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…the root (#9592) `npm link <path> --workspace=<ws>` did not scope the operation to the target workspace. The linked dependency was attached to the root project instead, and with `--save` (or `--save-dev`/`--save-optional`/etc.) the `file:` spec was written to the root `package.json` rather than `<ws>/package.json`. `npm install <path> --workspace=<ws> --save` behaved correctly, so only `npm link` was affected. The cause is in `Link.linkInstall()` in `lib/commands/link.js`, which built the local Arborist without the `workspaces` option and passed `workspaces` only to `reify()`. Arborist decides which node receives the `add` request from `this.options.workspaces`, which is captured at construction time, not from the reify-time option. `buildIdealTree` merges reify options into a local variable and `#parseSettings` never copies `options.workspaces` into `this.options`, so the reify-time value never reached `#applyUserRequests`. With `this.options.workspaces` left empty, the `add` and the save were applied to the root node. The fix passes `workspaces: this.workspaceNames` to the local Arborist constructor, matching how `lib/commands/install.js` already does it. Physical placement is unchanged: under the default `hoisted` strategy the symlink still hoists to the root `node_modules`, identical to `npm install --workspace`. ## References <!-- List any relevant issues, pull requests, or external references --> Fixes #9590 Related #9589
…irs (#9586) Implements the accepted RFC [npm/rfcs#903](npm/rfcs#903): a root-owned `.npm-extension.mjs` / `.npm-extension.cjs` file exporting `transformManifest(pkg, context)` that imperatively repairs third-party dependency manifests **before** Arborist finalizes the ideal tree. It is the imperative counterpart to [`packageExtensions` (#9496)](#9496) and operates in the same pre-resolution phase, running **before** `packageExtensions`. ```js // .npm-extension.mjs export function transformManifest(pkg, context) { if (pkg.name === "foo" && pkg.version.startsWith("1.")) { pkg.dependencies = { ...pkg.dependencies, bar: "^2.0.0" }; context.log("added bar to foo@1"); } return pkg; } ``` ## Why `packageExtensions` is declarative JSON: it cannot carry comments or issue links, repeats itself across many packages, is add-only, and lives in `package.json` (so public packages cannot publish while it is present). `.npm-extension` covers the gap for advanced projects that need conditional repairs, deletion, range rewrites, repeated rules expressed as code, stale-repair guards, and a policy location outside the published manifest. ## What it does - **Discovery** — one root `.npm-extension.mjs` or `.npm-extension.cjs` (both present is an error). The `extension-file` config overrides discovery with a project-local path that must resolve inside the project root and use `.mjs`/`.cjs`. - **`transformManifest(pkg, context)`** — receives a deeply isolated copy of the normalized manifest; `context` exposes `log`, `root`, and `extensionPoint`. Must return a manifest synchronously; `null`/primitive/array/promise returns and throws fail the install with a `.npm-extension`-named error. - **Allowlist** — only `dependencies`, `optionalDependencies`, `peerDependencies`, and `peerDependenciesMeta` may change (add, replace, or delete). Any other changed field (`scripts`, `bin`, …) is rejected. pacote's cached manifest is never mutated. - **Caching** — runs at most once per resolved package identity (integrity, else resolved source + name@version); the entry file is hash-keyed so a changed file is reloaded rather than served stale from the module cache. - **Lockfile** — the root entry records `npmExtensionHash` (a format-tagged digest of the file bytes); affected entries record minimal `npmExtensionApplied` provenance. Extension state reuses the existing `lockfileVersion: 4` threshold. - **Re-resolution** — changing or removing the file re-resolves the affected packages on the next `npm install`, reverting transforms that no longer apply. - **`npm ci`** — never imports or executes the file; it validates the recorded hash and reifies the locked graph (which already carries the extension-influenced edges). - **Configs** — `ignore-extension` disables import/execution; `ignore-scripts` implies it; `extension-file` is honored only from project config or the command line, never from user/global/builtin sources. - **Workspaces** — a `.npm-extension` file in a non-root workspace is ignored with a warning; only the workspace root's file is honored. - **Visibility** — `npm explain` annotates extension-changed edges and `npm ls` (human + `--json`) surfaces the provenance. - **Publish** — companion change in `npm-packlist` force-excludes root `.npm-extension.{mjs,cjs}` from package tarballs. ## Companion change Requires [npm/npm-packlist#294](npm/npm-packlist#294) to exclude root `.npm-extension.{mjs,cjs}` from tarballs. `pacote`/CLI will pick this up via a version bump once that publishes. ## Notes / out of scope for this PR One item is deferred for a genuine structural reason the RFC itself flags: - **Local `file:`/`link:`/directory sources.** `transformManifest` applies to fetched manifests (registry, git, remote tarball, `file:` tarballs) and is re-derived on the installed tree across all install strategies including `install-strategy=linked`. It is **not yet** applied to local sources that create `Link` nodes directly and bypass the fetch phase — the RFC flags this as net-new wiring ("npm must add an analogous pre-edge-read transform path for the `Link` target"). Follow-up. ## References Implements npm/rfcs#903 Builds on #9496 Companion: npm/npm-packlist#294
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