fix: resolve Windows build/check crash and npm shrinkwrap registry 404

[SHJordan]

This PR fixes two issues:

1. Windows build/check crash:

   • In scripts/build-all.mjs and scripts/run-web-ui-check.mjs, the script was trying to evaluate native binaries (such as pnpm.exe on Windows, which is set in npm_execpath by newer pnpm installations) using Node.js, causing a SyntaxError. We fixed this by detecting if the execpath does not end in .js/.cjs (which indicates a native binary) and running it directly instead of wrapping it via Node.

2. Package shrinkwrap dependency registry 404 error:

   • The generated npm-shrinkwrap.json for @code-yeongyu/senpi contained registry references to internal, private workspace packages (like @earendil-works/pi-tui) which are bundled but not actually published to the public registry. This resulted in 404 Not Found errors when users tried to install @code-yeongyu/senpi.
   • We updated scripts/generate-coding-agent-shrinkwrap.mjs to mark internal dependencies as "inBundle": true and omit resolved URL registry references, forcing npm to resolve them from the bundled contents.

---

Summary by cubic

Fixes Windows build/check crashes by executing native package manager binaries directly. Also updates shrinkwrap generation to bundle internal packages, avoiding registry 404s when installing @code-yeongyu/senpi.

• Bug Fixes
  • Detect native package manager execpaths (e.g., pnpm.exe) and run them directly in build/check scripts; otherwise load .js/.cjs via Node.
  • Mark internal workspace deps (@earendil-works/pi-agent-core, @earendil-works/pi-ai, @earendil-works/pi-tui) as "inBundle": true and omit resolved URLs in the generated npm-shrinkwrap.json.

^{Written for commit 59e2bec. Summary will update on new commits.}

[cubic-dev-ai]

No issues found across 4 files

_{Re-trigger cubic}

[code-yeongyu]

[sisyphus-bot] Rebased this branch onto the latest main and merged it via a merge commit.

The only conflict was the generated packages/coding-agent/npm-shrinkwrap.json. Rather than hand-merging it, I resolved it by regenerating the lockfile from scratch (node scripts/generate-coding-agent-shrinkwrap.mjs) on top of current main, then validated with node scripts/generate-coding-agent-shrinkwrap.mjs --check, which exits 0. The regeneration preserved your core fix: the internal @earendil-works/pi-* workspace deps are marked inBundle: true instead of carrying a resolved registry URL that 404s.

I verified both fixes:

• The native package-manager guard pm.execpath && (pm.cmd === "bun" || !/\.[cm]?js$/i.test(pm.execpath)) is present in both scripts/build-all.mjs and scripts/run-web-ui-check.mjs. This is backward-compatible: for bun/npm/pnpm-as-.js it behaves exactly as before, and the new branch only triggers for non-.js execpaths such as pnpm.exe. The Windows-specific path can't be exercised on the macOS CI here, so it was reviewed rather than run on Windows.
• The shrinkwrap generator change (inBundle added to the field order and set on internal workspace deps) is in place, and the --check validation passes.

Thanks for the careful fix, @SHJordan.