pac copilot mcp --run writes "Loading FeatureFlags from file: ..." to stdout — breaks MCP JSON-RPC transport

[jt-thrivara]

Summary

`pac copilot mcp --run` (and the `dnx Microsoft.PowerApps.CLI.Tool --yes copilot mcp --run` equivalent) writes one non-JSON line to stdout before entering MCP protocol mode:

```
Loading FeatureFlags from file: C:\Users<user>.nuget\packages\microsoft.powerapps.cli.tool\2.7.4\tools\net10.0\any\featureflags.json
```

The MCP stdio transport requires stdout to be exclusively JSON-RPC. Any non-JSON line on stdout breaks the host parser. Claude Desktop surfaces this as a toast:

MCP pac-cli: Unexpected token 'L', "Loading Fe"... is not valid JSON

The server then fails to register and its tools are unavailable to the host.

Repro

```powershell
$tmpOut = New-TemporaryFile
$tmpErr = New-TemporaryFile
$p = Start-Process -FilePath "dnx" `
-ArgumentList "Microsoft.PowerApps.CLI.Tool","--yes","copilot","mcp","--run" `
-NoNewWindow -PassThru -RedirectStandardOutput $tmpOut -RedirectStandardError $tmpErr
Start-Sleep -Seconds 6
Stop-Process -Id $p.Id -Force
Get-Content $tmpOut # <-- contains the offending FeatureFlags line
Get-Content $tmpErr | Select-Object -First 6 # <-- clean info: lines (correct behavior)
```

Captured stdout (the problem):
```
Loading FeatureFlags from file: C:\Users<user>.nuget\packages\microsoft.powerapps.cli.tool\2.7.4\tools\net10.0\any\featureflags.json
```

Captured stderr (correctly routed, MCP ignores stderr):
```
info: ModelContextProtocol.Server.StdioServerTransport[857250842]
Server (stream) (Power Platform Management MCP Server) transport reading messages.
info: Microsoft.Hosting.Lifetime[0]
Application started. Press Ctrl+C to shut down.
info: Microsoft.Hosting.Lifetime[0]
Hosting environment: Production
```

Expected

All bootstrap logging (FeatureFlags loader, lifecycle messages, anything diagnostic) should write to stderr. Stdout must be reserved exclusively for JSON-RPC frames. This is the documented requirement of the MCP stdio transport.

Actual

Exactly one line — the FeatureFlags-loader log — goes to stdout, breaking every MCP host that connects via stdio.

Workaround

A Node stdio proxy that filters non-JSON lines off stdout works:

```js
const { spawn } = require('child_process');
const readline = require('readline');
const isWin = process.platform === 'win32';
const command = isWin ? 'cmd.exe' : 'dnx';
const args = isWin
? ['/c', 'dnx', 'Microsoft.PowerApps.CLI.Tool', '--yes', 'copilot', 'mcp', '--run']
: ['Microsoft.PowerApps.CLI.Tool', '--yes', 'copilot', 'mcp', '--run'];
const child = spawn(command, args, { stdio: ['pipe', 'pipe', 'inherit'] });
process.stdin.pipe(child.stdin);
readline.createInterface({ input: child.stdout })
.on('line', line => { if (line.startsWith('{')) process.stdout.write(line + '\n'); });
child.on('exit', code => process.exit(code ?? 0));
```

But every user running pac MCP via Claude Desktop, GitHub Copilot, VS Code, etc. has to either deploy a wrapper like this or disable pac MCP entirely.

Suggested fix

Route the FeatureFlags loader's diagnostic write to `Console.Error` (or the configured stderr logger) instead of stdout. The lifecycle logger already routes correctly to stderr — only the FeatureFlags path is misrouted.

Environment

• pac CLI 2.7.4 (resolved via `dnx Microsoft.PowerApps.CLI.Tool --yes` on 2026-05-29)
• .NET 10.0.7
• Windows 11 (Build 10.0.26200)
• MCP host: Claude Desktop (latest)

Related

• PAC MCP Server fails to start - Missing Microsoft.Extensions.Configuration.EnvironmentVariables assembly #1260 — separate `pac copilot mcp` startup bug (missing assembly), not a duplicate of this stdout-routing issue.
• Discussion Preview: PAC CLI ships with local MCP server #1182 — original PAC MCP announcement; another user noted needing a `.cmd` wrapper for related output-stream issues without root-cause analysis.