fix(mcp): surface command output and run tools in the requested directory

[ryzizub]

Status

READY

Description

The very_good_cli MCP test, packages_get, and packages_check_licenses tools had two problems:

1. Command output was discarded. A failed run returned only "<tool>" failed with exit code 69. — the actual failing tests, compile errors, and logs (written by the in-process mason Logger to stdout/stderr, which the stdio transport shares with the JSON-RPC stream) never reached the client. Agents saw an opaque exit code and could not diagnose failures.
2. directory did nothing useful. It was appended as a positional CLI argument; the commands resolve their target from the process current directory, so in a monorepo the tool ran from the wrong place and failed with exit code 66.

Changes

• Capture the in-process command output by redirecting stdout/stderr to a buffer via IOOverrides.runZoned, constructing the mason Logger inside the zone (mason pins IOOverrides.current at construction, so a Logger built outside would still write to the real stdout). The captured output is returned in CallToolResult.content with isError on success and every failure path, and non-JSON is kept off the real stdout that carries the MCP JSON-RPC stream (per the stdio transport spec).
• Apply directory as the real working directory (Directory.current) for the run and restore it in finally; remove the positional misuse.
• Serialize tool runs behind an async mutex so the process-global working-directory switch is safe under concurrent/pipelined tool calls (the json_rpc_2 transport can dispatch handlers concurrently).
• Ignore generated *.vm.json test artifacts.

Connections

• Closes fix: MCP tools report only an exit code and discard the command output #1611
• Overlaps with fix(mcp): apply directory argument as the working directory #1600 / vgv-ai-flutter-plugin feat #70 doesn't work #1599: this PR also reworks directory into a working-directory switch. The approach here is concurrency-safe (serialized) and additionally surfaces command output — coordinate to avoid duplicate/conflicting changes.
• Refs fix: very_good_cli MCP 'test' tool hangs vgv-ai-flutter-plugin#94 (downstream symptom: opaque MCP test results blocked the /build flow).

Verification

• MCP suite: 40 tests pass, lib/src/mcp/mcp_server.dart at 100% coverage.
• dart analyze --fatal-infos --fatal-warnings clean; dart format clean.
• Verified live through the MCP test tool: a failing package now returns the real failure output and runs in the requested directory. The concurrency fix is covered by a mutation-proven regression test.

Type of Change

• ✨ New feature (non-breaking change which adds functionality)
• 🛠️ Bug fix (non-breaking change which fixes an issue)
• ❌ Breaking change (fix or feature that would cause existing functionality to change)
• 🧹 Code refactor
• ✅ Build configuration change
• 📝 Documentation
• 🗑️ Chore

🤖 Generated with Claude Code

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