test(snapshot): Refresh recorded fixture values

Update recorded snapshot fixture values that changed during the latest focused runs. Keep these separate from harness and normalisation logic for easier review.

Co-Authored-By: Codex <noreply@openai.com>

Author: cameroncooke

src/snapshot-tests/__fixtures__/json/macos/test--success.json

@@ -41,14 +41,7 @@
       }
     },
     "diagnostics": {
-      "warnings": [
-        {
-          "message": "<HOME>/Library/Developer/XcodeBuildMCP/DerivedData/Build/Products/Debug/MCPTest.app/Contents/Frameworks/XCTestCore.framework/Versions/A/XCTestCore: Failed to parse executable: Attempting to read past the size of the binary data. startingAt: 2179072, typeSize: 4 (UInt32), dataSize: 458752"
-        },
-        {
-          "message": "<HOME>/Library/Developer/XcodeBuildMCP/DerivedData/Build/Products/Debug/MCPTest.app/Contents/Frameworks/Testing.framework/Versions/A/Testing: Failed to parse executable: Attempting to read past the size of the binary data. startingAt: 3604480, typeSize: 4 (UInt32), dataSize: 589824"
-        }
-      ],
+      "warnings": [],
       "errors": [],
       "testFailures": []
     }

src/snapshot-tests/__fixtures__/json/swift-package/run--success.json

@@ -27,7 +27,7 @@
       "stderr": [
         "Building for debugging...",
         "[0/6] Write sources",
-        "[0/6] Write spm-entitlement.plist",
+        "[1/6] Write spm-entitlement.plist",
         "[2/6] Write swift-version--6988338F2F200930.txt",
         "[4/8] Compiling spm main.swift",
         "[5/8] Emitting module spm",

src/snapshot-tests/__fixtures__/mcp/resources/doctor--success.txt

@@ -36,7 +36,6 @@ Process Tree
    <PID> (ppid <PID>): <PROCESS>
    <PID> (ppid <PID>): <PROCESS>
    <PID> (ppid <PID>): <PROCESS>
-   <PID> (ppid <PID>): <PROCESS>
 
 Xcode Information
   version: <XCODE_VERSION>