Configuration file doesn't work for many flags

[LesnyRumcajs]

Describe the bug

Providing a configuration file, either via --config or through other means, doesn't work with a bunch of flags that get overridden in to_config after parsing the aforementioned file.

To Reproduce
Steps to reproduce the behavior:

1. Create a config file with one of the faulty entries, e.g.,

[client]
halt_after_import = true

3. Run forest --config <FILE>
4. See that the flag gets ignored (Forest will continue to sync)
5. See that forest --config <FILE> --halt-after-import works fine.

Expected behaviour

Configuration file parameters are not overridden by CliOpts defaults.

Screenshots

Environment (please complete the following information):

• OS: Fedora Linux 37
• Rust version(e.g. rustc --version)
• Branch/commit 5903083

Other information and links