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.}

[cursor]

macOS MCPTest reuses iOS Calculator bundle identifier

Medium Severity

The macOS MCPTest app's PRODUCT_BUNDLE_IDENTIFIER was updated to io.sentry.calculatorapp. This bundle ID is already in use by the iOS Calculator example app. Sharing the same bundle ID across two distinct example apps can lead to issues with app identification, automation, snapshot tests, and Keychain collisions.

 

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

[sentry]

Bug: Processing streamed output in chunks can merge lines across chunk boundaries, breaking regex matching for benchmark milestones and resulting in incorrect metrics.
_{Severity: MEDIUM}

Suggested Fix

Buffer the incoming data chunks and process the stream line-by-line instead of chunk-by-chunk. This ensures that normalizeTerminalTranscript and any subsequent pattern matching operate on complete lines, preventing milestone markers from being broken apart.

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: scripts/benchmark-simulator-test.ts#L140

Potential issue: When processing streamed output, the `normalizeTerminalTranscript`
function is called on each data chunk. This function joins lines without a trailing
newline. If a log line containing a benchmark milestone (e.g., `/🛠️\s*Compiling/`) is
split across two chunks, the last part of the line from the first chunk and the first
part from the next are concatenated. This breaks the pattern matching, leading to
incorrect metrics.

_{Did we get this right? 👍 / 👎 to inform future reviews.}

[cameroncooke]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• 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: The macOS MCPTest app's bundle identifier is identical to the iOS Calculator app's, which could cause collisions for tools targeting by bundle ID.
_{Severity: MEDIUM}

Suggested Fix

Assign a unique bundle identifier to the macOS MCPTest application to differentiate it from the iOS Calculator app. For example, you could use a platform-specific suffix like io.sentry.calculatorapp.macOS.

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: example_projects/macOS/MCPTest.xcodeproj/project.pbxproj#L341

Potential issue: The bundle identifier for the macOS `MCPTest` application has been set
to `io.sentry.calculatorapp`, which is identical to the one used by the iOS Calculator
application. This duplication creates a collision, causing ambiguity for tools that
target applications by their bundle ID, such as `launch_app_sim` or `stop_app_sim`.
These tools might inadvertently target the wrong application if both are present in the
same environment, for instance, on a simulator capable of running both iOS and macOS
apps.