Values in config file not used unless passed as CLI flags

[lolasanchezzz]

Generated the config file using:

LS_Metadata_reader --c

Set CS and Gainref_FlipRotate, which were saved correctly in the config file.

However, when running:

LS_Metadata_reader -o test.json /path/to/OffloadData/Images-Disc1/

those values are not included in the output JSON.

When running with CLI flags:

LS_Metadata_reader --cs 2.7 --gain_flip_rotate 0,0,0 -o test2.json /path/to/OffloadData/Images-Disc1/

they are correctly included.

Looks like the config file is ignored unless values are passed explicitly via CLI.