Fix publish workflow + switch internal alias to subpath imports

[0x80]

Two independent changes on this branch.

Publish workflow fix

The publish workflow (.github/workflows/publish.yml) was failing at the Bump version step with:

npm error Git working directory not clean.

Root cause: tsdown.config.ts had exports: true, which makes tsdown rewrite package.json's bin and exports fields from the entry config on every build. With the entries named index and isolate-bin, tsdown strips the isolate bin alias that PR #188 explicitly restored alongside isolate-package for backwards compatibility. Locally that just leaves a dirty diff after pnpm build; in CI, pnpm build dirties the tree and the subsequent npm version aborts.

Fix: remove exports: true so the manually maintained bin/exports in package.json is the source of truth, and pnpm build no longer mutates the working tree.

Internal alias: ~/* -> #/* via subpath imports

Replace the TypeScript-only ~/* path alias with Node subpath imports. The mapping now lives in package.json as "imports": { "#/*": "./src/*" }, which is understood natively by Node, bundlers, and TypeScript — not only by tsc via tsconfig paths.

A matching paths entry remains in tsconfig.json because TS's bundler resolution of the imports field does not do directory-index fallback (so barrel imports like #/lib/utils -> src/lib/utils/index.ts would otherwise fail in tsc). The package.json imports field is the source of truth at runtime.

Engines is already >=22.22.1, well above the 14.6 cutoff for stable subpath imports.

Scope: packages (isolate-package), infra (publish workflow)
Visibility: internal

[coderabbitai]

Walkthrough

This PR migrates the project's module import alias system from the ~ prefix to the # prefix. The tsconfig.json and package.json are updated to map the new #/* prefix to ./src/*. All source and test files throughout the codebase are then updated to import from the new #/ paths instead of the old ~/ paths. Test files also update their Vitest vi.mock() setup to intercept the new alias paths. The build configuration (tsdown.config.ts) removes an unused exports option.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The PR title clearly identifies the two main changes: fixing the publish workflow and switching from the internal ~/* alias to subpath imports (#/*).
Description check	✅ Passed	The PR description comprehensively explains both independent changes with clear rationale, implementation details, and scope information aligned with the changeset.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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[coderabbitai]

Actionable comments posted: 1

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ℹ️ Review info

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Configuration used: Organization UI

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Run ID: 66a1c811-ab4a-4cb7-af9a-b8678010186b

📥 Commits

Reviewing files that changed from the base of the PR and between 673508a and 862b546.

📒 Files selected for processing (34)

• package.json
• src/get-internal-package-names.test.ts
• src/lib/config.test.ts
• src/lib/lockfile/helpers/generate-bun-lockfile.test.ts
• src/lib/lockfile/helpers/generate-bun-lockfile.ts
• src/lib/lockfile/helpers/generate-npm-lockfile.ts
• src/lib/lockfile/helpers/generate-pnpm-lockfile.test.ts
• src/lib/lockfile/helpers/generate-pnpm-lockfile.ts
• src/lib/lockfile/helpers/generate-yarn-lockfile.ts
• src/lib/lockfile/process-lockfile.test.ts
• src/lib/manifest/helpers/adapt-internal-package-manifests.test.ts
• src/lib/manifest/helpers/adapt-internal-package-manifests.ts
• src/lib/manifest/helpers/adapt-manifest-internal-deps.ts
• src/lib/manifest/helpers/adopt-pnpm-fields-from-root.test.ts
• src/lib/manifest/helpers/adopt-pnpm-fields-from-root.ts
• src/lib/manifest/helpers/resolve-catalog-dependencies.test.ts
• src/lib/manifest/helpers/resolve-catalog-dependencies.ts
• src/lib/package-manager/helpers/infer-from-files.ts
• src/lib/package-manager/helpers/infer-from-manifest.ts
• src/lib/patches/collect-installed-names-bun.test.ts
• src/lib/patches/collect-installed-names-bun.ts
• src/lib/patches/collect-installed-names-pnpm.test.ts
• src/lib/patches/collect-installed-names-pnpm.ts
• src/lib/patches/copy-patches.test.ts
• src/lib/patches/copy-patches.ts
• src/lib/patches/write-isolate-pnpm-workspace.test.ts
• src/lib/patches/write-isolate-pnpm-workspace.ts
• src/lib/registry/collect-reachable-package-names.test.ts
• src/lib/registry/list-internal-packages.test.ts
• src/lib/utils/filter-patched-dependencies.test.ts
• src/lib/utils/filter-patched-dependencies.ts
• src/testing/setup.ts
• tsconfig.json
• tsdown.config.ts

💤 Files with no reviewable changes (1)

• tsdown.config.ts

[coderabbitai]

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Add the required ~/* path alias mapping.

Line 5 introduces only #/*; the required ~/* mapping is missing from tsconfig.json.

Suggested patch

   "compilerOptions": {
     "paths": {
+      "~/*": ["./src/*"],
       "`#/`*": ["./src/*"]
     }
   }

As per coding guidelines: tsconfig.json: Use path aliases with ~ mapping to src/ directory.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	"#/*": ["./src/*"]
	"~/*": ["./src/*"],
	"`#/`*": ["./src/*"]