Respect log level from rc files

[saidM]

Fixes #2132

Log level flags defined in .fpm config files were being ignored because option parsing set the default logger level after reading the config options.

This fix ensures log levels specified in configuration files are respected, while still allowing explicit CLI flags to take precedence.

Changes

• Apply log level settings loaded from config files.
• Keep CLI arguments as the highest precedence.

Testing

• Tested passing log level options via .fpm file.
• Verified CLI flags still override file config as expected.