refactor(11/12): update manifests, config, docs, and example projects

[cameroncooke]

Summary

This is PR 11 of 12 in a stacked PR series that decouples the rendering pipeline from MCP transport. Depends on PR 10 (boundary rewiring).

Updates all configuration files, YAML manifests, documentation, and example projects to reflect the rendering pipeline refactor. No behavioral code changes -- this is metadata, documentation, and project configuration.

Manifest YAML updates (28 files)

All tool manifests updated to reflect the simplified handler contract. Changes are consistent across all manifests:

• Removed output format configuration that is now handled by the render session
• Updated parameter descriptions where they referenced the old rendering model

New resource manifests

Added manifests/resources/ directory with resource manifest definitions that were previously inline.

Configuration

• package.json + package-lock.json: Dependency updates and script changes
• knip.json: Dead code analysis configuration for the new module structure
• vitest.config.ts: Minor updates for new test paths
• vitest.flowdeck.config.ts + vitest.snapshot.config.ts: New vitest configs for flowdeck integration tests and snapshot tests respectively

Documentation

New developer documentation explaining the rendering pipeline architecture:

• RENDERING_PIPELINE.md: Architecture overview for contributors
• RENDERING_PIPELINE_REFACTOR.md: Migration guide and decision log
• QUERY_TOOL_FORMAT_SPEC.md: Specification for query tool output formatting
• FIXTURE_DESIGNS.md: Snapshot test fixture design documentation
• STRUCTURED_XCODEBUILD_EVENTS_PLAN.md: Design document for the xcodebuild event model
• Updated ARCHITECTURE.md, TESTING.md, MANIFEST_FORMAT.md, TOOL_DISCOVERY_LOGIC.md

Example projects

Minor updates to example projects to work with the updated tool interfaces. Updated test files and project configuration.

Other

• AGENTS.md: Updated project rules
• New test infrastructure: test-helpers.ts, vitest-executor-safety.setup.ts
• Build scripts updated: removed copy-build-assets.js (no longer needed), added benchmark and capture wrapper scripts

Stack navigation

• PR 1-10/12: All code changes
• PR 11/12 (this PR): Manifests, config, docs, examples
• PR 12/12: Snapshot test fixtures and benchmarks

Test plan

• npx vitest run passes
• Manifest validation passes for all YAML files
• Documentation renders correctly in GitHub
• Example projects build successfully

[cursor]

Cursor Bugbot has reviewed your changes and found 2 potential issues.

^{❌ Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

^{Reviewed by Cursor Bugbot for commit 55a323e. Configure here.}

[cameroncooke]

• refactor(12/12): add snapshot test fixtures and benchmarks #330
• refactor(11/12): update manifests, config, docs, and example projects #329 👈 (View in Graphite)
• refactor(10/12): rewire CLI, daemon, and MCP server boundaries #328
• refactor(9/12): migrate debugging, swift-package, and remaining tools #327
• refactor(8/12): migrate UI automation tools to event-based handlers #326
• refactor(7/12): migrate device and macOS tools to event-based handlers #325
• refactor(6/12): migrate simulator tools to event-based handlers #324
• refactor(5/12): change handler contract to event-based emission #323
• refactor(4/12): extract build/test utilities, platform steps, and xcodebuild pipeline #322
• refactor(3/12): add rendering engine and output formatting #321
• refactor(2/12): add pipeline event types, parsers, and event builders #320
• refactor(1/12): remove deprecated logging tools #319
• main

This stack of pull requests is managed by Graphite. Learn more about stacking.

[sentry]

Bug: If the request('pause') call fails in pauseExecution, the abandoned waitForEvent promise can cause an unhandled rejection, crashing the process.
_{Severity: HIGH}

Suggested Fix

Wrap the request and waitForEvent calls in a try...finally block. In the finally block, ensure the waitForEvent promise is either awaited with a catch or otherwise handled to prevent an unhandled rejection if the request call fails.

Prompt for AI Agent

Review the code at the location below. A potential bug has been identified by an AI
agent.
Verify if this is a real issue. If it is, propose a fix; if not, explain why it's not
valid.

Location: src/utils/debugger/backends/dap-backend.ts#L416-L428

Potential issue: In the `pauseExecution` function, a call is made to
`this.request('pause', ...)`. If this request fails and throws an error, the `catch`
block will handle it, but the promise returned by `waitForEvent('stopped', ...)` is left
pending. This `waitForEvent` call has an internal timeout. When this timeout is
eventually reached, it will reject the promise. Since nothing is awaiting or handling
this rejection, it becomes an unhandled promise rejection, which can terminate the
Node.js process.

[cameroncooke]

Merge activity

• Apr 10, 12:18 PM UTC: A user started a stack merge that includes this pull request via Graphite.
• Apr 10, 12:33 PM UTC: Graphite rebased this pull request as part of a merge.
• Apr 10, 12:33 PM UTC: @cameroncooke merged this pull request with Graphite.