Address comprehensive code review feedback and improve MCP security

Security & Quality Improvements:
- Add security validation for GitHub URLs with XSS/injection prevention
- Implement user confirmation prompt for GitHub clone operations
- Add security warning for remote code execution risks
- Replace duplicate authentication logic with DRY helper function
- Fix bearer token/password exposure in debug logs (now properly masked)
- Add proper exit codes for different error types (auth, network, config, etc.)
- Disable WebSocket transport in CLI until implementation is complete
- Add comprehensive input sanitization and validation

Protocol & Reliability:
- Replace magic strings with named constants (MCP_PROTOCOL_VERSION, etc.)
- Implement request ID overflow protection with MAX_REQUEST_ID limit
- Improve Cargo.toml parsing with robust TOML section detection
- Add HTTP timeouts and better error context
- Implement stdio process lifecycle management with auto-cleanup
- Add proper configuration load priority (env vars override file configs)

Code Quality:
- Extract authenticated request builder to eliminate code duplication
- Fix base64 deprecation warning with new Engine API
- Improve error messages with actionable troubleshooting guidance
- Add comprehensive constants for maintainability
- Better async stdio communication with response validation
- Enhanced debug logging with appropriate verbosity levels

All tests passing, production ready

Co-authored-by: 0xrinegade <[email protected]>

Author: Copilot

src/clparse.rs

@@ -849,9 +849,9 @@ pub fn parse_command_line() -> clap::ArgMatches {
                             Arg::new("transport")
                                 .long("transport")
                                 .value_name("TYPE")
-                                .value_parser(clap::builder::PossibleValuesParser::new(["http", "websocket", "stdio"]))
+                                .value_parser(clap::builder::PossibleValuesParser::new(["http", "stdio"]))
                                 .default_value("http")
-                                .help("Transport type for communication")
+                                .help("Transport type for communication (websocket not yet implemented)")
                         )
                         .arg(
                             Arg::new("auth_type")