chore(deps): upgrade dependencies and fix docker-e2e Vitest RPC timeout

[arabold]

Summary

• Fixes npm run test:docker reporting a false-positive failure: test/docker-e2e.test.ts used spawnSync for docker build/docker run, which blocks Node's event loop for the whole command duration. Vitest's worker↔main-thread RPC heartbeat has a hardcoded 60s timeout, so any long-running synchronous call tripped [vitest-worker]: Timeout calling "onTaskUpdate" and failed the run even though every test assertion passed. Switched to async spawn-based helpers so the event loop stays responsive.
• Upgrades all dependencies except typescript and tree-sitter (see below), after reviewing each changelog for breaking changes:
  • @fastify/static 9→10, @kreuzberg/node 4.4→4.10 (kept tilde-pinned given its license churned MIT→Elastic→MIT across minors), @types/archiver 7→8 (now matches archiver@8's ESM exports — removed the @ts-expect-error workarounds), @types/yauzl 2→3, @types/node 24→26, defuddle 0.18→0.19, vite-plugin-dts 4→5 (confirmed unused in this repo).
  • vite/vite-node/vitest bumped together (7→8 / 5→6 / 3→4) since Vitest 3 doesn't support Vite 8.
• Fixes required by the Vitest 4 bump:
  • Vitest 4 mock constructors use real new semantics, so arrow-function mockImplementations used to mock classes now throw "is not a constructor". Converted the affected call sites across test files to function expressions, and extended the existing test-file Biome override to disable useArrowFunction (which otherwise fights this fix).
  • Re-spying an already-spied prototype method no longer resets its call count, which broke HtmlPipeline/MarkdownPipeline middleware-count assertions; added afterEach(() => vi.restoreAllMocks()).
• @kreuzberg/node 4.10.2 stopped embedding the sheet name inside XLSX table markdown; DocumentPipeline now reconstructs it from metadata.sheetNames so indexed spreadsheet content doesn't silently lose that context.
• Cleaned up lint drift from the Biome 2.4→2.5 bump (formatter reflow of it.each calls) plus two small fixes (unused param, optional chain).
• typescript stays on ^5.9.3: bumping breaks npm ci outright (ERESOLVE — @kitajs/ts-html-plugin@4.1.4 peer-depends on typescript@^5.9.3). Its only newer-TS-compatible release is a 5.0.0-next.2 prerelease pinned to the exact typescript@6.0.2 and requiring a @kitajs/html@5.0.0-next.1 prerelease bump too — holding off until a stable release exists.
• tree-sitter/tree-sitter-javascript/tree-sitter-python are intentionally left unchanged (no mutually compatible newer versions available).

Test plan

• npm run typecheck
• npm run lint (clean — 0 errors/warnings/info)
• npm run build
• npm test — 130/130 test files, 1874/1874 tests passing
• npm run test:docker — all 5 Docker image tests passing, no more spurious RPC-timeout failure

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR updates the repo’s dependency set (notably Vite/Vitest/Biome and related tooling) and adjusts tests + pipeline behavior to stay compatible, while also fixing npm run test:docker flakiness by avoiding long-running spawnSync calls that block Vitest’s worker heartbeat.

Changes:

• Replace spawnSync Docker invocations in test/docker-e2e.test.ts with async spawn helpers to keep the event loop responsive during long Docker operations.
• Upgrade dependencies (incl. @fastify/static, @kreuzberg/node, Vite/Vitest, Biome) and apply the required test/mocking updates for Vitest 4 semantics.
• Restore XLSX sheet-name context in DocumentPipeline output when Kreuzberg no longer includes it in per-table markdown.

Reviewed changes

Copilot reviewed 31 out of 32 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
test/docker-e2e.test.ts	Switch Docker build/run to async helpers to prevent Vitest RPC timeouts during long operations
test/archive-integration.test.ts	Remove obsolete @ts-expect-error now that archiver typings match exports
src/web/main.client.ts	Simplify HTMX xhr header check using optional chaining
src/utils/archive/ArchiveFactory.test.ts	Biome-driven it.each formatting change
src/tools/ScrapeTool.test.ts	Update mock constructor implementation for Vitest 4 “new” semantics + formatting
src/tools/CancelJobTool.test.ts	Biome-driven it.each formatting change
src/telemetry/telemetry.test.ts	Convert mocked class constructor to function expression for Vitest 4 semantics
src/telemetry/postHogClient.test.ts	Convert mocked constructor to function expression for Vitest 4 semantics
src/store/DocumentManagementService.test.ts	Convert mocked constructors to function expressions for Vitest 4 semantics
src/splitter/splitters/TextContentSplitter.test.ts	Tighten spy typing and update vitest import types
src/splitter/SemanticMarkdownSplitter.test.ts	Remove unused param warning by prefixing with _
src/scraper/utils/sandbox.test.ts	Convert JSDOM mock implementations to function expressions for Vitest 4 semantics
src/scraper/strategies/GitHubScraperStrategy.test.ts	Convert mockImplementation to function expression for Vitest 4 semantics
src/scraper/pipelines/MarkdownPipeline.test.ts	Add afterEach(vi.restoreAllMocks) to prevent spy call-count leakage in Vitest 4
src/scraper/pipelines/HtmlPipeline.test.ts	Add afterEach(vi.restoreAllMocks) to prevent spy call-count leakage in Vitest 4
src/scraper/pipelines/DocumentPipeline.ts	Reconstruct XLSX sheet-name headings from Kreuzberg metadata when available
src/pipeline/PipelineManager.test.ts	Convert mocked worker constructor to function expression + formatting
src/index.test.ts	Convert mocked service constructor to function expression for Vitest 4 semantics
src/cli/index.test.ts	Convert multiple mocked constructors/tools to function expressions for Vitest 4 semantics
src/cli/commands/search.test.ts	Convert mocked tool constructor to function expression
src/cli/commands/scrape.test.ts	Convert mocked tool/event bus constructors to function expressions
src/cli/commands/refresh.test.ts	Convert mocked tool/event bus constructors to function expressions
src/cli/commands/mcp.test.ts	Convert mocked store constructors to function expressions
src/cli/commands/list.test.ts	Convert mocked tool constructor to function expression
src/cli/commands/findVersion.test.ts	Convert mocked tool constructor to function expression
src/cli/commands/fetchUrl.test.ts	Convert mocked fetchers/tools to function expressions
src/cli/commands/default.test.ts	Convert mocked store constructor to function expression
src/auth/ProxyAuthManager.test.ts	Adjust proxy provider mock + Biome formatting
src/app/AppServer.test.ts	Convert mocked auth manager constructor to function expression
package.json	Upgrade runtime/dev dependencies (Fastify static, Kreuzberg, Vite/Vitest, typings, etc.)
package-lock.json	Lockfile updates corresponding to dependency upgrades
biome.json	Bump Biome schema + disable useArrowFunction for src/**/*.test.ts to avoid fighting Vitest 4 constructor-mocking needs

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