docs: convert command guidance to bun invocation

[code-yeongyu]

Motivation

The fleet standard is Bun-only for JavaScript/TypeScript command invocation. Agent and developer documentation was guiding agents toward npm/npx/node commands, including package-scoped Vitest commands, which conflicts with that standard. This PR updates documentation command guidance only; Vitest remains the test framework.

Conversion table

Before	After
npm run <script>	bun run <script>
npm test	bun run test
npm --prefix <dir> test -- <args>	bun run --cwd <dir> test <args>
npm --prefix <dir> run <script>	bun run --cwd <dir> <script>
npm --prefix <dir> exec vitest -- <args>	bunx --cwd <dir> vitest <args>
npx <cli>	bunx <cli>
node scripts/<file>.mjs / .js	bun scripts/<file>.mjs / .js
Agent-facing npm install	bun install

Contributor-facing npm install examples in README.md/CONTRIBUTING.md remain available with Bun alternatives alongside them, as requested. node --test guidance was not converted because Bun node:test compatibility is not proven; those references remain intentionally inventoried exceptions. No package.json, lockfile, workflow, source, CHANGELOG.md, or changes.md files were changed.

Spot verification (remote mengmotaMac)

All commands were run remotely with ssh mengmotaMac 'cd ~/local-workspaces/senpi && ...'; no tests/builds were run on the local machine.

• bun run --cwd packages/coding-agent test test/compaction/overflow-retry-bound.test.ts
  • Vitest v4.1.11
  • 1 test file passed
  • 4 tests passed
  • Duration: 960ms
• bun run check:ts-imports
  • Executed node scripts/check-ts-relative-imports.mjs
  • Passed with exit code 0
• bun run check:model-data
  • Executed the existing package script chain (npm --prefix packages/ai run check:model-data)
  • Output: Generated model data is valid.
  • Passed with exit code 0

Follow-up inventory: untouched npm internals

These are intentionally not changed in this documentation-only PR and should be handled as a separate runtime/CI migration proposal:

• package.json script chains: multiple package scripts still call npm run, npm --prefix, npm install, npm version, or node scripts/...; notable examples include root check, test, refresh-lock, version/publish scripts, coding-agent build:binary, and package prepublishOnly chains.
• CI workflows: .github/workflows/ci.yml, perf-trend.yml, npm-audit.yml, issue-analysis.yml, native-prebuilds.yml, changelog-gate.yml, releasability.yml, publish-npm.yml, build-binaries.yml, and publish-model-catalog.yml still contain npm/npx/node invocations. These were explicitly out of scope.
• node --test guidance: intentional exceptions remain in AGENTS.md and packages/tui/AGENTS.md for the TUI/scripts node:test runners.
• Historical/runtime prose: npm registry/package identity, npm package-manager behavior, audit/publishing details, and quoted historical material were preserved rather than rewritten.

Scope verification

• git diff --name-only contains Markdown files only.
• git diff --check passes.
• AGENTS.md COMMANDS/VALIDATION sections contain Bun invocation guidance; intentional node --test runner notes remain as inventory exceptions.

---

Summary by cubic

Updates documentation command guidance from npm/npx/node to Bun (bun, bunx) so agent and developer docs match the fleet-standard Bun-only invocation. Vitest remains the test framework; this is a docs-only change.

• Converts npm run, npm test, npm --prefix, npx, node scripts/..., and install guidance (npm install, npm install -g, npm --package-lock-only, npm ci) to bun run, bun run --cwd, bunx, bun scripts/..., bun add -g, bun install --lockfile-only, and bun install --frozen-lockfile.
• Keeps contributor-facing npm install examples in root and package README.md files and CONTRIBUTING.md with Bun alternatives alongside.
• Leaves node --test guidance in TUI/scripts docs unchanged because Bun node:test compatibility is not proven.
• No package.json, lockfile, workflow, source, CHANGELOG.md, or changes.md files were changed; npm in CI workflow files and package script chains remains for a separate runtime/CI migration.

^{Written for commit a99450d. Summary will update on new commits.}