gjc --worktree shares the origin checkout's node_modules, contaminating worktree module resolution

[Yeachan-Heo]

Problem

ensureReusableNodeModules (packages/coding-agent/src/gjc-runtime/launch-worktree.ts:453) symlinks the entire node_modules from the origin checkout into a freshly created launch worktree:

export function ensureReusableNodeModules(sourceRoot: string, worktreePath: string): "symlink" | "present" | "missing" {
	const target = path.join(worktreePath, "node_modules");
	if (fs.existsSync(target)) return "present";
	const source = path.join(sourceRoot, "node_modules");
	if (!fs.existsSync(source)) return "missing";
	fs.symlinkSync(source, target, "junction");
	return "symlink";
}

Because Bun workspace installs link @gajae-code/* packages back to the origin checkout's packages/*, every workspace import in the worktree resolves to the origin checkout's live sources, not the worktree's own commit. Two concrete failure classes observed while verifying the 0.14.0 release worktree (frozen head c83ffe3d7f):

1. Cannot find module '@gajae-code/ai/utils/json-parse' from '/Users/.../gajae-code/packages/agent/src/proxy.ts' — the main checkout's proxy.ts was pulled into the worktree's test run, and its import graph disagreed with the worktree's dependency state. Any divergence between the two checkouts (different branch, mid-rebase, uncommitted edits) produces arbitrary, hard-to-attribute failures.
2. Worse, mutations flow backwards: running bun install inside the worktree (after deleting a broken package link) rewrote the origin checkout's node_modules workspace links to point into the worktree. Deleting the worktree afterwards would strand the origin checkout with dangling links.

Non-workspace deps also break: the shared node_modules may not satisfy the worktree branch's bun.lock (new/updated deps on the worktree branch are simply missing), and compiled native addon state (packages/natives/native/*.node) is per-checkout, so worktree natives resolve to the origin checkout's build (or its absence).

Impact

• Test/verification results obtained inside a gjc --worktree tree are not trustworthy for the worktree's commit — they exercise a hybrid of two checkouts.
• Worktree-side installs corrupt the origin checkout's node_modules.
• This monorepo itself already documents the symptom class: natives-augment.d.ts notes "Linked sibling checkouts sharing the root node_modules can dedupe @gajae-code/natives declarations by package ID to an older generated file".

Suggested direction

For workspace repos (root package.json with workspaces), do not share node_modules; run a real bun install --frozen-lockfile in the worktree (or at minimum copy the lockfile and install). The symlink reuse is only safe for repos whose node_modules contains no links back into the repo itself. A cheap heuristic: share only when the origin node_modules contains no symlink whose target resolves inside sourceRoot.

Environment

• gjc dev @ c83ffe3d7f (release/0.14.0 freeze), Bun 1.3.14, macOS arm64

[Yeachan-Heo]

Fix implemented and delivered in #4626 (fix/issue-4620-worktree-node-modules, targeting dev).

Reproduction (pre-fix) — both failure classes from this issue confirmed live against a bun workspace install:

1. Cross-checkout resolution: with the origin carrying uncommitted edits (export const marker = "foo-DIRTY-ORIGIN"), a clean worktree at the original commit imported the origin's dirty source — bun -e 'import { value } from "@repro/bar"' inside the shared worktree printed the origin's marker, because node_modules/@repro/foo -> ../../packages/foo resolved through the shared tree into the origin checkout.
2. Reverse mutation: bun install run inside the worktree (after the shared symlink was in place) wrote picomatch/left-pad into the origin's node_modules top level — the worktree's install mutated the origin's tree, exactly the "mutations flow backwards" class.

Fix — ensureReusableNodeModules no longer shares blindly:

• Scans the origin node_modules for symlinks resolving inside the origin repo root (bun/npm hoisted, bun isolated .bun/node_modules, pnpm scoped .pnpm depth-5 layouts; fails closed on unreadable links). Workspace trees are left unshared — the worktree gets no node_modules, never a cross-checkout symlink, so it resolves its own commit after its own install.
• Never shares an origin node_modules that is itself a symlink (vendored inside the repo, or a nested-repo parent-workspace hoist): its entries belong to another checkout's install graph.
• Remediates already-contaminated worktrees: a stale node_modules symlink pointing into the source repo is removed on next launch; worktree-owned real directories are never touched; dangling links no longer crash with EEXIST.

Verification on the PR head: 39-test launch-worktree suite (10 new isolation regressions), adjacent cli-root-flags + sdk-broker-lifecycle-e2e suites, workspace check:ts, bun run build, and a dogfood run of the real built CLI (dist/gjc --worktree against a workspace repo with a live bun install): the worktree was left without node_modules, resolved its own commit's sources after its own install, and the origin's tree stayed untouched. A red-team lane ran 46 adversarial cases (deep nesting, root-link escapes, EACCES targets, loops, prefix collisions, concurrency); every actionable finding is fixed and pinned by tests.

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[Yeachan-Heo]

Linked-PR disposition for #4620 — reconciliation census (2026-08-18, issue-lane owner)

This issue lane does not duplicate the fix: PR #4626 (fix/issue-4620-worktree-node-modules → dev) credibly owns it, and this lane stays evidence/closure owner only until that PR is merged.

Exact PR state (verified via API at post time):

• Head: b6a8d19665a479638301dbfce3777b3d02cc7f6e; PR event base: dev@50b032e9b4a2532a02240354ff28d26afaee22a0; state: open, not merged.
• Review: 7 × CHANGES_REQUESTED, no approval. Latest is snowykr at exact head b6a8d196 (2026-08-18T08:02:35Z). Earlier rounds: snowykr @ 1c0ce5a7, 22eab0ea, 8fe7875, d4af0a7c, c07f76b6; probepark @ b5bb5a67 (3 majors).
• CI at head: Validate exact-head PR contract ✗, Affected path validation / plan ✗ ("Exact-head CI requires this PR head to contain base 50b032e9…; rebase onto current dev"), evidence producer ✗, PR contract bootstrap ✗. All non-contract jobs that ran are green.

Does it still fully address worktree node_modules contamination? Direction yes — at the audited head the launcher refuses to share origin node_modules for workspace repos, remediates only positively-identified launcher links, and creates a marker-owned worktree-local member boundary (63-test launch-worktree suite). But it is not currently mergeable and five standing blockers remain, independently re-verified against the actual head source:

1. Stale base (merge gate): head's merge-base with dev is 416201eb; 50b032e9 is not an ancestor (and dev has since moved to 2bd7b4a4). Needs rebase + refreshed exact-head contract/CI evidence.
2. Manifest symlink escape (launch-worktree.ts:890/948): .gjc-node-modules-links.json is read/written via follow-symlink APIs without an lstat regular-file guard; a checkout-supplied symlink can redirect the write outside node_modules.
3. External node_modules link accepted unproven (:601-603): a link whose realpath merely differs from sourceRoot/node_modules returns present without the complete-boundary proof applied to unmarked directories.
4. Non-directory obstruction (:639-640): file/FIFO/socket at worktree/node_modules returns present; ancestor walk-up stays reachable.
5. Pattern-order re-inclusion (:780-795): all positives are collected before all negations, so pnpm ordered semantics (['packages/*', '!packages/legacy', 'packages/legacy'] must re-include) are violated.

Live dev census: dev@2bd7b4a4 still carries the vulnerable ensureReusableNodeModules (launch-worktree.ts:453, unconditional origin→worktree node_modules symlink), so the issue remains unfixed on dev and stays open. #4621 (merged) is unrelated release prep; no other open PR owns this fix.

This issue will be closed only after #4626 is dev-merged with exact-head approval and green exact-head CI, with the merged-commit evidence posted here.

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gaebal-gajae

[Yeachan-Heo]

Linked-PR reconciliation update for #4620 — census at 2026-08-18T14:46Z (issue-lane owner)

PR #4626 (sole fix owner) remains open/unmerged: head b6a8d19665a479638301dbfce3777b3d02cc7f6e, event base dev@50b032e9, head merge-base with dev still 416201eb — the rebase gate stays failed. dev tip is now ceb31349c2 (2026-08-18T14:07Z).

Reviews: now 8 × CHANGES_REQUESTED, zero approvals. Latest: probepark at exact head (2026-08-18T13:50:16Z) — confirms a long list of prior findings closed (backlink detector identity/case handling, fail-closed traversal/identity errors, remediation safety, marker/reconciliation protocol, boundary completeness, manifest validation, trailing pnpm negations), and blocks with:

• the five standing majors (external resolved symlink accepted without boundary proof, non-directory node_modules accepted as present, pattern-order re-inclusion, ownership manifest read/written through symlinks, stale base/rebase), and
• new major: non-atomic link replacement (launch-worktree.ts:739-755) can degrade a marker-owned boundary into a silently accepted partial boundary (ENOSPC/EACCES/interruption window → next launch drops the missing link from ownership and returns success, resolving through an ancestor with no error), plus a same-target concurrency note; minor: readFileSync/writeFileSync vs the Bun.file()/Bun.write() contract; nit: console.log in a test probe.

Live dev census: dev@ceb31349c2 still carries the vulnerable ensureReusableNodeModules (launch-worktree.ts:453, unconditional origin→worktree node_modules junction), so this issue remains unfixed on dev and stays open.

Lane policy unchanged: this issue lane owns issue-side evidence and closure only; it does not mutate PR #4626 and will not duplicate the fix. Closure happens when #4626 is dev-merged with exact-head approval + green exact-head CI, and the exact merged commit is posted here.

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