Keep pnpm links intact when running Deno

[dahlia]

Deno 2.9 can replace pnpm's workspace links, leaving pnpm pack unable to resolve workspace: dependencies. Setting nodeModulesDir to "none" in deno.json keeps Deno's npm cache separate from pnpm's installation. Development dependencies are declared explicitly because Deno no longer supplies the links. Fresh loads its Vite config natively so its build continues to work.

An isolated regression test checks that Deno preserves pnpm's links and that pnpm pack still runs prepack and resolves workspace versions. CI also checks that nodeModulesDir remains "none".

Tested packing on Deno 2.7.7/2.9.7, affected package suites on Deno/Node.js/Bun, Fresh/docs builds, and Workers tests. The full Deno suite still reports a docloader timer leak; the parallel Node.js run stalled, though the isolated vocabulary suite passed.

Fixes #1259.

[coderabbitai]

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ℹ️ Recent review info

⚙️ Run configuration

• Configuration used: Repository UI
• Review profile: ASSERTIVE
• Plan: Advanced
• Run ID: da8e2f88-2816-4643-9e66-91812f796daf

📥 Commits

Reviewing files that changed from the base of the PR and between a2414f9 and 664b54a.

⛔ Files ignored due to path filters (1)

• pnpm-lock.yaml is excluded by !**/pnpm-lock.yaml

📒 Files selected for processing (8)

• deno.json
• docs/package.json
• examples/fresh/deno.json
• mise.toml
• packages/fastify/package.json
• packages/sqlite/package.json
• packages/testing/package.json
• scripts/test_pack.mjs

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📝 Walkthrough

Walkthrough

The change sets Deno’s nodeModulesDir to none and checks that setting. It updates workspace development dependencies and the Fresh example’s Vite tasks. A new integration test checks installed links and packed package metadata.

Changes

Workspace tooling

Layer / File(s)	Summary
Set and check the Deno node_modules mode deno.json, mise.toml	The root Deno configuration sets nodeModulesDir to none. The check task now fails if the setting differs.
Update workspace tooling declarations and commands docs/package.json, packages/fastify/package.json, packages/sqlite/package.json, packages/testing/package.json, examples/fresh/deno.json	The package manifests add development dependencies. The Fresh example’s dev and build tasks run Vite through Deno with --configLoader native.
Test packing after Deno checks mise.toml, scripts/test_pack.mjs	The new test:pack task runs an integration test. The test installs a temporary workspace, checks installed links before and after Deno, packs an adapter, and verifies the prepack side effect and packed peer dependency.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Bug fix · Severity of issue fixed: Medium

Merge Risk: ⚪ Minimal · up to 664b5

The change sets Deno's nodeModulesDir to none to keep pnpm links intact, adds a regression test for it, and declares the workspace dev dependencies. No concrete merge-blocking risk was found.

🚥 Pre-merge checks | ✅ 3 | ❌ 1 | ❓ 1

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 5 functions across 1 files. (7 skipped: 7 …	Write docstrings for the functions missing them to satisfy the coverage threshold.
Linked Issues check	❓ Inconclusive	Issue #1259 covers affected branches 2.0–2.3. This PR targets 2.0 and changes nodeModulesDir to "none"; its regression test checks pnpm links and packing. The available evidence does not establish…	Provide evidence of the relevant configuration or equivalent protection on branches 2.1–2.3 to determine whether the full issue scope is covered.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly describes the main change: preserving pnpm workspace links when running Deno.
Description check	✅ Passed	The description explains the Deno and pnpm link issue, the changes made, and the regression test and validation work.
Out of Scope Changes check	✅ Passed	The added package development dependencies and Fresh Vite task changes support operation with Deno no longer managing node_modules. The regression test and CI check verify the linked issue’s fix. Th…

Full details: Linked Issues check

Explanation

Issue #1259 covers affected branches 2.0–2.3. This PR targets 2.0 and changes nodeModulesDir to "none"; its regression test checks pnpm links and packing. The available evidence does not establish whether branches 2.1–2.3 also preserve the links.

Full details: Docstring Coverage

Explanation

Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 5 functions across 1 files. (7 skipped: 7 unsupported.)

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.
see 1 file with indirect coverage changes

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