Merge latest main and resolve scope discovery conflicts

Author: ksumitathenahealth

.changeset/cap_protocol_version_negotiation_on_stateful_transports.md

@@ -0,0 +1,32 @@
+name: MCP conformance
+on:
+  workflow_dispatch:
+
+jobs:
+  conformance:
+    name: MCP conformance (${{ matrix.revision }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        revision: ['2025-11-25', '2026-07-28']
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions-rust-lang/setup-rust-toolchain@v1
+      - uses: actions/setup-node@v6
+        with:
+          node-version: 22
+          cache: npm
+          cache-dependency-path: e2e/conformance/package-lock.json
+      - name: Run production server conformance
+        run: bash e2e/conformance/run.sh --revision ${{ matrix.revision }}
+      - name: Upload conformance results and logs
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: mcp-conformance-${{ matrix.revision }}
+          path: e2e/conformance/artifacts/
+          if-no-files-found: warn

.changeset/clarify_security_boundaries_in_documentation.md

@@ -62,10 +62,11 @@ cargo llvm-cov --all-features --workspace --codecov --output-path codecov.json
 
 ## Workspace Structure
 
-The project is a Rust workspace with three crates:
+The project is a Rust workspace with four crates:
 
 - **apollo-mcp-server** (`crates/apollo-mcp-server/`) - Main binary. MCP protocol handler, HTTP/WebSocket transport, GraphQL execution, auth, telemetry.
 - **apollo-mcp-registry** (`crates/apollo-mcp-registry/`) - Schema and operations provider. Handles schema sources (Uplink, local files) and operation sources (Platform API collections, persisted queries, local files).
+- **apollo-mcp-rhai** (`crates/apollo-mcp-rhai/`) - Rhai scripting support. Script engine, lifecycle hook functions, and checkpoints.
 - **apollo-schema-index** (`crates/apollo-schema-index/`) - GraphQL schema indexing using Tantivy for full-text search.
 
 ## Key Architecture Patterns
@@ -87,7 +88,7 @@ The project is a Rust workspace with three crates:
 
 ## Key Dependencies
 
-- `rmcp 3.2` - MCP protocol implementation (aligned with MCP 2025-11-25)
+- `rmcp` - MCP protocol implementation (the official Rust SDK)
 - `apollo-compiler`, `apollo-federation` - GraphQL parsing and schema handling
 - `axum 0.8` - HTTP server
 - `tokio` - Async runtime