packageManager": "pnpm@12.15.0",
  "scripts": { "hello": "node -e 1" },
  "dependencies": { "is-number": "7.0.0" }
}

pnpm-workspace.yaml:

dedupePeers: true

.pnpmfile.cjs:

module.exports = { hooks: { readPackage: (pkg) => pkg } }

pnpm install
printf '\n' >> pnpm-lock.yaml   # any lockfile change, e.g. a git checkout
pnpm hello
pnpm hello
pnpm hello

Expected behavior

The first pnpm hello runs the verifyDepsBeforeRun install once. Later runs see node_modules as up to date and run the script directly, as on 12.14.0.

Actual behavior

Every pnpm run and pnpm exec installs again and warns:

Already up to date
[WARN] The install that ran before the script left node_modules out of date, so the next run installs again. a lockfile setting drifted from the current configuration

The loop stops only after a plain pnpm install. Each later lockfile change starts it again.

With TRACE=pacquet::install=debug:

DEBUG pacquet::install: repeat-install content check: lockfile settings drift, error: `dedupePeers` in the lockfile (true) doesn't match the current config (false)

Additional information

The loop needs all three: dedupePeers: true, an active pnpmfile (local or from a config dependency), and a lockfile changed since the last validation. Without the pnpmfile, or with dedupePeers: false, it does not happen.

The pre-run gate hardcodes dedupe_peers: false in check_deps_status_before_run (pnpm/crates/package-manager/src/optimistic_repeat_install/deps_status.rs), so the lockfile settings comparison always fails when the workspace sets dedupePeers: true. The gate can never record the tree as proven, and the frozen install it starts finds nothing to do. 12.15.0 routes both gates through the shared check_freshness (#17181), which is likely when this comparison started to apply to the run gate.

Passing config.dedupe_peers there, as the install gate does, should fix it.

Node.js version

v26.5.0

Operating System

Windows