Consolidate logging packages (logger vs logging)

[NP-compete]

Summary

There are two logging-related packages with confusing names:

• `internal/logger/` - Application logging (zerolog wrapper)
• `internal/logging/` - MCP server-to-client logging

Current State

```
internal/
├── logger/
│ └── logger.go # App logging with zerolog
└── logging/
├── logging.go # MCP notifications
└── logging_test.go
```

Problem

1. Names are too similar, causing confusion
2. `logger.go` has dead code (`GetUvicornLogConfig` is Python-specific)
3. Inconsistent usage patterns across codebase

Expected Outcome

Option A: Rename for clarity

```
internal/
├── applog/ # Renamed from logger
│ └── applog.go
└── mcplog/ # Renamed from logging
├── mcplog.go
└── mcplog_test.go
```

Option B: Merge into single package

```
internal/
└── log/
├── app.go # Application logging
├── mcp.go # MCP notifications
└── mcp_test.go
```

Additional Cleanup

1. Remove `GetUvicornLogConfig` - Python-specific dead code
2. Standardize logging patterns across codebase
3. Add structured logging fields consistently

Acceptance Criteria

• Packages renamed or merged for clarity
• Dead code removed
• All imports updated
• Consistent logging patterns documented
• All tests pass