fix(linker): point bin shim NODE_PATH at the hidden modules dir

[jdx]

Summary

Two stacked bugs caused astro check (and any tool that loads a transitive via require('typescript') from a shimmed bin) to fail on an aube install while it worked on pnpm:

1. preferSymlinkedExecutables defaulted to symlink under the isolated linker. A symlink can't export env vars, silently making extendNodePath=true a no-op on every default install. pnpm's actual default flips based on the linker (symlink for node-linker=hoisted, shim for isolated); aube now mirrors that.
2. The shim's NODE_PATH only covered the project's top-level node_modules/. Auto-installed peers hoisted to .aube/node_modules/ were invisible to Node's resolver when launched from a shim. The shim now emits a two-entry NODE_PATH covering both directories, matching the load-bearing entries of pnpm's own shim.

Repro

Astro project with @astrojs/check as a direct devDep and typescript only auto-installed as the package's peer:

$ aube install
$ ./node_modules/.bin/astro check
To continue, Astro requires the following dependency to be installed: typescript.
  pnpm add typescript

typescript@5.9.3 was on disk at node_modules/.aube/typescript@5.9.3/node_modules/typescript, but the shim's NODE_PATH pointed at the root node_modules/ which doesn't contain transitives.

After the fix:

$ ./node_modules/.bin/astro check
[content] Synced content
[types] Generated 57ms
[check] Getting diagnostics for Astro files in /tmp/cmp-aube-with-pnpm-lock...
Result (0 files): - 0 errors - 0 warnings - 0 hints

The same shim now reads:

export NODE_PATH="$basedir/..:$basedir/../.aube/node_modules"

Test plan

• cargo test -p aube-linker --lib — 77 pass (new create_bin_shim_appends_hidden_modules_to_node_path covers the two-entry NODE_PATH)
• cargo test -p aube --bin aube — 463 pass
• cargo test --workspace --lib — all green
• cargo clippy --workspace --all-targets -- -D warnings — clean
• cargo fmt --all -- --check — clean
• End-to-end on /tmp/cmp-aube-with-pnpm-lock (Astro + Vite + @astrojs/check with existing pnpm-lock.yaml): aube install + astro check succeeds, matching pnpm behavior

🤖 Generated with Claude Code

---

Note

Medium Risk
Changes default POSIX .bin entry type (symlink → shim) under the isolated linker and alters NODE_PATH construction across platforms, which may affect how executables resolve dependencies and how tools observe .bin files.

Overview
Fixes isolated installs where shimmed CLIs couldn’t resolve transitives/auto-installed peers by expanding shim NODE_PATH to include both the top-level node_modules and the hidden virtual-store modules dir (.aube/node_modules).

On POSIX, preferSymlinkedExecutables now defaults to shims under the isolated linker (to make extendNodePath effective) while keeping the symlink default under nodeLinker=hoisted; global installs explicitly pass no hidden-modules path. Windows shims are updated to build multi-entry NODE_PATH correctly (always using ; as the delimiter), and tests/docs are updated to reflect the new defaults and NODE_PATH contents.

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[greptile-apps]

Greptile Summary

Fixes two compounding bugs that caused shimmed bins (e.g. astro check) to fail under the isolated linker because auto-installed peers were invisible to Node's resolver. The fix adds a hidden_modules_dir field to BinShimOptions and introduces shim_node_path to build a complete two-entry NODE_PATH string that covers both the top-level node_modules/ and the virtual store's hidden node_modules/.

• shim_node_path refactor: shim generators now receive the fully-assembled NODE_PATH value (with $basedir/ / %~dp0 prefixes already embedded) rather than a bare relative path, which is the only way to express a multi-entry list without repeating prefix logic in each generator.
• Default preferSymlinkedExecutables flip: isolated-linker installs now default to shim (not symlink) so extendNodePath is effective; hoisted installs keep the symlink default. Both install and rebuild guard hidden_modules_dir with isolated.then_some(...), so hoisted users don't get a spurious .aube/node_modules entry.
• Tests and docs: bats integration tests are updated to match the new shim-first default; new unit tests cover the two-entry POSIX and Windows NODE_PATH shapes.

Confidence Score: 5/5

Safe to merge — shim and default changes are well-guarded and tested end-to-end.

The isolated.then_some(...) guard in both install/mod.rs and rebuild.rs correctly limits the hidden-modules NODE_PATH entry to isolated layouts, so hoisted users see no change in their shim output. The shim_node_path refactor consolidates prefix construction into one place, reducing per-platform divergence. New unit tests cover the two-entry POSIX and Windows (cmd/ps1/sh) shapes explicitly, and the bats integration tests are updated to match the new shim-first default.

No files require special attention.

Important Files Changed

Filename	Overview
crates/aube-linker/src/sys.rs	Core shim generation refactored: BinShimOptions gains hidden_modules_dir, shim_node_path builds the complete NODE_PATH value with correct platform separators, and generator functions updated to accept the pre-built value. New unit tests cover POSIX and Windows two-entry paths.
crates/aube/src/commands/install/mod.rs	Adds isolated flag to gate hidden_modules_dir and the new preferSymlinkedExecutables default; correctly passes None for hoisted layouts so no spurious shim entry is emitted.
crates/aube/src/commands/rebuild.rs	Mirrors the same isolated/prefer_symlinked_executables logic from install/mod.rs; hidden_modules_dir is correctly gated with isolated.then_some(...).
crates/aube/src/commands/add.rs	Global install correctly passes hidden_modules_dir: None since the global layout is hoisted-shaped and needs no second NODE_PATH entry.
test/optimistic_and_bin_settings.bats	Integration tests updated to reflect the new shim-first default: the old symlink assertion becomes a shim assertion, and the two-entry NODE_PATH grep pattern is updated accordingly.
test/workspace.bats	Symlink-specific test -L / readlink -f checks replaced with shim-agnostic test -f + test -x + shim-marker grep, correctly handling both symlink and shim layouts.

_{Reviews (2): Last reviewed commit: "fix(linker): use `;` on Windows + skip h..." | Re-trigger Greptile}

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[jdx]

Pushed 9362ecd addressing the review feedback and the bats-serial CI failures:

Greptile (both files): gated hidden_modules_dir on node_linker != Hoisted in install/mod.rs and rebuild.rs. Under the hoisted layout that path doesn't exist, so it would have shown up as a non-existent NODE_PATH entry on Windows. add.rs already had this guard for its hoisted-shaped global installs.

Cursor Bugbot (Windows separator): real bug — NODE_PATH is parsed by Node.js, which always splits on ; on Windows regardless of the launching shell. The prior helper used : for the ps1 / Git-Bash .sh shims because their paths use /, but I'd conflated path separator with list separator. All three Windows shim variants now join with ; — Node sees both entries correctly. Added create_bin_shim_appends_hidden_modules_on_windows_uses_semicolon to lock the cmd/ps1/sh assertions.

bats: updated optimistic_and_bin_settings.bats for the new default (shim under isolated, with a two-entry NODE_PATH) and reworked workspace.bats's workspace-bin test so it accepts both shim and symlink outputs by reading the v1 marker comment when the entry isn't a symlink.

Verified: mise run ci:bats:serial passes locally end-to-end (92/92 plus the new ones), cargo test --workspace --lib is green, clippy/fmt clean, and the end-to-end Astro+Vite repro still resolves typescript from the shim.

This comment was generated by Claude.